 |
PDBsum entry 1zaa
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transcription/DNA
|
PDB id
|
|
|
|
1zaa
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Science
252:809-817
(1991)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A.
|
|
N.P.Pavletich,
C.O.Pabo.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The zinc finger DNA-binding motif occurs in many proteins that regulate
eukaryotic gene expression. The crystal structure of a complex containing the
three zinc fingers from Zif268 (a mouse immediate early protein) and a consensus
DNA-binding site has been determined at 2.1 angstroms resolution and refined to
a crystallographic R factor of 18.2 percent. In this complex, the zinc fingers
bind in the major groove of B-DNA and wrap part way around the double helix.
Each finger has a similar relation to the DNA and makes its primary contacts in
a three-base pair subsite. Residues from the amino-terminal portion of an alpha
helix contact the bases, and most of the contracts are made with the
guanine-rich strand of the DNA. This structure provides a framework for
understanding how zinc fingers recognize DNA and suggests that this motif may
provide a useful basis for the design of novel DNA-binding proteins.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
B.Yang,
Y.Zhu,
Y.Wang,
and
G.Chen
(2011).
Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study.
|
| |
J Comput Chem,
32,
416-428.
|
|
|
|
|
|
|
C.P.Ponting
(2011).
What are the genomic drivers of the rapid evolution of PRDM9?
|
| |
Trends Genet,
27,
165-171.
|
|
|
|
|
|
|
E.A.Alemu,
E.Sjøttem,
H.Outzen,
K.B.Larsen,
T.Holm,
G.Bjørkøy,
and
T.Johansen
(2011).
Transforming growth factor-β-inducible early response gene 1 is a novel substrate for atypical protein kinase Cs.
|
| |
Cell Mol Life Sci,
68,
1953-1968.
|
|
|
|
|
|
|
G.Nagy,
B.Gyurcsik,
E.A.Hoffmann,
and
T.Körtvélyesi
(2011).
Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods.
|
| |
J Mol Graph Model,
29,
928-934.
|
|
|
|
|
|
|
J.J.Young,
J.M.Cherone,
Y.Doyon,
I.Ankoudinova,
F.M.Faraji,
A.H.Lee,
C.Ngo,
D.Y.Guschin,
D.E.Paschon,
J.C.Miller,
L.Zhang,
E.J.Rebar,
P.D.Gregory,
F.D.Urnov,
R.M.Harland,
and
B.Zeitler
(2011).
Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases.
|
| |
Proc Natl Acad Sci U S A,
108,
7052-7057.
|
|
|
|
|
|
|
K.Yusa,
S.T.Rashid,
H.Strick-Marchand,
I.Varela,
P.Q.Liu,
D.E.Paschon,
E.Miranda,
A.Ordóñez,
N.R.Hannan,
F.J.Rouhani,
S.Darche,
G.Alexander,
S.J.Marciniak,
N.Fusaki,
M.Hasegawa,
M.C.Holmes,
J.P.Di Santo,
D.A.Lomas,
A.Bradley,
and
L.Vallier
(2011).
Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells.
|
| |
Nature,
478,
391-394.
|
|
|
|
|
|
|
N.M.Jensen,
T.Dalsgaard,
M.Jakobsen,
R.R.Nielsen,
C.B.Sørensen,
L.Bolund,
and
T.G.Jensen
(2011).
An update on targeted gene repair in mammalian cells: methods and mechanisms.
|
| |
J Biomed Sci,
18,
10.
|
|
|
|
|
|
|
P.Tumbale,
C.D.Appel,
R.Kraehenbuehl,
P.D.Robertson,
J.S.Williams,
J.Krahn,
I.Ahel,
and
R.S.Williams
(2011).
Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.
|
| |
Nat Struct Mol Biol,
18,
1189-1195.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Kothinti,
N.M.Tabatabai,
and
D.H.Petering
(2011).
Electrophoretic mobility shift assay of zinc finger proteins: competition for Zn(2+) bound to Sp1 in protocols including EDTA.
|
| |
J Inorg Biochem,
105,
569-576.
|
|
|
|
|
|
|
S.M.Quintal,
Q.A.dePaula,
and
N.P.Farrell
(2011).
Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences.
|
| |
Metallomics,
3,
121-139.
|
|
|
|
|
|
|
A.Klug
(2010).
The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation.
|
| |
Q Rev Biophys,
43,
1.
|
|
|
|
|
|
|
A.Klug
(2010).
The discovery of zinc fingers and their applications in gene regulation and genome manipulation.
|
| |
Annu Rev Biochem,
79,
213-231.
|
|
|
|
|
|
|
A.M.Geurts,
and
C.Moreno
(2010).
Zinc-finger nucleases: new strategies to target the rat genome.
|
| |
Clin Sci (Lond),
119,
303-311.
|
|
|
|
|
|
|
A.Sabogal,
A.Y.Lyubimov,
J.E.Corn,
J.M.Berger,
and
D.C.Rio
(2010).
THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves.
|
| |
Nat Struct Mol Biol,
17,
117-123.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.Gonzalez,
L.J.Schwimmer,
R.P.Fuller,
Y.Ye,
L.Asawapornmongkol,
and
C.F.Barbas
(2010).
Modular system for the construction of zinc-finger libraries and proteins.
|
| |
Nat Protoc,
5,
791-810.
|
|
|
|
|
|
|
C.A.Hogarth,
D.Mitchell,
C.Small,
and
M.Griswold
(2010).
EGR4 displays both a cell- and intracellular-specific localization pattern in the developing murine testis.
|
| |
Dev Dyn,
239,
3106-3114.
|
|
|
|
|
|
|
C.C.Chou,
M.Rajasekaran,
and
C.Chen
(2010).
An effective approach for generating a three-Cys2His2 zinc-finger-DNA complex model by docking.
|
| |
BMC Bioinformatics,
11,
334.
|
|
|
|
|
|
|
C.C.Chou,
Y.C.Lou,
T.K.Tang,
and
C.Chen
(2010).
Structure and DNA binding characteristics of the three-Cys(2)His(2) domain of mouse testis zinc finger protein.
|
| |
Proteins,
78,
2202-2212.
|
|
|
|
|
|
|
C.W.am Ende,
H.Y.Meng,
M.Ye,
A.K.Pandey,
and
N.J.Zondlo
(2010).
Design of lanthanide fingers: compact lanthanide-binding metalloproteins.
|
| |
Chembiochem,
11,
1738-1747.
|
|
|
|
|
|
|
D.Jantz,
and
J.M.Berg
(2010).
Probing the DNA-binding affinity and specificity of designed zinc finger proteins.
|
| |
Biophys J,
98,
852-860.
|
|
|
|
|
|
|
F.D.Urnov,
E.J.Rebar,
M.C.Holmes,
H.S.Zhang,
and
P.D.Gregory
(2010).
Genome editing with engineered zinc finger nucleases.
|
| |
Nat Rev Genet,
11,
636-646.
|
|
|
|
|
|
|
F.Zhang,
M.L.Maeder,
E.Unger-Wallace,
J.P.Hoshaw,
D.Reyon,
M.Christian,
X.Li,
C.J.Pierick,
D.Dobbs,
T.Peterson,
J.K.Joung,
and
D.F.Voytas
(2010).
High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases.
|
| |
Proc Natl Acad Sci U S A,
107,
12028-12033.
|
|
|
|
|
|
|
J.D.Sander,
M.L.Maeder,
D.Reyon,
D.F.Voytas,
J.K.Joung,
and
D.Dobbs
(2010).
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.
|
| |
Nucleic Acids Res,
38,
W462-W468.
|
|
|
|
|
|
|
K.Zhang,
L.Zhang,
F.Rao,
B.Brar,
J.L.Rodriguez-Flores,
L.Taupenot,
and
D.T.O'Connor
(2010).
Human tyrosine hydroxylase natural genetic variation: delineation of functional transcriptional control motifs disrupted in the proximal promoter.
|
| |
Circ Cardiovasc Genet,
3,
187-198.
|
|
|
|
|
|
|
M.Hatayama,
and
J.Aruga
(2010).
Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.
|
| |
BMC Evol Biol,
10,
53.
|
|
|
|
|
|
|
M.Imanishi,
T.Nakaya,
T.Morisaki,
D.Noshiro,
S.Futaki,
and
Y.Sugiura
(2010).
Metal-stimulated regulation of transcription by an artificial zinc-finger protein.
|
| |
Chembiochem,
11,
1653-1655.
|
|
|
|
|
|
|
N.A.Temiz,
A.Trapp,
O.A.Prokopyev,
and
C.J.Camacho
(2010).
Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting.
|
| |
Bioinformatics,
26,
319-325.
|
|
|
|
|
|
|
P.Lorenz,
S.Dietmann,
T.Wilhelm,
D.Koczan,
S.Autran,
S.Gad,
G.Wen,
G.Ding,
Y.Li,
M.F.Rousseau-Merck,
and
H.J.Thiesen
(2010).
The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues.
|
| |
BMC Genomics,
11,
206.
|
|
|
|
|
|
|
R.Iida,
M.Ueki,
and
T.Yasuda
(2010).
A novel transcriptional repressor, Rhit, is involved in heat-inducible and age-dependent expression of Mpv17-like protein, a participant in reactive oxygen species metabolism.
|
| |
Mol Cell Biol,
30,
2306-2315.
|
|
|
|
|
|
|
R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
|
| |
Annu Rev Biochem,
79,
233-269.
|
|
|
|
|
|
|
S.D.Lim,
W.C.Yim,
J.C.Moon,
D.S.Kim,
B.M.Lee,
and
C.S.Jang
(2010).
A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes.
|
| |
Plant Mol Biol,
72,
369-380.
|
|
|
|
|
|
|
S.J.Orlando,
Y.Santiago,
R.C.DeKelver,
Y.Freyvert,
E.A.Boydston,
E.A.Moehle,
V.M.Choi,
S.M.Gopalan,
J.F.Lou,
J.Li,
J.C.Miller,
M.C.Holmes,
P.D.Gregory,
F.D.Urnov,
and
G.J.Cost
(2010).
Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology.
|
| |
Nucleic Acids Res,
38,
e152.
|
|
|
|
|
|
|
T.J.Cradick,
K.Keck,
S.Bradshaw,
A.C.Jamieson,
and
A.P.McCaffrey
(2010).
Zinc-finger nucleases as a novel therapeutic strategy for targeting hepatitis B virus DNAs.
|
| |
Mol Ther,
18,
947-954.
|
|
|
|
|
|
|
T.Morisaki,
M.Imanishi,
S.Futaki,
and
Y.Sugiura
(2010).
[Artificial transcription factors based on multi-zinc finger motifs]
|
| |
Yakugaku Zasshi,
130,
45-48.
|
|
|
|
|
|
|
X.Feng,
A.L.Bednarz,
and
S.D.Colloms
(2010).
Precise targeted integration by a chimaeric transposase zinc-finger fusion protein.
|
| |
Nucleic Acids Res,
38,
1204-1216.
|
|
|
|
|
|
|
A.N.Zaykov,
K.R.MacKenzie,
and
Z.T.Ball
(2009).
Controlling peptide structure with coordination chemistry: robust and reversible peptide-dirhodium ligation.
|
| |
Chemistry,
15,
8961-8965.
|
|
|
|
|
|
|
A.Nomura,
and
A.Okamoto
(2009).
Photoresponsive tandem zinc finger peptide.
|
| |
Chem Commun (Camb),
(),
1906-1908.
|
|
|
|
|
|
|
A.V.Persikov,
R.Osada,
and
M.Singh
(2009).
Predicting DNA recognition by Cys2His2 zinc finger proteins.
|
| |
Bioinformatics,
25,
22-29.
|
|
|
|
|
|
|
A.Zykovich,
I.Korf,
and
D.J.Segal
(2009).
Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.
|
| |
Nucleic Acids Res,
37,
e151.
|
|
|
|
|
|
|
C.M.Phillips,
X.Meng,
L.Zhang,
J.H.Chretien,
F.D.Urnov,
and
A.F.Dernburg
(2009).
Identification of chromosome sequence motifs that mediate meiotic pairing and synapsis in C. elegans.
|
| |
Nat Cell Biol,
11,
934-942.
|
|
|
|
|
|
|
C.Q.Cai,
Y.Doyon,
W.M.Ainley,
J.C.Miller,
R.C.Dekelver,
E.A.Moehle,
J.M.Rock,
Y.L.Lee,
R.Garrison,
L.Schulenberg,
R.Blue,
A.Worden,
L.Baker,
F.Faraji,
L.Zhang,
M.C.Holmes,
E.J.Rebar,
T.N.Collingwood,
B.Rubin-Wilson,
P.D.Gregory,
F.D.Urnov,
and
J.F.Petolino
(2009).
Targeted transgene integration in plant cells using designed zinc finger nucleases.
|
| |
Plant Mol Biol,
69,
699-709.
|
|
|
|
|
|
|
D.F.Voytas,
and
J.K.Joung
(2009).
Plant science. DNA binding made easy.
|
| |
Science,
326,
1491-1492.
|
|
|
|
|
|
|
D.Mittelman,
C.Moye,
J.Morton,
K.Sykoudis,
Y.Lin,
D.Carroll,
and
J.H.Wilson
(2009).
Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells.
|
| |
Proc Natl Acad Sci U S A,
106,
9607-9612.
|
|
|
|
|
|
|
E.M.Händel,
S.Alwin,
and
T.Cathomen
(2009).
Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity.
|
| |
Mol Ther,
17,
104-111.
|
|
|
|
|
|
|
F.Cui,
and
V.B.Zhurkin
(2009).
Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA.
|
| |
Nucleic Acids Res,
37,
2818-2829.
|
|
|
|
|
|
|
F.E.Loughlin,
R.E.Mansfield,
P.M.Vaz,
A.P.McGrath,
S.Setiyaputra,
R.Gamsjaeger,
E.S.Chen,
B.J.Morris,
J.M.Guss,
and
J.P.Mackay
(2009).
The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences.
|
| |
Proc Natl Acad Sci U S A,
106,
5581-5586.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Katada,
and
M.Komiyama
(2009).
Artificial restriction DNA cutters as new tools for gene manipulation.
|
| |
Chembiochem,
10,
1279-1288.
|
|
|
|
|
|
|
J.Ashworth,
and
D.Baker
(2009).
Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
|
| |
Nucleic Acids Res,
37,
e73.
|
|
|
|
|
|
|
J.D.Sander,
P.Zaback,
J.K.Joung,
D.F.Voytas,
and
D.Dobbs
(2009).
An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.
|
| |
Nucleic Acids Res,
37,
506-515.
|
|
|
|
|
|
|
J.H.Thomas,
R.O.Emerson,
and
J.Shendure
(2009).
Extraordinary molecular evolution in the PRDM9 fertility gene.
|
| |
PLoS One,
4,
e8505.
|
|
|
|
|
|
|
J.M.Vaquerizas,
S.K.Kummerfeld,
S.A.Teichmann,
and
N.M.Luscombe
(2009).
A census of human transcription factors: function, expression and evolution.
|
| |
Nat Rev Genet,
10,
252-263.
|
|
|
|
|
|
|
K.Kandavelou,
and
S.Chandrasegaran
(2009).
Custom-designed molecular scissors for site-specific manipulation of the plant and mammalian genomes.
|
| |
Methods Mol Biol,
544,
617-636.
|
|
|
|
|
|
|
K.Su,
D.Wang,
J.Ye,
Y.C.Kim,
and
S.A.Chow
(2009).
Site-specific integration of retroviral DNA in human cells using fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc-finger protein E2C.
|
| |
Methods,
47,
269-276.
|
|
|
|
|
|
|
M.Muzzioli,
R.Stecconi,
R.Moresi,
and
M.Provinciali
(2009).
Zinc improves the development of human CD34+ cell progenitors towards NK cells and increases the expression of GATA-3 transcription factor in young and old ages.
|
| |
Biogerontology,
10,
593-604.
|
|
|
|
|
|
|
S.C.Parker,
L.Hansen,
H.O.Abaan,
T.D.Tullius,
and
E.H.Margulies
(2009).
Local DNA topography correlates with functional noncoding regions of the human genome.
|
| |
Science,
324,
389-392.
|
|
|
|
|
|
|
S.J.Maerkl,
and
S.R.Quake
(2009).
Experimental determination of the evolvability of a transcription factor.
|
| |
Proc Natl Acad Sci U S A,
106,
18650-18655.
|
|
|
|
|
|
|
S.Sakkhachornphop,
S.Jiranusornkul,
K.Kodchakorn,
S.Nangola,
T.Sirisanthana,
and
C.Tayapiwatana
(2009).
Designed zinc finger protein interacting with the HIV-1 integrase recognition sequence at 2-LTR-circle junctions.
|
| |
Protein Sci,
18,
2219-2230.
|
|
|
|
|
|
|
T.Sera
(2009).
Zinc-finger-based artificial transcription factors and their applications.
|
| |
Adv Drug Deliv Rev,
61,
513-526.
|
|
|
|
|
|
|
V.K.Shukla,
Y.Doyon,
J.C.Miller,
R.C.DeKelver,
E.A.Moehle,
S.E.Worden,
J.C.Mitchell,
N.L.Arnold,
S.Gopalan,
X.Meng,
V.M.Choi,
J.M.Rock,
Y.Y.Wu,
G.E.Katibah,
G.Zhifang,
D.McCaskill,
M.A.Simpson,
B.Blakeslee,
S.A.Greenwalt,
H.J.Butler,
S.J.Hinkley,
L.Zhang,
E.J.Rebar,
P.D.Gregory,
and
F.D.Urnov
(2009).
Precise genome modification in the crop species Zea mays using zinc-finger nucleases.
|
| |
Nature,
459,
437-441.
|
|
|
|
|
|
|
Y.Shimizu,
M.S.Bhakta,
and
D.J.Segal
(2009).
Restricted spacer tolerance of a zinc finger nuclease with a six amino acid linker.
|
| |
Bioorg Med Chem Lett,
19,
3970-3972.
|
|
|
|
|
|
|
Z.Yang,
H.J.Wen,
V.Minhas,
and
C.Wood
(2009).
The zinc finger DNA-binding domain of K-RBP plays an important role in regulating Kaposi's sarcoma-associated herpesvirus RTA-mediated gene expression.
|
| |
Virology,
391,
221-231.
|
|
|
|
|
|
|
A.D.Kelleher,
and
D.F.Purcell
(2008).
Controlling HIV infection: HIV co-receptor gets the finger.
|
| |
Immunol Cell Biol,
86,
641-642.
|
|
|
|
|
|
|
A.Marabotti,
F.Spyrakis,
A.Facchiano,
P.Cozzini,
S.Alberti,
G.E.Kellogg,
and
A.Mozzarelli
(2008).
Energy-based prediction of amino acid-nucleotide base recognition.
|
| |
J Comput Chem,
29,
1955-1969.
|
|
|
|
|
|
|
C.B.Gocke,
and
H.Yu
(2008).
ZNF198 stabilizes the LSD1-CoREST-HDAC1 complex on chromatin through its MYM-type zinc fingers.
|
| |
PLoS ONE,
3,
e3255.
|
|
|
|
|
|
|
D.Pantoja-Uceda,
M.T.Pastor,
J.Salgado,
A.Pineda-Lucena,
and
E.Pérez-Payá
(2008).
Design of a bivalent peptide with two independent elements of secondary structure able to fold autonomously.
|
| |
J Pept Sci,
14,
845-854.
|
|
|
|
|
|
|
E.M.Warren,
S.Vaithiyalingam,
J.Haworth,
B.Greer,
A.K.Bielinsky,
W.J.Chazin,
and
B.F.Eichman
(2008).
Structural basis for DNA binding by replication initiator Mcm10.
|
| |
Structure,
16,
1892-1901.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Pearson
(2008).
Protein engineering: The fate of fingers.
|
| |
Nature,
455,
160-164.
|
|
|
|
|
|
|
J.Liu,
and
G.D.Stormo
(2008).
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.
|
| |
Bioinformatics,
24,
1850-1857.
|
|
|
|
|
|
|
K.J.Brayer,
and
D.J.Segal
(2008).
Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains.
|
| |
Cell Biochem Biophys,
50,
111-131.
|
|
|
|
|
|
|
K.J.Brayer,
S.Kulshreshtha,
and
D.J.Segal
(2008).
The protein-binding potential of C2H2 zinc finger domains.
|
| |
Cell Biochem Biophys,
51,
9.
|
|
|
|
|
|
|
M.Hatayama,
T.Tomizawa,
K.Sakai-Kato,
P.Bouvagnet,
S.Kose,
N.Imamoto,
S.Yokoyama,
N.Utsunomiya-Tate,
K.Mikoshiba,
T.Kigawa,
and
J.Aruga
(2008).
Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain.
|
| |
Hum Mol Genet,
17,
3459-3473.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Nowotny,
S.M.Cerritelli,
R.Ghirlando,
S.A.Gaidamakov,
R.J.Crouch,
and
W.Yang
(2008).
Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD.
|
| |
EMBO J,
27,
1172-1181.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.M.Pruett-Miller,
J.P.Connelly,
M.L.Maeder,
J.K.Joung,
and
M.H.Porteus
(2008).
Comparison of zinc finger nucleases for use in gene targeting in mammalian cells.
|
| |
Mol Ther,
16,
707-717.
|
|
|
|
|
|
|
S.M.Shimeld
(2008).
C2H2 zinc finger genes of the Gli, Zic, KLF, SP, Wilms' tumour, Huckebein, Snail, Ovo, Spalt, Odd, Blimp-1, Fez and related gene families from Branchiostoma floridae.
|
| |
Dev Genes Evol,
218,
639-649.
|
|
|
|
|
|
|
T.Cathomen,
and
J.K.Joung
(2008).
Zinc-finger nucleases: the next generation emerges.
|
| |
Mol Ther,
16,
1200-1207.
|
|
|
|
|
|
|
T.I.Cornu,
S.Thibodeau-Beganny,
E.Guhl,
S.Alwin,
M.Eichtinger,
J.Joung,
and
T.Cathomen
(2008).
DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.
|
| |
Mol Ther,
16,
352-358.
|
|
|
|
|
|
|
W.J.Liu,
Y.S.Chang,
H.C.Wang,
J.H.Leu,
G.H.Kou,
and
C.F.Lo
(2008).
Transactivation, dimerization, and DNA-binding activity of white spot syndrome virus immediate-early protein IE1.
|
| |
J Virol,
82,
11362-11373.
|
|
|
|
|
|
|
Y.Chen,
J.Mandic,
and
G.Varani
(2008).
Cell-free selection of RNA-binding proteins using in vitro compartmentalization.
|
| |
Nucleic Acids Res,
36,
e128.
|
|
|
|
|
|
|
Y.Doyon,
J.M.McCammon,
J.C.Miller,
F.Faraji,
C.Ngo,
G.E.Katibah,
R.Amora,
T.D.Hocking,
L.Zhang,
E.J.Rebar,
P.D.Gregory,
F.D.Urnov,
and
S.L.Amacher
(2008).
Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases.
|
| |
Nat Biotechnol,
26,
702-708.
|
|
|
|
|
|
|
Y.Osawa,
K.Ikebukuro,
H.Motoki,
T.Matsuo,
M.Horiuchi,
and
K.Sode
(2008).
The simple and rapid detection of specific PCR products from bacterial genomes using Zn finger proteins.
|
| |
Nucleic Acids Res,
36,
e68.
|
|
|
|
|
|
|
Y.Zheng,
J.Kief,
K.Auffarth,
J.W.Farfsing,
M.Mahlert,
F.Nieto,
and
C.W.Basse
(2008).
The Ustilago maydis Cys2His2-type zinc finger transcription factor Mzr1 regulates fungal gene expression during the biotrophic growth stage.
|
| |
Mol Microbiol,
68,
1450-1470.
|
|
|
|
|
|
|
B.J.You,
M.Choquer,
and
K.R.Chung
(2007).
The Colletotrichum acutatum gene encoding a putative pH-responsive transcription regulator is a key virulence determinant during fungal pathogenesis on citrus.
|
| |
Mol Plant Microbe Interact,
20,
1149-1160.
|
|
|
|
|
|
|
D.Lu,
and
A.Klug
(2007).
Invariance of the zinc finger module: a comparison of the free structure with those in nucleic-acid complexes.
|
| |
Proteins,
67,
508-512.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.A.Moehle,
E.A.Moehle,
J.M.Rock,
J.M.Rock,
Y.L.Lee,
Y.L.Lee,
Y.Jouvenot,
Y.Jouvenot,
R.C.DeKelver,
R.C.Dekelver,
P.D.Gregory,
P.D.Gregory,
F.D.Urnov,
F.D.Urnov,
M.C.Holmes,
and
M.C.Holmes
(2007).
Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases.
|
| |
Proc Natl Acad Sci U S A,
104,
3055-3060.
|
|
|
|
|
|
|
J.C.Shieh,
Y.C.Cheng,
M.C.Su,
M.Moore,
Y.Choo,
and
A.Klug
(2007).
Tailor-made zinc-finger transcription factors activate FLO11 gene expression with phenotypic consequences in the yeast Saccharomyces cerevisiae.
|
| |
PLoS ONE,
2,
e746.
|
|
|
|
|
|
|
J.F.Etchberger,
A.Lorch,
M.C.Sleumer,
R.Zapf,
S.J.Jones,
M.A.Marra,
R.A.Holt,
D.G.Moerman,
and
O.Hobert
(2007).
The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron.
|
| |
Genes Dev,
21,
1653-1674.
|
|
|
|
|
|
|
J.Wu,
K.Kandavelou,
and
S.Chandrasegaran
(2007).
Custom-designed zinc finger nucleases: what is next?
|
| |
Cell Mol Life Sci,
64,
2933-2944.
|
|
|
|
|
|
|
K.Rothfels,
O.Rowland,
and
J.Segall
(2007).
Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5 S RNA gene.
|
| |
Nucleic Acids Res,
35,
4869-4881.
|
|
|
|
|
|
|
M.Egli,
and
P.S.Pallan
(2007).
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
|
| |
Annu Rev Biophys Biomol Struct,
36,
281-305.
|
|
|
|
|
|
|
M.Kitahashi,
Y.Sato,
L.Fujimura,
C.Ozeki,
M.Arima,
A.Sakamoto,
S.Yamamoto,
T.Tokuhisa,
and
M.Hatano
(2007).
Identification of the consensus DNA sequence for Nczf binding.
|
| |
DNA Cell Biol,
26,
395-401.
|
|
|
|
|
|
|
M.Muzzioli,
R.Stecconi,
A.Donnini,
F.Re,
and
M.Provinciali
(2007).
Zinc improves the development of human CD34+ cell progenitors towards Natural Killer cells and induces the expression of GATA-3 transcription factor.
|
| |
Int J Biochem Cell Biol,
39,
955-965.
|
|
|
|
|
|
|
N.G.Nickols,
and
P.B.Dervan
(2007).
Suppression of androgen receptor-mediated gene expression by a sequence-specific DNA-binding polyamide.
|
| |
Proc Natl Acad Sci U S A,
104,
10418-10423.
|
|
|
|
|
|
|
P.S.Pallan,
P.Lubini,
M.Bolli,
and
M.Egli
(2007).
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing.
|
| |
Nucleic Acids Res,
35,
6611-6624.
|
|
|
|
|
|
|
P.Seale,
S.Kajimura,
W.Yang,
S.Chin,
L.M.Rohas,
M.Uldry,
G.Tavernier,
D.Langin,
and
B.M.Spiegelman
(2007).
Transcriptional control of brown fat determination by PRDM16.
|
| |
Cell Metab,
6,
38-54.
|
|
|
|
|
|
|
S.J.Bruce,
B.B.Gardiner,
L.J.Burke,
M.M.Gongora,
S.M.Grimmond,
and
A.C.Perkins
(2007).
Dynamic transcription programs during ES cell differentiation towards mesoderm in serum versus serum-freeBMP4 culture.
|
| |
BMC Genomics,
8,
365.
|
|
|
|
|
|
|
S.Mahony,
P.E.Auron,
and
P.V.Benos
(2007).
Inferring protein-DNA dependencies using motif alignments and mutual information.
|
| |
Bioinformatics,
23,
i297-i304.
|
|
|
|
|
|
|
X.Meng,
S.Thibodeau-Beganny,
T.Jiang,
J.K.Joung,
and
S.A.Wolfe
(2007).
Profiling the DNA-binding specificities of engineered Cys2His2 zinc finger domains using a rapid cell-based method.
|
| |
Nucleic Acids Res,
35,
e81.
|
|
|
|
|
|
|
A.Beltran,
Y.Liu,
S.Parikh,
B.Temple,
and
P.Blancafort
(2006).
Interrogating genomes with combinatorial artificial transcription factor libraries: asking zinc finger questions.
|
| |
Assay Drug Dev Technol,
4,
317-331.
|
|
|
|
|
|
|
A.M.Pilon,
D.G.Nilson,
D.Zhou,
J.Sangerman,
T.M.Townes,
D.M.Bodine,
and
P.G.Gallagher
(2006).
Alterations in expression and chromatin configuration of the alpha hemoglobin-stabilizing protein gene in erythroid Kruppel-like factor-deficient mice.
|
| |
Mol Cell Biol,
26,
4368-4377.
|
|
|
|
|
|
|
B.Taneja,
A.Patel,
A.Slesarev,
and
A.Mondragón
(2006).
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
|
| |
EMBO J,
25,
398-408.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
D.Carroll,
J.J.Morton,
K.J.Beumer,
and
D.J.Segal
(2006).
Design, construction and in vitro testing of zinc finger nucleases.
|
| |
Nat Protoc,
1,
1329-1341.
|
|
|
|
|
|
|
G.Grigoryan,
F.Zhou,
S.R.Lustig,
G.Ceder,
D.Morgan,
and
A.E.Keating
(2006).
Ultra-fast evaluation of protein energies directly from sequence.
|
| |
PLoS Comput Biol,
2,
e63.
|
|
|
|
|
|
|
G.Yin,
C.Ji,
L.Zeng,
Z.Wang,
J.Wang,
Z.Shen,
T.Wu,
S.Gu,
Y.Xie,
and
Y.Mao
(2006).
Cloning and characterization of a novel KRAB-domain-containing zinc finger gene (ZNF284L).
|
| |
Mol Biol Rep,
33,
137-144.
|
|
|
|
|
|
|
J.Morton,
M.W.Davis,
E.M.Jorgensen,
and
D.Carroll
(2006).
Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells.
|
| |
Proc Natl Acad Sci U S A,
103,
16370-16375.
|
|
|
|
|
|
|
J.Wang,
S.Zhang,
R.M.Schultz,
and
H.Tseng
(2006).
Search for basonuclin target genes.
|
| |
Biochem Biophys Res Commun,
348,
1261-1271.
|
|
|
|
|
|
|
K.Beumer,
G.Bhattacharyya,
M.Bibikova,
J.K.Trautman,
and
D.Carroll
(2006).
Efficient gene targeting in Drosophila with zinc-finger nucleases.
|
| |
Genetics,
172,
2391-2403.
|
|
|
|
|
|
|
S.H.Mishra,
C.M.Shelley,
D.J.Barrow,
M.K.Darby,
and
M.W.Germann
(2006).
Solution structures and characterization of human immunodeficiency virus Rev responsive element IIB RNA targeting zinc finger proteins.
|
| |
Biopolymers,
83,
352-364.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Ladame,
J.A.Schouten,
J.Roldan,
J.E.Redman,
S.Neidle,
and
S.Balasubramanian
(2006).
Exploring the recognition of quadruplex DNA by an engineered Cys2-His2 zinc finger protein.
|
| |
Biochemistry,
45,
1393-1399.
|
|
|
|
|
|
|
S.M.Gopal,
and
W.Wenzel
(2006).
De novo folding of the DNA-binding ATF-2 zinc finger motif in an all-atom free-energy forcefield.
|
| |
Angew Chem Int Ed Engl,
45,
7726-7728.
|
|
|
|
|
|
|
S.Negi,
M.Dhanasekaran,
T.Hirata,
H.Urata,
and
Y.Sugiura
(2006).
Biomolecular mirror-image recognition: reciprocal chiral-specific DNA binding of synthetic enantiomers of zinc finger domain from GAGA factor.
|
| |
Chirality,
18,
254-258.
|
|
|
|
|
|
|
S.P.Sripathy,
J.Stevens,
and
D.C.Schultz
(2006).
The KAP1 corepressor functions to coordinate the assembly of de novo HP1-demarcated microenvironments of heterochromatin required for KRAB zinc finger protein-mediated transcriptional repression.
|
| |
Mol Cell Biol,
26,
8623-8638.
|
|
|
|
|
|
|
T.Yamamoto,
T.Matsuda,
T.Inoue,
H.Matsumura,
M.Morikawa,
S.Kanaya,
and
Y.Kai
(2006).
Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA.
|
| |
Protein Sci,
15,
152-161.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
W.Tan,
Z.Dong,
T.A.Wilkinson,
C.F.Barbas,
and
S.A.Chow
(2006).
Human immunodeficiency virus type 1 incorporated with fusion proteins consisting of integrase and the designed polydactyl zinc finger protein E2C can bias integration of viral DNA into a predetermined chromosomal region in human cells.
|
| |
J Virol,
80,
1939-1948.
|
|
|
|
|
|
|
W.Zhang,
B.Li,
R.Singh,
U.Narendra,
L.Zhu,
and
M.A.Weiss
(2006).
Regulation of sexual dimorphism: mutational and chemogenetic analysis of the doublesex DM domain.
|
| |
Mol Cell Biol,
26,
535-547.
|
|
|
|
|
|
|
Y.Li,
T.Kimura,
J.H.Laity,
and
G.K.Andrews
(2006).
The zinc-sensing mechanism of mouse MTF-1 involves linker peptides between the zinc fingers.
|
| |
Mol Cell Biol,
26,
5580-5587.
|
|
|
|
|
|
|
Z.Birtle,
and
C.P.Ponting
(2006).
Meisetz and the birth of the KRAB motif.
|
| |
Bioinformatics,
22,
2841-2845.
|
|
|
|
|
|
|
A.Al-Sarraj,
R.M.Day,
and
G.Thiel
(2005).
Specificity of transcriptional regulation by the zinc finger transcription factors Sp1, Sp3, and Egr-1.
|
| |
J Cell Biochem,
94,
153-167.
|
|
|
|
|
|
|
A.J.Edgar,
S.L.Dover,
M.N.Lodrick,
I.J.McKay,
F.J.Hughes,
and
W.Turner
(2005).
Bone morphogenetic protein-2 induces expression of murine zinc finger transcription factor ZNF450.
|
| |
J Cell Biochem,
94,
202-215.
|
|
|
|
|
|
|
C.T.Workman,
Y.Yin,
D.L.Corcoran,
T.Ideker,
G.D.Stormo,
and
P.V.Benos
(2005).
enoLOGOS: a versatile web tool for energy normalized sequence logos.
|
| |
Nucleic Acids Res,
33,
W389-W392.
|
|
|
|
|
|
|
F.D.Urnov,
J.C.Miller,
Y.L.Lee,
C.M.Beausejour,
J.M.Rock,
S.Augustus,
A.C.Jamieson,
M.H.Porteus,
P.D.Gregory,
and
M.C.Holmes
(2005).
Highly efficient endogenous human gene correction using designed zinc-finger nucleases.
|
| |
Nature,
435,
646-651.
|
|
|
|
|
|
|
J.Liu,
and
G.D.Stormo
(2005).
Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein.
|
| |
BMC Bioinformatics,
6,
176.
|
|
|
|
|
|
|
J.Stetefeld,
and
M.A.Ruegg
(2005).
Structural and functional diversity generated by alternative mRNA splicing.
|
| |
Trends Biochem Sci,
30,
515-521.
|
|
|
|
|
|
|
M.D.Hughes,
Z.R.Zhang,
A.J.Sutherland,
A.F.Santos,
and
A.V.Hine
(2005).
Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins.
|
| |
Nucleic Acids Res,
33,
e32.
|
|
|
|
|
|
|
M.H.Porteus,
and
D.Carroll
(2005).
Gene targeting using zinc finger nucleases.
|
| |
Nat Biotechnol,
23,
967-973.
|
|
|
|
|
|
|
M.Isalan,
M.I.Santori,
C.Gonzalez,
and
L.Serrano
(2005).
Localized transfection on arrays of magnetic beads coated with PCR products.
|
| |
Nat Methods,
2,
113-118.
|
|
|
|
|
|
|
R.Stefl,
L.Skrisovska,
and
F.H.Allain
(2005).
RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle.
|
| |
EMBO Rep,
6,
33-38.
|
|
|
|
|
|
|
S.Durai,
M.Mani,
K.Kandavelou,
J.Wu,
M.H.Porteus,
and
S.Chandrasegaran
(2005).
Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.
|
| |
Nucleic Acids Res,
33,
5978-5990.
|
|
|
|
|
|
|
S.Zolotukhin
(2005).
Gene therapy for obesity.
|
| |
Expert Opin Biol Ther,
5,
347-357.
|
|
|
|
|
|
|
T.Clouaire,
M.Roussigne,
V.Ecochard,
C.Mathe,
F.Amalric,
and
J.P.Girard
(2005).
The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity.
|
| |
Proc Natl Acad Sci U S A,
102,
6907-6912.
|
|
|
|
|
|
|
T.H.Jenkins,
J.Li,
C.P.Scutt,
and
P.M.Gilmartin
(2005).
Analysis of members of the Silene latifolia Cys2/His2 zinc-finger transcription factor family during dioecious flower development and in a novel stamen-defective mutant ssf1.
|
| |
Planta,
220,
559-571.
|
|
|
|
|
|
|
T.Kaplan,
N.Friedman,
and
H.Margalit
(2005).
Ab initio prediction of transcription factor targets using structural knowledge.
|
| |
PLoS Comput Biol,
1,
e1.
|
|
|
|
|
|
|
T.M.Hall
(2005).
Multiple modes of RNA recognition by zinc finger proteins.
|
| |
Curr Opin Struct Biol,
15,
367-373.
|
|
|
|
|
|
|
Y.Chen,
S.D.Carrington-Lawrence,
P.Bai,
and
S.K.Weller
(2005).
Mutations in the putative zinc-binding motif of UL52 demonstrate a complex interdependence between the UL5 and UL52 subunits of the human herpes simplex virus type 1 helicase/primase complex.
|
| |
J Virol,
79,
9088-9096.
|
|
|
|
|
|
|
A.Kozaki,
S.Hake,
and
J.Colasanti
(2004).
The maize ID1 flowering time regulator is a zinc finger protein with novel DNA binding properties.
|
| |
Nucleic Acids Res,
32,
1710-1720.
|
|
|
|
|
|
|
A.Vanhoutteghem,
and
P.Djian
(2004).
Basonuclin 2: an extremely conserved homolog of the zinc finger protein basonuclin.
|
| |
Proc Natl Acad Sci U S A,
101,
3468-3473.
|
|
|
|
|
|
|
C.V.Mello,
T.A.Velho,
and
R.Pinaud
(2004).
Song-induced gene expression: a window on song auditory processing and perception.
|
| |
Ann N Y Acad Sci,
1016,
263-281.
|
|
|
|
|
|
|
E.Knapska,
and
L.Kaczmarek
(2004).
A gene for neuronal plasticity in the mammalian brain: Zif268/Egr-1/NGFI-A/Krox-24/TIS8/ZENK?
|
| |
Prog Neurobiol,
74,
183-211.
|
|
|
|
|
|
|
H.Jafar-Nejad,
H.J.Bellen,
and
H.J.Bellen
(2004).
Gfi/Pag-3/senseless zinc finger proteins: a unifying theme?
|
| |
Mol Cell Biol,
24,
8803-8812.
|
|
|
|
|
|
|
M.J.Lachenmann,
J.E.Ladbury,
X.Qian,
K.Huang,
R.Singh,
and
M.A.Weiss
(2004).
Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice.
|
| |
Protein Sci,
13,
3115-3126.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.H.Kim,
J.K.Hong,
S.C.Lee,
K.H.Sohn,
H.W.Jung,
and
B.K.Hwang
(2004).
CAZFP1, Cys2/His2-type zinc-finger transcription factor gene functions as a pathogen-induced early-defense gene in Capsicum annuum.
|
| |
Plant Mol Biol,
55,
883-904.
|
|
|
|
|
|
|
W.Tan,
K.Zhu,
D.J.Segal,
C.F.Barbas,
and
S.A.Chow
(2004).
Fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc finger protein E2C direct integration of viral DNA into specific sites.
|
| |
J Virol,
78,
1301-1313.
|
|
|
|
|
|
|
A.C.Jamieson,
J.C.Miller,
and
C.O.Pabo
(2003).
Drug discovery with engineered zinc-finger proteins.
|
| |
Nat Rev Drug Discov,
2,
361-368.
|
|
|
|
|
|
|
A.H.Kwan,
D.A.Gell,
A.Verger,
M.Crossley,
J.M.Matthews,
and
J.P.Mackay
(2003).
Engineering a protein scaffold from a PHD finger.
|
| |
Structure,
11,
803-813.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Z.Ansari
(2003).
Fingers reach for the genome.
|
| |
Nat Biotechnol,
21,
242-243.
|
|
|
|
|
|
|
G.Li,
G.V.Tolstonog,
and
P.Traub
(2003).
Interaction in vitro of type III intermediate filament proteins with Z-DNA and B-Z-DNA junctions.
|
| |
DNA Cell Biol,
22,
141-169.
|
|
|
|
|
|
|
H.R.Chrisman,
and
D.J.Tindall
(2003).
Identification and characterization of a consensus DNA binding element for the zinc finger transcription factor TIEG/EGRalpha.
|
| |
DNA Cell Biol,
22,
187-199.
|
|
|
|
|
|
|
K.H.Bae,
Y.D.Kwon,
H.C.Shin,
M.S.Hwang,
E.H.Ryu,
K.S.Park,
H.Y.Yang,
D.K.Lee,
Y.Lee,
J.Park,
H.S.Kwon,
H.W.Kim,
B.I.Yeh,
H.W.Lee,
S.H.Sohn,
J.Yoon,
W.Seol,
and
J.S.Kim
(2003).
Human zinc fingers as building blocks in the construction of artificial transcription factors.
|
| |
Nat Biotechnol,
21,
275-280.
|
|
|
|
|
|
|
M.Papworth,
M.Moore,
M.Isalan,
M.Minczuk,
Y.Choo,
and
A.Klug
(2003).
Inhibition of herpes simplex virus 1 gene expression by designer zinc-finger transcription factors.
|
| |
Proc Natl Acad Sci U S A,
100,
1621-1626.
|
|
|
|
|
|
|
P.A.Reynolds,
G.A.Smolen,
R.E.Palmer,
D.Sgroi,
V.Yajnik,
W.L.Gerald,
and
D.A.Haber
(2003).
Identification of a DNA-binding site and transcriptional target for the EWS-WT1(+KTS) oncoprotein.
|
| |
Genes Dev,
17,
2094-2107.
|
|
|
|
|
|
|
R.Jauch,
G.P.Bourenkov,
H.R.Chung,
H.Urlaub,
U.Reidt,
H.Jäckle,
and
M.C.Wahl
(2003).
The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinc-coordinating protein-protein interaction module.
|
| |
Structure,
11,
1393-1402.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.W.Blume,
Z.Meng,
K.Shrestha,
R.C.Snyder,
and
P.D.Emanuel
(2003).
The 5'-untranslated RNA of the human dhfr minor transcript alters transcription pre-initiation complex assembly at the major (core) promoter.
|
| |
J Cell Biochem,
88,
165-180.
|
|
|
|
|
|
|
W.Nomura,
and
Y.Sugiura
(2003).
Effects of length and position of an extended linker on sequence-selective DNA recognition of zinc finger peptides.
|
| |
Biochemistry,
42,
14805-14813.
|
|
|
|
|
|
|
A.Gordon-Shaag,
O.Ben-Nun-Shaul,
V.Roitman,
Y.Yosef,
and
A.Oppenheim
(2002).
Cellular transcription factor Sp1 recruits simian virus 40 capsid proteins to the viral packaging signal, ses.
|
| |
J Virol,
76,
5915-5924.
|
|
|
|
|
|
|
C.J.Wilds,
M.A.Maier,
V.Tereshko,
M.Manoharan,
and
M.Egli
(2002).
Direct observation of a cytosine analogue that forms five hydrogen bonds to guanosine: guanidino G-clamp.
|
| |
Angew Chem Int Ed Engl,
41,
115-117.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
E.Hinoi,
V.J.Balcar,
N.Kuramoto,
N.Nakamichi,
and
Y.Yoneda
(2002).
Nuclear transcription factors in the hippocampus.
|
| |
Prog Neurobiol,
68,
145-165.
|
|
|
|
|
|
|
F.D.Urnov,
E.J.Rebar,
A.Reik,
and
P.P.Pandolfi
(2002).
Designed transcription factors as structural, functional and therapeutic probes of chromatin in vivo. Fourth in review series on chromatin dynamics.
|
| |
EMBO Rep,
3,
610-615.
|
|
|
|
|
|
|
G.Thiel,
and
G.Cibelli
(2002).
Regulation of life and death by the zinc finger transcription factor Egr-1.
|
| |
J Cell Physiol,
193,
287-292.
|
|
|
|
|
|
|
H.L.Ng,
and
R.E.Dickerson
(2002).
Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.
|
| |
Nucleic Acids Res,
30,
4061-4067.
|
|
|
|
|
|
|
J.A.Benanti,
D.K.Williams,
K.L.Robinson,
H.L.Ozer,
and
D.A.Galloway
(2002).
Induction of extracellular matrix-remodeling genes by the senescence-associated protein APA-1.
|
| |
Mol Cell Biol,
22,
7385-7397.
|
|
|
|
|
|
|
M.J.Sui,
L.C.Tsai,
K.C.Hsia,
L.G.Doudeva,
W.Y.Ku,
G.W.Han,
and
H.S.Yuan
(2002).
Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions.
|
| |
Protein Sci,
11,
2947-2957.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.L.Bulyk,
P.L.Johnson,
and
G.M.Church
(2002).
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.
|
| |
Nucleic Acids Res,
30,
1255-1261.
|
|
|
|
|
|
|
M.Sagasser,
G.H.Lu,
K.Hahlbrock,
and
B.Weisshaar
(2002).
A. thaliana TRANSPARENT TESTA 1 is involved in seed coat development and defines the WIP subfamily of plant zinc finger proteins.
|
| |
Genes Dev,
16,
138-149.
|
|
|
|
|
|
|
M.Shiraishi,
A.J.Oates,
and
T.Sekiya
(2002).
An overview of the analysis of DNA methylation in mammalian genomes.
|
| |
Biol Chem,
383,
893-906.
|
|
|
|
|
|
|
M.Tang,
M.Waterman,
and
S.Yooseph
(2002).
Zinc finger gene clusters and tandem gene duplication.
|
| |
J Comput Biol,
9,
429-446.
|
|
|
|
|
|
|
N.Dathan,
L.Zaccaro,
S.Esposito,
C.Isernia,
J.G.Omichinski,
A.Riccio,
C.Pedone,
B.Di Blasio,
R.Fattorusso,
and
P.V.Pedone
(2002).
The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif.
|
| |
Nucleic Acids Res,
30,
4945-4951.
|
|
|
|
|
|
|
P.J.Wilder,
C.T.Bernadt,
J.H.Kim,
and
A.Rizzino
(2002).
Stimulation of the murine type II transforming growth factor-beta receptor promoter by the transcription factor Egr-1.
|
| |
Mol Reprod Dev,
63,
282-290.
|
|
|
|
|
|
|
P.V.Benos,
A.S.Lapedes,
and
G.D.Stormo
(2002).
Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .
|
| |
Bioessays,
24,
466-475.
|
|
|
|
|
|
|
P.V.Benos,
M.L.Bulyk,
and
G.D.Stormo
(2002).
Additivity in protein-DNA interactions: how good an approximation is it?
|
| |
Nucleic Acids Res,
30,
4442-4451.
|
|
|
|
|
|
|
R.J.Kim,
S.Moine,
D.K.Reese,
and
P.A.Bullock
(2002).
Peptides containing cyclin/Cdk-nuclear localization signal motifs derived from viral initiator proteins bind to DNA when unphosphorylated.
|
| |
J Virol,
76,
11785-11792.
|
|
|
|
|
|
|
X.Gao,
D.J.Rowley,
X.Gai,
and
D.F.Voytas
(2002).
Ty5 gag mutations increase retrotransposition and suggest a role for hydrogen bonding in the function of the nucleocapsid zinc finger.
|
| |
J Virol,
76,
3240-3247.
|
|
|
|
|
|
|
B.Gebelein,
and
R.Urrutia
(2001).
Sequence-specific transcriptional repression by KS1, a multiple-zinc-finger-Krüppel-associated box protein.
|
| |
Mol Cell Biol,
21,
928-939.
|
|
|
|
|
|
|
C.K.Hwang,
U.M.D'Souza,
A.J.Eisch,
S.Yajima,
C.H.Lammers,
Y.Yang,
S.H.Lee,
Y.M.Kim,
E.J.Nestler,
and
M.M.Mouradian
(2001).
Dopamine receptor regulating factor, DRRF: a zinc finger transcription factor.
|
| |
Proc Natl Acad Sci U S A,
98,
7558-7563.
|
|
|
|
|
|
|
C.O.Pabo,
E.Peisach,
and
R.A.Grant
(2001).
Design and selection of novel Cys2His2 zinc finger proteins.
|
| |
Annu Rev Biochem,
70,
313-340.
|
|
|
|
|
|
|
C.W.Garvie,
and
C.Wolberger
(2001).
Recognition of specific DNA sequences.
|
| |
Mol Cell,
8,
937-946.
|
|
|
|
|
|
|
D.E.Wilcox,
A.D.Schenk,
B.M.Feldman,
and
Y.Xu
(2001).
Oxidation of zinc-binding cysteine residues in transcription factor proteins.
|
| |
Antioxid Redox Signal,
3,
549-564.
|
|
|
|
|
|
|
D.P.Giedroc,
X.Chen,
and
J.L.Apuy
(2001).
Metal response element (MRE)-binding transcription factor-1 (MTF-1): structure, function, and regulation.
|
| |
Antioxid Redox Signal,
3,
577-596.
|
|
|
|
|
|
|
G.Zhai,
M.Iskandar,
K.Barilla,
and
P.J.Romaniuk
(2001).
Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1.
|
| |
Biochemistry,
40,
2032-2040.
|
|
|
|
|
|
|
H.B.Houbaviy,
and
S.K.Burley
(2001).
Thermodynamic analysis of the interaction between YY1 and the AAV P5 promoter initiator element.
|
| |
Chem Biol,
8,
179-187.
|
|
|
|
|
|
|
J.H.Laity,
B.M.Lee,
and
P.E.Wright
(2001).
Zinc finger proteins: new insights into structural and functional diversity.
|
| |
Curr Opin Struct Biol,
11,
39-46.
|
|
|
|
|
|
|
J.S.Rodgers,
J.R.Hocker,
R.J.Hanas,
E.C.Nwosu,
and
J.S.Hanas
(2001).
Mercuric ion inhibition of eukaryotic transcription factor binding to DNA.
|
| |
Biochem Pharmacol,
61,
1543-1550.
|
|
|
|
|
|
|
M.Amorós,
and
F.Estruch
(2001).
Hsf1p and Msn2/4p cooperate in the expression of Saccharomyces cerevisiae genes HSP26 and HSP104 in a gene- and stress type-dependent manner.
|
| |
Mol Microbiol,
39,
1523-1532.
|
|
|
|
|
|
|
M.Isalan,
A.Klug,
and
Y.Choo
(2001).
A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.
|
| |
Nat Biotechnol,
19,
656-660.
|
|
|
|
|
|
|
M.Isalan,
S.D.Patel,
S.Balasubramanian,
and
Y.Choo
(2001).
Selection of zinc fingers that bind single-stranded telomeric DNA in the G-quadruplex conformation.
|
| |
Biochemistry,
40,
830-836.
|
|
|
|
|
|
|
M.L.Bulyk,
X.Huang,
Y.Choo,
and
G.M.Church
(2001).
Exploring the DNA-binding specificities of zinc fingers with DNA microarrays.
|
| |
Proc Natl Acad Sci U S A,
98,
7158-7163.
|
|
|
|
|
|
|
M.Nagaoka,
T.Kaji,
M.Imanishi,
Y.Hori,
W.Nomura,
and
Y.Sugiura
(2001).
Multiconnection of identical zinc finger: implication for DNA binding affinity and unit modulation of the three zinc finger domain.
|
| |
Biochemistry,
40,
2932-2941.
|
|
|
|
|
|
|
M.Nagaoka,
Y.Shiraishi,
and
Y.Sugiura
(2001).
Selected base sequence outside the target binding site of zinc finger protein Sp1.
|
| |
Nucleic Acids Res,
29,
4920-4929.
|
|
|
|
|
|
|
R.I.Boysen,
and
M.T.Hearn
(2001).
The metal binding properties of the CCCH motif of the 50S ribosomal protein L36 from Thermus thermophilus.
|
| |
J Pept Res,
57,
19-28.
|
|
|
|
|
|
|
W.Zhang,
S.Kadam,
B.M.Emerson,
and
J.J.Bieker
(2001).
Site-specific acetylation by p300 or CREB binding protein regulates erythroid Krüppel-like factor transcriptional activity via its interaction with the SWI-SNF complex.
|
| |
Mol Cell Biol,
21,
2413-2422.
|
|
|
|
|
|
|
Y.Uno,
K.Matsushita,
M.Nagaoka,
and
Y.Sugiura
(2001).
Finger-positional change in three zinc finger protein Sp1: influence of terminal finger in DNA recognition.
|
| |
Biochemistry,
40,
1787-1795.
|
|
|
|
|
|
|
A.Hata,
J.Seoane,
G.Lagna,
E.Montalvo,
A.Hemmati-Brivanlou,
and
J.Massagué
(2000).
OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-Smad and Olf signaling pathways.
|
| |
Cell,
100,
229-240.
|
|
|
|
|
|
|
A.Lombardi,
C.M.Summa,
S.Geremia,
L.Randaccio,
V.Pavone,
and
W.F.DeGrado
(2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
|
| |
Proc Natl Acad Sci U S A,
97,
6298-6305.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.R.McNamara,
and
K.G.Ford
(2000).
A novel four zinc-finger protein targeted against p190(BcrAbl) fusion oncogene cDNA: utilisation of zinc-finger recognition codes.
|
| |
Nucleic Acids Res,
28,
4865-4872.
|
|
|
|
|
|
|
B.Burke,
F.Yang,
F.Chen,
C.Stehlin,
B.Chan,
and
K.Musier-Forsyth
(2000).
Evolutionary coadaptation of the motif 2--acceptor stem interaction in the class II prolyl-tRNA synthetase system.
|
| |
Biochemistry,
39,
15540-15547.
|
|
|
|
|
|
|
D.J.Segal,
and
C.F.Barbas
(2000).
Design of novel sequence-specific DNA-binding proteins.
|
| |
Curr Opin Chem Biol,
4,
34-39.
|
|
|
|
|
|
|
H.D.Rupprecht,
Y.Akagi,
A.Keil,
and
G.Hofer
(2000).
Nitric oxide inhibits growth of glomerular mesangial cells: role of the transcription factor EGR-1.
|
| |
Kidney Int,
57,
70-82.
|
|
|
|
|
|
|
J.H.Laity,
H.J.Dyson,
and
P.E.Wright
(2000).
Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein.
|
| |
Proc Natl Acad Sci U S A,
97,
11932-11935.
|
|
|
|
|
|
|
J.M.Matthews,
K.Kowalski,
C.K.Liew,
B.K.Sharpe,
A.H.Fox,
M.Crossley,
and
J.P.MacKay
(2000).
A class of zinc fingers involved in protein-protein interactions biophysical characterization of CCHC fingers from fog and U-shaped.
|
| |
Eur J Biochem,
267,
1030-1038.
|
|
|
|
|
|
|
J.Smith,
M.Bibikova,
F.G.Whitby,
A.R.Reddy,
S.Chandrasegaran,
and
D.Carroll
(2000).
Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains.
|
| |
Nucleic Acids Res,
28,
3361-3369.
|
|
|
|
|
|
|
K.J.O'Donovan,
Y.Levkovitz,
D.Ahn,
and
J.M.Baraban
(2000).
Functional comparison of Egr3 transcription factor isoforms: identification of an activation domain in the N-terminal segment absent from Egr3beta, a major isoform expressed in brain.
|
| |
J Neurochem,
75,
1352-1357.
|
|
|
|
|
|
|
M.Imanishi,
Y.Hori,
M.Nagaoka,
and
Y.Sugiura
(2000).
DNA-bending finger: artificial design of 6-zinc finger peptides with polyglycine linker and induction of DNA bending.
|
| |
Biochemistry,
39,
4383-4390.
|
|
|
|
|
|
|
M.Razmiafshari,
and
N.H.Zawia
(2000).
Utilization of a synthetic peptide as a tool to study the interaction of heavy metals with the zinc finger domain of proteins critical for gene expression in the developing brain.
|
| |
Toxicol Appl Pharmacol,
166,
1.
|
|
|
|
|
|
|
M.Schaub,
A.Krol,
and
P.Carbon
(2000).
Structural organization of Staf-DNA complexes.
|
| |
Nucleic Acids Res,
28,
2114-2121.
|
|
|
|
|
|
|
M.Thompson,
and
N.W.Woodbury
(2000).
Fluorescent and photochemical properties of a single zinc finger conjugated to a fluorescent DNA-binding probe.
|
| |
Biochemistry,
39,
4327-4338.
|
|
|
|
|
|
|
M.Worbs,
R.Huber,
and
M.C.Wahl
(2000).
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon.
|
| |
EMBO J,
19,
807-818.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
N.M.Luscombe,
S.E.Austin,
H.M.Berman,
and
J.M.Thornton
(2000).
An overview of the structures of protein-DNA complexes.
|
| |
Genome Biol,
1,
REVIEWS001.
|
|
|
|
|
|
|
P.C.Hsieh,
J.P.Xiao,
D.O'loane,
and
S.Y.Xu
(2000).
Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
|
| |
J Bacteriol,
182,
949-955.
|
|
|
|
|
|
|
P.Nissen,
M.Kjeldgaard,
and
J.Nyborg
(2000).
Macromolecular mimicry.
|
| |
EMBO J,
19,
489-495.
|
|
|
|
|
|
|
S.A.Wolfe,
E.I.Ramm,
and
C.O.Pabo
(2000).
Combining structure-based design with phage display to create new Cys(2)His(2) zinc finger dimers.
|
| |
Structure,
8,
739-750.
|
|
|
|
|
|
|
S.A.Wolfe,
L.Nekludova,
and
C.O.Pabo
(2000).
DNA recognition by Cys2His2 zinc finger proteins.
|
| |
Annu Rev Biophys Biomol Struct,
29,
183-212.
|
|
|
|
|
|
|
S.Lee,
and
M.D.Garfinkel
(2000).
Characterization of Drosophila OVO protein DNA binding specificity using random DNA oligomer selection suggests zinc finger degeneration.
|
| |
Nucleic Acids Res,
28,
826-834.
|
|
|
|
|
|
|
T.D.Stephens,
C.J.Bunde,
and
B.J.Fillmore
(2000).
Mechanism of action in thalidomide teratogenesis.
|
| |
Biochem Pharmacol,
59,
1489-1499.
|
|
|
|
|
|
|
T.Nakamura,
Y.Yamazaki,
Y.Saiki,
M.Moriyama,
D.A.Largaespada,
N.A.Jenkins,
and
N.G.Copeland
(2000).
Evi9 encodes a novel zinc finger protein that physically interacts with BCL6, a known human B-cell proto-oncogene product.
|
| |
Mol Cell Biol,
20,
3178-3186.
|
|
|
|
|
|
|
Y.Choo,
and
M.Isalan
(2000).
Advances in zinc finger engineering.
|
| |
Curr Opin Struct Biol,
10,
411-416.
|
|
|
|
|
|
|
A.Perkins
(1999).
Erythroid Kruppel like factor: from fishing expedition to gourmet meal.
|
| |
Int J Biochem Cell Biol,
31,
1175-1192.
|
|
|
|
|
|
|
A.T.Petkova,
J.G.Hu,
M.Bizounok,
M.Simpson,
R.G.Griffin,
and
J.Herzfeld
(1999).
Arginine activity in the proton-motive photocycle of bacteriorhodopsin: solid-state NMR studies of the wild-type and D85N proteins.
|
| |
Biochemistry,
38,
1562-1572.
|
|
|
|
|
|
|
B.S.Wang,
and
C.O.Pabo
(1999).
Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences.
|
| |
Proc Natl Acad Sci U S A,
96,
9568-9573.
|
|
|
|
|
|
|
C.Huang,
N.Kohno,
H.Inufusa,
K.Kodama,
T.Taki,
and
M.Miyake
(1999).
Overexpression of bax associated with mutations in the loop-sheet-helix motif of p53.
|
| |
Am J Pathol,
155,
955-965.
|
|
|
|
|
|
|
D.Avram,
M.Leid,
and
A.T.Bakalinsky
(1999).
Fzf1p of Saccharomyces cerevisiae is a positive regulator of SSU1 transcription and its first zinc finger region is required for DNA binding.
|
| |
Yeast,
15,
473-480.
|
|
|
|
|
|
|
D.J.McColl,
C.D.Honchell,
and
A.D.Frankel
(1999).
Structure-based design of an RNA-binding zinc finger.
|
| |
Proc Natl Acad Sci U S A,
96,
9521-9526.
|
|
|
|
|
|
|
D.J.Segal,
B.Dreier,
R.R.Beerli,
and
C.F.Barbas
(1999).
Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5'-GNN-3' DNA target sequences.
|
| |
Proc Natl Acad Sci U S A,
96,
2758-2763.
|
|
|
|
|
|
|
F.S.Santiago,
D.G.Atkins,
and
L.M.Khachigian
(1999).
Vascular smooth muscle cell proliferation and regrowth after mechanical injury in vitro are Egr-1/NGFI-A-dependent.
|
| |
Am J Pathol,
155,
897-905.
|
|
|
|
|
|
|
H.Chan,
D.P.Bartos,
and
L.B.Owen-Schaub
(1999).
Activation-dependent transcriptional regulation of the human Fas promoter requires NF-kappaB p50-p65 recruitment.
|
| |
Mol Cell Biol,
19,
2098-2108.
|
|
|
|
|
|
|
H.E.Xu,
M.A.Rould,
W.Xu,
J.A.Epstein,
R.L.Maas,
and
C.O.Pabo
(1999).
Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding.
|
| |
Genes Dev,
13,
1263-1275.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.J.Tremblay,
and
J.Drouin
(1999).
Egr-1 is a downstream effector of GnRH and synergizes by direct interaction with Ptx1 and SF-1 to enhance luteinizing hormone beta gene transcription.
|
| |
Mol Cell Biol,
19,
2567-2576.
|
|
|
|
|
|
|
K.E.Hightower,
and
C.A.Fierke
(1999).
Zinc-catalyzed sulfur alkyation:insights from protein farnesyltransferase.
|
| |
Curr Opin Chem Biol,
3,
176-181.
|
|
|
|
|
|
|
K.J.O'Donovan,
W.G.Tourtellotte,
J.Millbrandt,
and
J.M.Baraban
(1999).
The EGR family of transcription-regulatory factors: progress at the interface of molecular and systems neuroscience.
|
| |
Trends Neurosci,
22,
167-173.
|
|
|
|
|
|
|
K.Miyagawa,
Y.Hayashi,
T.Fukuda,
K.Mitani,
H.Hirai,
and
K.Kamiya
(1999).
Mutations of the WT1 gene in childhood nonlymphoid hematological malignancies.
|
| |
Genes Chromosomes Cancer,
25,
176-183.
|
|
|
|
|
|
|
L.Fan,
P.C.Sanschagrin,
L.S.Kaguni,
and
L.A.Kuhn
(1999).
The accessory subunit of mtDNA polymerase shares structural homology with aminoacyl-tRNA synthetases: implications for a dual role as a primer recognition factor and processivity clamp.
|
| |
Proc Natl Acad Sci U S A,
96,
9527-9532.
|
|
|
|
|
|
|
L.Wang,
Y.Duan,
R.Shortle,
B.Imperiali,
and
P.A.Kollman
(1999).
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures.
|
| |
Protein Sci,
8,
1292-1304.
|
|
|
|
|
|
|
N.Adachi,
M.Matsumoto,
S.Hasegawa,
T.Yamamoto,
and
M.Horikoshi
(1999).
Analysis of TFIIH subunit through isolation of the gene from Schizosaccharomyces pombe corresponding to that of Saccharomyces cerevisiae SSL1, reveals the presence of conserved structural motifs.
|
| |
Yeast,
15,
255-262.
|
|
|
|
|
|
|
P.Blancafort,
S.V.Steinberg,
B.Paquin,
R.Klinck,
J.K.Scott,
and
R.Cedergren
(1999).
The recognition of a noncanonical RNA base pair by a zinc finger protein.
|
| |
Chem Biol,
6,
585-597.
|
|
|
|
|
|
|
S.Chandrasegaran,
and
J.Smith
(1999).
Chimeric restriction enzymes: what is next?
|
| |
Biol Chem,
380,
841-848.
|
|
|
|
|
|
|
S.Philipsen,
and
G.Suske
(1999).
A tale of three fingers: the family of mammalian Sp/XKLF transcription factors.
|
| |
Nucleic Acids Res,
27,
2991-3000.
|
|
|
|
|
|
|
T.P.Ko,
C.C.Liao,
W.Y.Ku,
K.F.Chak,
and
H.S.Yuan
(1999).
The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.
|
| |
Structure,
7,
91.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Duarte,
A.Caricasole,
C.F.Graham,
and
A.Ward
(1998).
Wilms' tumour-suppressor protein isoforms have opposite effects on Igf2 expression in primary embryonic cells, independently of p53 genotype.
|
| |
Br J Cancer,
77,
253-259.
|
|
|
|
|
|
|
A.K.Aggarwal,
and
D.A.Wah
(1998).
Novel site-specific DNA endonucleases.
|
| |
Curr Opin Struct Biol,
8,
19-25.
|
|
|
|
|
|
|
B.Imperiali,
and
J.J.Ottesen
(1998).
Design strategies for the construction of independently folded polypeptide motifs.
|
| |
Biopolymers,
47,
23-29.
|
|
|
|
|
|
|
F.Hirano,
H.Tanaka,
Y.Hirano,
M.Hiramoto,
H.Handa,
I.Makino,
and
C.Scheidereit
(1998).
Functional interference of Sp1 and NF-kappaB through the same DNA binding site.
|
| |
Mol Cell Biol,
18,
1266-1274.
|
|
|
|
|
|
|
H.H.Thorp
(1998).
Bioinorganic chemistry and drug design: here comes zinc again.
|
| |
Chem Biol,
5,
R125-R127.
|
|
|
|
|
|
|
J.L.Pomerantz,
S.A.Wolfe,
and
C.O.Pabo
(1998).
Structure-based design of a dimeric zinc finger protein.
|
| |
Biochemistry,
37,
965-970.
|
|
|
|
|
|
|
J.M.Madison,
A.M.Dudley,
and
F.Winston
(1998).
Identification and analysis of Mot3, a zinc finger protein that binds to the retrotransposon Ty long terminal repeat (delta) in Saccharomyces cerevisiae.
|
| |
Mol Cell Biol,
18,
1879-1890.
|
|
|
|
|
|
|
J.S.Kim,
and
C.O.Pabo
(1998).
Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants.
|
| |
Proc Natl Acad Sci U S A,
95,
2812-2817.
|
|
|
|
|
|
|
J.Woda,
B.Schneider,
K.Patel,
K.Mistry,
and
H.M.Berman
(1998).
An analysis of the relationship between hydration and protein-DNA interactions.
|
| |
Biophys J,
75,
2170-2177.
|
|
|
|
|
|
|
K.Kubo,
A.Sakamoto,
A.Kobayashi,
Z.Rybka,
Y.Kanno,
H.Nakagawa,
and
H.Takatsuji
(1998).
Cys2/His2 zinc-finger protein family of petunia: evolution and general mechanism of target-sequence recognition.
|
| |
Nucleic Acids Res,
26,
608-615.
|
|
|
|
|
|
|
L.E.Warner,
P.Mancias,
I.J.Butler,
C.M.McDonald,
L.Keppen,
K.G.Koob,
and
J.R.Lupski
(1998).
Mutations in the early growth response 2 (EGR2) gene are associated with hereditary myelinopathies.
|
| |
Nat Genet,
18,
382-384.
|
|
|
|
|
|
|
L.L.Lutfiyya,
V.R.Iyer,
J.DeRisi,
M.J.DeVit,
P.O.Brown,
and
M.Johnston
(1998).
Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae.
|
| |
Genetics,
150,
1377-1391.
|
|
|
|
|
|
|
L.Regan
(1998).
Proteins to order?
|
| |
Structure,
6,
1-4.
|
|
|
|
|
|
|
M.D.Mendenhall,
and
A.E.Hodge
(1998).
Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae.
|
| |
Microbiol Mol Biol Rev,
62,
1191-1243.
|
|
|
|
|
|
|
M.Elrod-Erickson,
T.E.Benson,
and
C.O.Pabo
(1998).
High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.
|
| |
Structure,
6,
451-464.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Isalan,
A.Klug,
and
Y.Choo
(1998).
Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.
|
| |
Biochemistry,
37,
12026-12033.
|
|
|
|
|
|
|
M.S.Wisz,
C.Z.Garrett,
and
H.W.Hellinga
(1998).
Construction of a family of Cys2His2 zinc binding sites in the hydrophobic core of thioredoxin by structure-based design.
|
| |
Biochemistry,
37,
8269-8277.
|
|
|
|
|
|
|
M.Shimizu,
W.Li,
P.A.Covitz,
M.Hara,
H.Shindo,
and
A.P.Mitchell
(1998).
Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator IME1.
|
| |
Nucleic Acids Res,
26,
2329-2336.
|
|
|
|
|
|
|
M.Yokono,
N.Saegusa,
K.Matsushita,
and
Y.Sugiura
(1998).
Unique DNA binding mode of the N-terminal zinc finger of transcription factor Sp1.
|
| |
Biochemistry,
37,
6824-6832.
|
|
|
|
|
|
|
N.Bardeesy,
and
J.Pelletier
(1998).
Overlapping RNA and DNA binding domains of the wt1 tumor suppressor gene product.
|
| |
Nucleic Acids Res,
26,
1784-1792.
|
|
|
|
|
|
|
N.Gillemans,
R.Tewari,
F.Lindeboom,
R.Rottier,
T.de Wit,
M.Wijgerde,
F.Grosveld,
and
S.Philipsen
(1998).
Altered DNA-binding specificity mutants of EKLF and Sp1 show that EKLF is an activator of the beta-globin locus control region in vivo.
|
| |
Genes Dev,
12,
2863-2873.
|
|
|
|
|
|
|
R.F.Ryan,
and
M.K.Darby
(1998).
The role of zinc finger linkers in p43 and TFIIIA binding to 5S rRNA and DNA.
|
| |
Nucleic Acids Res,
26,
703-709.
|
|
|
|
|
|
|
R.I.Cukier,
and
D.G.Nocera
(1998).
Proton-coupled electron transfer.
|
| |
Annu Rev Phys Chem,
49,
337-369.
|
|
|
|
|
|
|
R.R.Beerli,
D.J.Segal,
B.Dreier,
and
C.F.Barbas
(1998).
Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks.
|
| |
Proc Natl Acad Sci U S A,
95,
14628-14633.
|
|
|
|
|
|
|
R.T.Nolte,
R.M.Conlin,
S.C.Harrison,
and
R.S.Brown
(1998).
Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex.
|
| |
Proc Natl Acad Sci U S A,
95,
2938-2943.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Y.Tsai,
and
R.R.Reed
(1998).
Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz.
|
| |
Mol Cell Biol,
18,
6447-6456.
|
|
|
|
|
|
|
S.L.Porello,
M.J.Cannon,
and
S.S.David
(1998).
A substrate recognition role for the [4Fe-4S]2+ cluster of the DNA repair glycosylase MutY.
|
| |
Biochemistry,
37,
6465-6475.
|
|
|
|
|
|
|
S.Mohammadi,
M.Perrée-Fauvet,
N.Gresh,
K.Hillairet,
and
E.Taillandier
(1998).
Joint molecular modeling and spectroscopic studies of DNA complexes of a bis(arginyl) conjugate of a tricationic porphyrin designed to target the major groove.
|
| |
Biochemistry,
37,
6165-6178.
|
|
|
|
|
|
|
S.Nanduri,
B.W.Carpick,
Y.Yang,
B.R.Williams,
and
J.Qin
(1998).
Structure of the double-stranded RNA-binding domain of the protein kinase PKR reveals the molecular basis of its dsRNA-mediated activation.
|
| |
EMBO J,
17,
5458-5465.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Tan,
and
T.J.Richmond
(1998).
Eukaryotic transcription factors.
|
| |
Curr Opin Struct Biol,
8,
41-48.
|
|
|
|
|
|
|
S.Y.Chiang,
J.C.Azizkhan,
and
T.A.Beerman
(1998).
A comparison of DNA-binding drugs as inhibitors of E2F1- and Sp1-DNA complexes and associated gene expression.
|
| |
Biochemistry,
37,
3109-3115.
|
|
|
|
|
|
|
T.B.Hamilton,
F.Borel,
and
P.J.Romaniuk
(1998).
Comparison of the DNA binding characteristics of the related zinc finger proteins WT1 and EGR1.
|
| |
Biochemistry,
37,
2051-2058.
|
|
|
|
|
|
|
V.Ramesh,
S.Gite,
and
U.L.RajBhandary
(1998).
Functional interaction of an arginine conserved in the sixteen amino acid insertion module of Escherichia coli methionyl-tRNA formyltransferase with determinants for formylation in the initiator tRNA.
|
| |
Biochemistry,
37,
15925-15932.
|
|
|
|
|
|
|
Y.Choo
(1998).
End effects in DNA recognition by zinc finger arrays.
|
| |
Nucleic Acids Res,
26,
554-557.
|
|
|
|
|
|
|
Y.G.Kim,
J.Smith,
M.Durgesha,
and
S.Chandrasegaran
(1998).
Chimeric restriction enzyme: Gal4 fusion to FokI cleavage domain.
|
| |
Biol Chem,
379,
489-495.
|
|
|
|
|
|
|
Y.Mandel-Gutfreund,
and
H.Margalit
(1998).
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites.
|
| |
Nucleic Acids Res,
26,
2306-2312.
|
|
|
|
|
|
|
B.A.Katz
(1997).
Structural and mechanistic determinants of affinity and specificity of ligands discovered or engineered by phage display.
|
| |
Annu Rev Biophys Biomol Struct,
26,
27-45.
|
|
|
|
|
|
|
D.Grate,
and
C.Wilson
(1997).
Role REVersal: understanding how RRE RNA binds its peptide ligand.
|
| |
Structure,
5,
7.
|
|
|
|
|
|
|
D.P.Matheos,
T.J.Kingsbury,
U.S.Ahsan,
and
K.W.Cunningham
(1997).
Tcn1p/Crz1p, a calcineurin-dependent transcription factor that differentially regulates gene expression in Saccharomyces cerevisiae.
|
| |
Genes Dev,
11,
3445-3458.
|
|
|
|
|
|
|
D.Suck
(1997).
DNA recognition by structure-selective nucleases.
|
| |
Biopolymers,
44,
405-421.
|
|
|
|
|
|
|
F.D.Bushman,
and
M.D.Miller
(1997).
Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites.
|
| |
J Virol,
71,
458-464.
|
|
|
|
|
|
|
F.Payre,
P.Buono,
N.Vanzo,
and
A.Vincent
(1997).
Two types of zinc fingers are required for dimerization of the serendipity delta transcriptional activator.
|
| |
Mol Cell Biol,
17,
3137-3145.
|
|
|
|
|
|
|
G.L.Xu,
and
T.H.Bestor
(1997).
Cytosine methylation targetted to pre-determined sequences.
|
| |
Nat Genet,
17,
376-378.
|
|
|
|
|
|
|
G.Patikoglou,
and
S.K.Burley
(1997).
Eukaryotic transcription factor-DNA complexes.
|
| |
Annu Rev Biophys Biomol Struct,
26,
289-325.
|
|
|
|
|
|
|
H.A.Greisman,
and
C.O.Pabo
(1997).
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites.
|
| |
Science,
275,
657-661.
|
|
|
|
|
|
|
H.D.Rupprecht,
G.Hofer,
R.B.Sterzel,
and
H.O.Schöcklmann
(1997).
[Egr-1 transcription factor regulates the growth of glomerular mesangium cells]
|
| |
Med Klin (Munich),
92,
68-73.
|
|
|
|
|
|
|
H.D.Rupprecht,
G.Hoffer,
E.de Heer,
R.B.Sterzel,
G.Faller,
and
H.O.Schoecklmann
(1997).
Expression of the transcriptional regulator Egr-1 in experimental glomerulonephritis: requirement for mesangial cell proliferation.
|
| |
Kidney Int,
51,
694-702.
|
|
|
|
|
|
|
H.Shao,
D.H.Kono,
L.Y.Chen,
E.M.Rubin,
and
J.Kaye
(1997).
Induction of the early growth response (Egr) family of transcription factors during thymic selection.
|
| |
J Exp Med,
185,
731-744.
|
|
|
|
|
|
|
J.G.Omichinski,
P.V.Pedone,
G.Felsenfeld,
A.M.Gronenborn,
and
G.M.Clore
(1997).
The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode.
|
| |
Nat Struct Biol,
4,
122-132.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Guo,
and
D.P.Giedroc
(1997).
Zinc site redesign in T4 gene 32 protein: structure and stability of cobalt(II) complexes formed by wild-type and metal ligand substitution mutants.
|
| |
Biochemistry,
36,
730-742.
|
|
|
|
|
|
|
J.M.Berg
(1997).
Letting your fingers do the walking.
|
| |
Nat Biotechnol,
15,
323.
|
|
|
|
|
|
|
J.S.Albert,
M.W.Peczuh,
and
A.D.Hamilton
(1997).
Design, synthesis and evaluation of synthetic receptors for the recognition of aspartate pairs in an alpha-helical conformation.
|
| |
Bioorg Med Chem,
5,
1455-1467.
|
|
|
|
|
|
|
J.S.Kim,
J.Kim,
K.L.Cepek,
P.A.Sharp,
and
C.O.Pabo
(1997).
Design of TATA box-binding protein/zinc finger fusions for targeted regulation of gene expression.
|
| |
Proc Natl Acad Sci U S A,
94,
3616-3620.
|
|
|
|
|
|
|
K.M.Galvin,
and
Y.Shi
(1997).
Multiple mechanisms of transcriptional repression by YY1.
|
| |
Mol Cell Biol,
17,
3723-3732.
|
|
|
|
|
|
|
M.Isalan,
Y.Choo,
and
A.Klug
(1997).
Synergy between adjacent zinc fingers in sequence-specific DNA recognition.
|
| |
Proc Natl Acad Sci U S A,
94,
5617-5621.
|
|
|
|
|
|
|
M.Lambert,
S.Blanchin-Roland,
F.Le Louedec,
A.Lepingle,
and
C.Gaillardin
(1997).
Genetic analysis of regulatory mutants affecting synthesis of extracellular proteinases in the yeast Yarrowia lipolytica: identification of a RIM101/pacC homolog.
|
| |
Mol Cell Biol,
17,
3966-3976.
|
|
|
|
|
|
|
M.P.Foster,
D.S.Wuttke,
I.Radhakrishnan,
D.A.Case,
J.M.Gottesfeld,
and
P.E.Wright
(1997).
Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.
|
| |
Nat Struct Biol,
4,
605-608.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.Schmiedeskamp,
P.Rajagopal,
and
R.E.Klevit
(1997).
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
|
| |
Protein Sci,
6,
1835-1848.
|
|
|
|
|
|
|
M.Schmiedeskamp,
and
R.E.Klevit
(1997).
Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein.
|
| |
Biochemistry,
36,
14003-14011.
|
|
|
|
|
|
|
N.M.Luscombe,
R.A.Laskowski,
and
J.M.Thornton
(1997).
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
|
| |
Nucleic Acids Res,
25,
4940-4945.
|
|
|
|
|
|
|
Q.Liu,
D.J.Segal,
J.B.Ghiara,
and
C.F.Barbas
(1997).
Design of polydactyl zinc-finger proteins for unique addressing within complex genomes.
|
| |
Proc Natl Acad Sci U S A,
94,
5525-5530.
|
|
|
|
|
|
|
R.E.Dickerson,
and
T.K.Chiu
(1997).
Helix bending as a factor in protein/DNA recognition.
|
| |
Biopolymers,
44,
361-403.
|
|
|
|
|
|
|
S.F.Bellon,
K.K.Rodgers,
D.G.Schatz,
J.E.Coleman,
and
T.A.Steitz
(1997).
Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster.
|
| |
Nat Struct Biol,
4,
586-591.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Arranz,
F.Harper,
Y.Florentin,
E.Puvion,
M.Kress,
and
M.Ernoult-Lange
(1997).
Human and mouse MOK2 proteins are associated with nuclear ribonucleoprotein components and bind specifically to RNA and DNA through their zinc finger domains.
|
| |
Mol Cell Biol,
17,
2116-2126.
|
|
|
|
|
|
|
Y.Choo,
and
A.Klug
(1997).
Physical basis of a protein-DNA recognition code.
|
| |
Curr Opin Struct Biol,
7,
117-125.
|
|
|
|
|
|
|
A.B.Hegvold,
and
O.S.Gabrielsen
(1996).
The importance of the linker connecting the repeats of the c-Myb oncoprotein may be due to a positioning function.
|
| |
Nucleic Acids Res,
24,
3990-3995.
|
|
|
|
|
|
|
A.C.Jamieson,
H.Wang,
and
S.H.Kim
(1996).
A zinc finger directory for high-affinity DNA recognition.
|
| |
Proc Natl Acad Sci U S A,
93,
12834-12839.
|
|
|
|
|
|
|
A.P.MacCabe,
J.P.Van den Hombergh,
J.Tilburn,
H.N.Arst,
and
J.Visser
(1996).
Identification, cloning and analysis of the Aspergillus niger gene pacC, a wide domain regulatory gene responsive to ambient pH.
|
| |
Mol Gen Genet,
250,
367-374.
|
|
|
|
|
|
|
B.Huang,
C.J.Schaeffer,
Q.Li,
and
M.D.Tsai
(1996).
Splase: a new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites.
|
| |
J Protein Chem,
15,
481-489.
|
|
|
|
|
|
|
B.W.Tague,
P.Gallant,
and
H.M.Goodman
(1996).
Expression analysis of an Arabidopsis C2H2 zinc finger protein gene.
|
| |
Plant Mol Biol,
32,
785-796.
|
|
|
|
|
|
|
C.A.Kim,
and
J.M.Berg
(1996).
A 2.2 A resolution crystal structure of a designed zinc finger protein bound to DNA.
|
| |
Nat Struct Biol,
3,
940-945.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.J.Schoenherr,
A.J.Paquette,
and
D.J.Anderson
(1996).
Identification of potential target genes for the neuron-restrictive silencer factor.
|
| |
Proc Natl Acad Sci U S A,
93,
9881-9886.
|
|
|
|
|
|
|
C.Vesque,
M.Maconochie,
S.Nonchev,
L.Ariza-McNaughton,
A.Kuroiwa,
P.Charnay,
and
R.Krumlauf
(1996).
Hoxb-2 transcriptional activation in rhombomeres 3 and 5 requires an evolutionarily conserved cis-acting element in addition to the Krox-20 binding site.
|
| |
EMBO J,
15,
5383-5396.
|
|
|
|
|
|
|
D.A.Erlanson,
M.Chytil,
and
G.L.Verdine
(1996).
The leucine zipper domain controls the orientation of AP-1 in the NFAT.AP-1.DNA complex.
|
| |
Chem Biol,
3,
981-991.
|
|
|
|
|
|
|
D.E.Wemmer
(1996).
New features in RNA recognition: a Tat-TAR complex.
|
| |
Chem Biol,
3,
17-19.
|
|
|
|
|
|
|
D.Moras,
and
A.Poterszman
(1996).
Getting into the major groove. Protein-RNA interactions.
|
| |
Curr Biol,
6,
530-532.
|
|
|
|
|
|
|
F.Borel,
K.C.Barilla,
T.B.Hamilton,
M.Iskandar,
and
P.J.Romaniuk
(1996).
Effects of Denys-Drash syndrome point mutations on the DNA binding activity of the Wilms' tumor suppressor protein WT1.
|
| |
Biochemistry,
35,
12070-12076.
|
|
|
|
|
|
|
F.Radtke,
M.Hug,
O.Georgiev,
K.Matsuo,
and
W.Schaffner
(1996).
Differential sensitivity of zinc finger transcription factors MTF-1, Sp1 and Krox-20 to CpG methylation of their binding sites.
|
| |
Biol Chem Hoppe Seyler,
377,
47-56.
|
|
|
|
|
|
|
H.B.Houbaviy,
A.Usheva,
T.Shenk,
and
S.K.Burley
(1996).
Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator.
|
| |
Proc Natl Acad Sci U S A,
93,
13577-13582.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Kawasaki,
M.Machida,
M.Komatsu,
H.O.Li,
T.Murata,
H.Tsutsui,
A.Fujita,
M.Matsumura,
Y.Kobayashi,
K.Taira,
and
K.K.Yokoyama
(1996).
Specific regulation of gene expression by antisense nucleic acids: a summary of methodologies and associated problems.
|
| |
Artif Organs,
20,
836-848.
|
|
|
|
|
|
|
J.A.Gogos,
J.Jin,
H.Wan,
M.Kokkinidis,
and
F.C.Kafatos
(1996).
Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements.
|
| |
Proc Natl Acad Sci U S A,
93,
2159-2164.
|
|
|
|
|
|
|
J.C.Reddy,
and
J.D.Licht
(1996).
The WT1 Wilms' tumor suppressor gene: how much do we really know?
|
| |
Biochim Biophys Acta,
1287,
1.
|
|
|
|
|
|
|
J.Kim,
B.Shen,
C.Rosen,
and
D.Dorsett
(1996).
The DNA-binding and enhancer-blocking domains of the Drosophila suppressor of Hairy-wing protein.
|
| |
Mol Cell Biol,
16,
3381-3392.
|
|
|
|
|
|
|
J.S.Hanas,
and
C.G.Gunn
(1996).
Inhibition of transcription factor IIIA-DNA interactions by xenobiotic metal ions.
|
| |
Nucleic Acids Res,
24,
924-930.
|
|
|
|
|
|
|
J.S.Maltzman,
J.A.Carman,
and
J.G.Monroe
(1996).
Role of EGR1 in regulation of stimulus-dependent CD44 transcription in B lymphocytes.
|
| |
Mol Cell Biol,
16,
2283-2294.
|
|
|
|
|
|
|
L.E.Benjamin,
W.J.Fredericks,
F.G.Barr,
and
F.J.Rauscher
(1996).
Fusion of the EWS1 and WT1 genes as a result of the t(11;22)(p13;q12) translocation in desmoplastic small round cell tumors.
|
| |
Med Pediatr Oncol,
27,
434-439.
|
|
|
|
|
|
|
L.L.Lutfiyya,
and
M.Johnston
(1996).
Two zinc-finger-containing repressors are responsible for glucose repression of SUC2 expression.
|
| |
Mol Cell Biol,
16,
4790-4797.
|
|
|
|
|
|
|
L.Wang,
and
D.E.Coulter
(1996).
bowel, an odd-skipped homolog, functions in the terminal pathway during Drosophila embryogenesis.
|
| |
EMBO J,
15,
3182-3196.
|
|
|
|
|
|
|
M.Elrod-Erickson,
M.A.Rould,
L.Nekludova,
and
C.O.Pabo
(1996).
Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions.
|
| |
Structure,
4,
1171-1180.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.H.Werner,
J.R.Huth,
A.M.Gronenborn,
and
G.M.Clore
(1996).
Molecular determinants of mammmalian sex.
|
| |
Trends Biochem Sci,
21,
302-308.
|
|
|
|
|
|
|
M.L'Haridon,
P.Paul,
J.G.Xerri,
H.Dastot,
C.Dolliger,
M.Schmid,
N.de Angelis,
L.Grollet,
F.Sigaux,
L.Degos,
and
C.Gazin
(1996).
Transcriptional regulation of the MHC class I HLA-A11 promoter by the zinc finger protein ZFX.
|
| |
Nucleic Acids Res,
24,
1928-1935.
|
|
|
|
|
|
|
M.Nagaoka,
and
Y.Sugiura
(1996).
Distinct phosphate backbone contacts revealed by some mutant peptides of zinc finger protein Spl: effect of protein-induced bending on DNA recognition.
|
| |
Biochemistry,
35,
8761-8768.
|
|
|
|
|
|
|
M.T.Martínez-Pastor,
G.Marchler,
C.Schüller,
A.Marchler-Bauer,
H.Ruis,
and
F.Estruch
(1996).
The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE).
|
| |
EMBO J,
15,
2227-2235.
|
|
|
|
|
|
|
P.A.Zweidler-Mckay,
H.L.Grimes,
M.M.Flubacher,
and
P.N.Tsichlis
(1996).
Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor.
|
| |
Mol Cell Biol,
16,
4024-4034.
|
|
|
|
|
|
|
P.R.Dohrmann,
W.P.Voth,
and
D.J.Stillman
(1996).
Role of negative regulation in promoter specificity of the homologous transcriptional activators Ace2p and Swi5p.
|
| |
Mol Cell Biol,
16,
1746-1758.
|
|
|
|
|
|
|
P.V.Pedone,
R.Ghirlando,
G.M.Clore,
A.M.Gronenborn,
G.Felsenfeld,
and
J.G.Omichinski
(1996).
The single Cys2-His2 zinc finger domain of the GAGA protein flanked by basic residues is sufficient for high-affinity specific DNA binding.
|
| |
Proc Natl Acad Sci U S A,
93,
2822-2826.
|
|
|
|
|
|
|
Q.Zheng,
and
D.J.Kyle
(1996).
Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings.
|
| |
Proteins,
24,
209-217.
|
|
|
|
|
|
|
Q.Zheng,
and
D.J.Kyle
(1996).
Computational screening of combinatorial libraries.
|
| |
Bioorg Med Chem,
4,
631-638.
|
|
|
|
|
|
|
R.N.Dutnall,
D.Neuhaus,
and
D.Rhodes
(1996).
The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.
|
| |
Structure,
4,
599-611.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.J.McBryant,
B.Gedulin,
K.R.Clemens,
P.E.Wright,
and
J.M.Gottesfeld
(1996).
Assessment of major and minor groove DNA interactions by the zinc fingers of Xenopus transcription factor IIIA.
|
| |
Nucleic Acids Res,
24,
2567-2574.
|
|
|
|
|
|
|
S.L.Lee,
Y.Wang,
and
J.Milbrandt
(1996).
Unimpaired macrophage differentiation and activation in mice lacking the zinc finger transplantation factor NGFI-A (EGR1).
|
| |
Mol Cell Biol,
16,
4566-4572.
|
|
|
|
|
|
|
S.P.Lee,
and
M.K.Han
(1996).
Zinc stimulates Mg2+-dependent 3'-processing activity of human immunodeficiency virus type 1 integrase in vitro.
|
| |
Biochemistry,
35,
3837-3844.
|
|
|
|
|
|
|
W.I.Sundquist
(1996).
Tattle tales.
|
| |
Nat Struct Biol,
3,
8.
|
|
|
|
|
|
|
Y.G.Kim,
J.Cha,
and
S.Chandrasegaran
(1996).
Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.
|
| |
Proc Natl Acad Sci U S A,
93,
1156-1160.
|
|
|
|
|
|
|
Y.Kuroiwa,
T.Kaneko-Ishino,
F.Kagitani,
T.Kohda,
L.L.Li,
M.Tada,
R.Suzuki,
M.Yokoyama,
T.Shiroishi,
S.Wakana,
S.C.Barton,
F.Ishino,
and
M.A.Surani
(1996).
Peg3 imprinted gene on proximal chromosome 7 encodes for a zinc finger protein.
|
| |
Nat Genet,
12,
186-190.
|
|
|
|
|
|
|
Y.Shi,
and
J.M.Berg
(1996).
DNA unwinding induced by zinc finger protein binding.
|
| |
Biochemistry,
35,
3845-3848.
|
|
|
|
|
|
|
Y.Ye,
B.Raychaudhuri,
A.Gurney,
C.E.Campbell,
and
B.R.Williams
(1996).
Regulation of WT1 by phosphorylation: inhibition of DNA binding, alteration of transcriptional activity and cellular translocation.
|
| |
EMBO J,
15,
5606-5615.
|
|
|
|
|
|
|
A.H.Swirnoff,
and
J.Milbrandt
(1995).
DNA-binding specificity of NGFI-A and related zinc finger transcription factors.
|
| |
Mol Cell Biol,
15,
2275-2287.
|
|
|
|
|
|
|
A.Klug
(1995).
Gene regulatory proteins and their interaction with DNA.
|
| |
Ann N Y Acad Sci,
758,
143-160.
|
|
|
|
|
|
|
A.M.Gronenborn,
and
G.M.Clore
(1995).
Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy.
|
| |
Crit Rev Biochem Mol Biol,
30,
351-385.
|
|
|
|
|
|
|
A.Rodger,
S.Taylor,
G.Adlam,
I.S.Blagbrough,
and
I.S.Haworth
(1995).
Multiple DNA binding modes of anthracene-9-carbonyl-N1-spermine.
|
| |
Bioorg Med Chem,
3,
861-872.
|
|
|
|
|
|
|
A.Vortkamp,
M.Gessler,
and
K.H.Grzeschik
(1995).
Identification of optimized target sequences for the GLI3 zinc finger protein.
|
| |
DNA Cell Biol,
14,
629-634.
|
|
|
|
|
|
|
B.Lustig,
and
R.L.Jernigan
(1995).
Consistencies of individual DNA base-amino acid interactions in structures and sequences.
|
| |
Nucleic Acids Res,
23,
4707-4711.
|
|
|
|
|
|
|
B.W.Baron,
R.R.Stanger,
E.Hume,
A.Sadhu,
R.Mick,
J.P.Kerckaert,
C.Deweindt,
C.Bastard,
G.Nucifora,
and
N.Zeleznik-Le
(1995).
BCL6 encodes a sequence-specific DNA-binding protein.
|
| |
Genes Chromosomes Cancer,
13,
221-224.
|
|
|
|
|
|
|
H.Nakagama,
G.Heinrich,
J.Pelletier,
and
D.E.Housman
(1995).
Sequence and structural requirements for high-affinity DNA binding by the WT1 gene product.
|
| |
Mol Cell Biol,
15,
1489-1498.
|
|
|
|
|
|
|
H.Wu,
W.P.Yang,
and
C.F.Barbas
(1995).
Building zinc fingers by selection: toward a therapeutic application.
|
| |
Proc Natl Acad Sci U S A,
92,
344-348.
|
|
|
|
|
|
|
H.Zaima,
N.Ueyama,
H.Adachi,
and
A.Nakamura
(1995).
1H-, 13C-, and 113Cd-NMR study of the Cd(II) complex of a blocked peptide, Z-Cys-Ala-Pro-His-OMe, in organic solvents.
|
| |
Biopolymers,
35,
319-329.
|
|
|
|
|
|
|
J.A.Carman,
and
J.G.Monroe
(1995).
The EGR1 protein contains a discrete transcriptional regulatory domain whose deletion results in a truncated protein that blocks EGR1-induced transcription.
|
| |
DNA Cell Biol,
14,
581-589.
|
|
|
|
|
|
|
J.A.Chong,
J.Tapia-Ramírez,
S.Kim,
J.J.Toledo-Aral,
Y.Zheng,
M.C.Boutros,
Y.M.Altshuller,
M.A.Frohman,
S.D.Kraner,
and
G.Mandel
(1995).
REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons.
|
| |
Cell,
80,
949-957.
|
|
|
|
|
|
|
J.Janin
(1995).
Elusive affinities.
|
| |
Proteins,
21,
30-39.
|
|
|
|
|
|
|
J.L.Pomerantz,
C.O.Pabo,
and
P.A.Sharp
(1995).
Analysis of homeodomain function by structure-based design of a transcription factor.
|
| |
Proc Natl Acad Sci U S A,
92,
9752-9756.
|
|
|
|
|
|
|
J.Tilburn,
S.Sarkar,
D.A.Widdick,
E.A.Espeso,
M.Orejas,
J.Mungroo,
M.A.Peñalva,
and
H.N.Arst
(1995).
The Aspergillus PacC zinc finger transcription factor mediates regulation of both acid- and alkaline-expressed genes by ambient pH.
|
| |
EMBO J,
14,
779-790.
|
|
|
|
|
|
|
K.Harada,
and
A.D.Frankel
(1995).
Identification of two novel arginine binding DNAs.
|
| |
EMBO J,
14,
5798-5811.
|
|
|
|
|
|
|
K.P.Anderson,
C.B.Kern,
S.C.Crable,
and
J.B.Lingrel
(1995).
Isolation of a gene encoding a functional zinc finger protein homologous to erythroid Krüppel-like factor: identification of a new multigene family.
|
| |
Mol Cell Biol,
15,
5957-5965.
|
|
|
|
|
|
|
L.P.Casson,
and
T.Manser
(1995).
Random mutagenesis of two complementarity determining region amino acids yields an unexpectedly high frequency of antibodies with increased affinity for both cognate antigen and autoantigen.
|
| |
J Exp Med,
182,
743-750.
|
|
|
|
|
|
|
L.Shimoni,
and
J.P.Glusker
(1995).
Hydrogen bonding motifs of protein side chains: descriptions of binding of arginine and amide groups.
|
| |
Protein Sci,
4,
65-74.
|
|
|
|
|
|
|
M.A.Young,
G.Ravishanker,
D.L.Beveridge,
and
H.M.Berman
(1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
|
| |
Biophys J,
68,
2454-2468.
|
|
|
|
|
|
|
M.Abrink,
M.Aveskogh,
and
L.Hellman
(1995).
Isolation of cDNA clones for 42 different Krüppel-related zinc finger proteins expressed in the human monoblast cell line U-937.
|
| |
DNA Cell Biol,
14,
125-136.
|
|
|
|
|
|
|
M.Okagami,
M.Ueno,
K.Makino,
M.Shimomura,
I.Saito,
T.Morii,
and
Y.Sugiura
(1995).
Sequence-specific DNA binding by covalently constrained peptide dimers of the basic leucine zipper protein GCN4.
|
| |
Bioorg Med Chem,
3,
777-784.
|
|
|
|
|
|
|
M.Suzuki,
and
M.Gerstein
(1995).
Binding geometry of alpha-helices that recognize DNA.
|
| |
Proteins,
23,
525-535.
|
|
|
|
|
|
|
M.Suzuki,
and
N.Yagi
(1995).
Stereochemical basis of DNA bending by transcription factors.
|
| |
Nucleic Acids Res,
23,
2083-2091.
|
|
|
|
|
|
|
M.W.Russo,
B.R.Sevetson,
and
J.Milbrandt
(1995).
Identification of NAB1, a repressor of NGFI-A- and Krox20-mediated transcription.
|
| |
Proc Natl Acad Sci U S A,
92,
6873-6877.
|
|
|
|
|
|
|
R.Lints,
M.A.Davis,
and
M.J.Hynes
(1995).
The positively acting amdA gene of Aspergillus nidulans encodes a protein with two C2H2 zinc-finger motifs.
|
| |
Mol Microbiol,
15,
965-975.
|
|
|
|
|
|
|
S.H.Larsson,
J.P.Charlieu,
K.Miyagawa,
D.Engelkamp,
M.Rassoulzadegan,
A.Ross,
F.Cuzin,
V.van Heyningen,
and
N.D.Hastie
(1995).
Subnuclear localization of WT1 in splicing or transcription factor domains is regulated by alternative splicing.
|
| |
Cell,
81,
391-401.
|
|
|
|
|
|
|
S.Muthukkumar,
P.Nair,
S.F.Sells,
N.G.Maddiwar,
R.J.Jacob,
and
V.M.Rangnekar
(1995).
Role of EGR-1 in thapsigargin-inducible apoptosis in the melanoma cell line A375-C6.
|
| |
Mol Cell Biol,
15,
6262-6272.
|
|
|
|
|
|
|
S.Natesan,
and
M.Gilman
(1995).
YY1 facilitates the association of serum response factor with the c-fos serum response element.
|
| |
Mol Cell Biol,
15,
5975-5982.
|
|
|
|
|
|
|
S.Yanagisawa
(1995).
A novel DNA-binding domain that may form a single zinc finger motif.
|
| |
Nucleic Acids Res,
23,
3403-3410.
|
|
|
|
|
|
|
T.B.Hamilton,
K.C.Barilla,
and
P.J.Romaniuk
(1995).
High affinity binding sites for the Wilms' tumour suppressor protein WT1.
|
| |
Nucleic Acids Res,
23,
277-284.
|
|
|
|
|
|
|
T.Tullius
(1995).
Homeodomains: together again for the first time.
|
| |
Structure,
3,
1143-1145.
|
|
|
|
|
|
|
W.Bruening,
E.Winnett,
and
J.Pelletier
(1995).
Wilms' tumor: a paradigm for insights into development and cancer.
|
| |
Cancer Invest,
13,
431-443.
|
|
|
|
|
|
|
X.Ye,
R.A.Kumar,
and
D.J.Patel
(1995).
Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex.
|
| |
Chem Biol,
2,
827-840.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
Y.Choo,
and
A.Klug
(1995).
Designing DNA-binding proteins on the surface of filamentous phage.
|
| |
Curr Opin Biotechnol,
6,
431-436.
|
|
|
|
|
|
|
Y.Shi,
and
J.M.Berg
(1995).
A direct comparison of the properties of natural and designed zinc-finger proteins.
|
| |
Chem Biol,
2,
83-89.
|
|
|
|
|
|
|
A.E.Uv,
C.R.Thompson,
and
S.J.Bray
(1994).
The Drosophila tissue-specific factor Grainyhead contains novel DNA-binding and dimerization domains which are conserved in the human protein CP2.
|
| |
Mol Cell Biol,
14,
4020-4031.
|
|
|
|
|
|
|
A.J.Franklin,
T.L.Jetton,
K.D.Shelton,
and
M.A.Magnuson
(1994).
BZP, a novel serum-responsive zinc finger protein that inhibits gene transcription.
|
| |
Mol Cell Biol,
14,
6773-6788.
|
|
|
|
|
|
|
A.Molnár,
and
K.Georgopoulos
(1994).
The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins.
|
| |
Mol Cell Biol,
14,
8292-8303.
|
|
|
|
|
|
|
A.Shrivastava,
and
K.Calame
(1994).
An analysis of genes regulated by the multi-functional transcriptional regulator Yin Yang-1.
|
| |
Nucleic Acids Res,
22,
5151-5155.
|
|
|
|
|
|
|
B.Cubero,
and
C.Scazzocchio
(1994).
Two different, adjacent and divergent zinc finger binding sites are necessary for CREA-mediated carbon catabolite repression in the proline gene cluster of Aspergillus nidulans.
|
| |
EMBO J,
13,
407-415.
|
|
|
|
|
|
|
B.Shen,
J.Kim,
and
D.Dorsett
(1994).
The enhancer-blocking suppressor of Hairy-wing zinc finger protein of Drosophila melanogaster alters DNA structure.
|
| |
Mol Cell Biol,
14,
5645-5652.
|
|
|
|
|
|
|
C.Cheng,
N.Kacherovsky,
K.M.Dombek,
S.Camier,
S.K.Thukral,
E.Rhim,
and
E.T.Young
(1994).
Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1.
|
| |
Mol Cell Biol,
14,
3842-3852.
|
|
|
|
|
|
|
C.E.Pritchard,
J.A.Grasby,
F.Hamy,
A.M.Zacharek,
M.Singh,
J.Karn,
and
M.J.Gait
(1994).
Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins.
|
| |
Nucleic Acids Res,
22,
2592-2600.
|
|
|
|
|
|
|
C.Junien,
and
I.Henry
(1994).
Genetics of Wilms' tumor: a blend of aberrant development and genomic imprinting.
|
| |
Kidney Int,
46,
1264-1279.
|
|
|
|
|
|
|
C.T.Walsh,
H.H.Sandstead,
A.S.Prasad,
P.M.Newberne,
and
P.J.Fraker
(1994).
Zinc: health effects and research priorities for the 1990s.
|
| |
Environ Health Perspect,
102,
5.
|
|
|
|
|
|
|
D.A.Erlanson,
and
G.L.Verdine
(1994).
Falling out of the fold: tumorigenic mutations and p53.
|
| |
Chem Biol,
1,
79-84.
|
|
|
|
|
|
|
E.Rubin,
and
E.T.Kool
(1994).
Strong, Specific Binding of Six Different DNA Sequences by a Single Conformation-Switching DNA Macrocycle.
|
| |
Angew Chem Int Ed Engl,
33,
1004-1007.
|
|
|
|
|
|
|
F.G.Larsen,
J.J.Voorhees,
and
A.Aström
(1994).
Retinoic acid induces expression of early growth response gene-1 (Egr-1) in human skin in vivo and in cultured skin fibroblasts.
|
| |
J Invest Dermatol,
102,
730-733.
|
|
|
|
|
|
|
G.C.Pérez-Alvarado,
C.Miles,
J.W.Michelsen,
H.A.Louis,
D.R.Winge,
M.C.Beckerle,
and
M.F.Summers
(1994).
Structure of the carboxy-terminal LIM domain from the cysteine rich protein CRP.
|
| |
Nat Struct Biol,
1,
388-398.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.M.Clore,
and
A.M.Gronenborn
(1994).
Young Investigator Award Lecture. Structures of larger proteins, protein-ligand and protein-DNA complexes by multidimensional heteronuclear NMR.
|
| |
Protein Sci,
3,
372-390.
|
|
|
|
|
|
|
H.D.Rupprecht,
V.P.Sukhatme,
A.P.Rupprecht,
R.B.Sterzel,
and
D.L.Coleman
(1994).
Serum response elements mediate protein kinase C dependent transcriptional induction of early growth response gene-1 by arginine vasopressin in rat mesangial cells.
|
| |
J Cell Physiol,
159,
311-323.
|
|
|
|
|
|
|
I.A.Drummond,
H.D.Rupprecht,
P.Rohwer-Nutter,
J.M.Lopez-Guisa,
S.L.Madden,
F.J.Rauscher,
and
V.P.Sukhatme
(1994).
DNA recognition by splicing variants of the Wilms' tumor suppressor, WT1.
|
| |
Mol Cell Biol,
14,
3800-3809.
|
|
|
|
|
|
|
I.A.Drummond,
P.Rohwer-Nutter,
and
V.P.Sukhatme
(1994).
The zebrafish egr1 gene encodes a highly conserved, zinc-finger transcriptional regulator.
|
| |
DNA Cell Biol,
13,
953-961.
|
|
|
|
|
|
|
I.A.Drummond,
P.Rohwer-Nutter,
and
V.P.Sukhatme
(1994).
The zebrafish egr1 gene encodes a highly conserved, zinc-finger transcriptional regulator.
|
| |
DNA Cell Biol,
13,
1047-1055.
|
|
|
|
|
|
|
J.F.Morris,
R.Hromas,
and
F.J.Rauscher
(1994).
Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core.
|
| |
Mol Cell Biol,
14,
1786-1795.
|
|
|
|
|
|
|
J.Liu,
M.Sodeoka,
W.S.Lane,
and
G.L.Verdine
(1994).
Evidence for a non-alpha-helical DNA-binding motif in the Rel homology region.
|
| |
Proc Natl Acad Sci U S A,
91,
908-912.
|
|
|
|
|
|
|
J.R.Desjarlais,
and
J.M.Berg
(1994).
Length-encoded multiplex binding site determination: application to zinc finger proteins.
|
| |
Proc Natl Acad Sci U S A,
91,
11099-11103.
|
|
|
|
|
|
|
K.Ogata,
S.Morikawa,
H.Nakamura,
A.Sekikawa,
T.Inoue,
H.Kanai,
A.Sarai,
S.Ishii,
and
Y.Nishimura
(1994).
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices.
|
| |
Cell,
79,
639-648.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
L.Nekludova,
and
C.O.Pabo
(1994).
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
|
| |
Proc Natl Acad Sci U S A,
91,
6948-6952.
|
|
|
|
|
|
|
L.V.Mendelman,
B.B.Beauchamp,
and
C.C.Richardson
(1994).
Requirement for a zinc motif for template recognition by the bacteriophage T7 primase.
|
| |
EMBO J,
13,
3909-3916.
|
|
|
|
|
|
|
L.von Kalm,
K.Crossgrove,
D.Von Seggern,
G.M.Guild,
and
S.K.Beckendorf
(1994).
The Broad-Complex directly controls a tissue-specific response to the steroid hormone ecdysone at the onset of Drosophila metamorphosis.
|
| |
EMBO J,
13,
3505-3516.
|
|
|
|
|
|
|
M.Hülskamp,
W.Lukowitz,
A.Beermann,
G.Glaser,
and
D.Tautz
(1994).
Differential regulation of target genes by different alleles of the segmentation gene hunchback in Drosophila.
|
| |
Genetics,
138,
125-134.
|
|
|
|
|
|
|
M.L.Nedved,
and
G.R.Moe
(1994).
Cooperative, non-specific binding of a zinc finger peptide to DNA.
|
| |
Nucleic Acids Res,
22,
4705-4711.
|
|
|
|
|
|
|
M.Lundin,
J.O.Nehlin,
and
H.Ronne
(1994).
Importance of a flanking AT-rich region in target site recognition by the GC box-binding zinc finger protein MIG1.
|
| |
Mol Cell Biol,
14,
1979-1985.
|
|
|
|
|
|
|
M.S.Lee,
D.S.Sem,
S.A.Kliewer,
J.Provencal,
R.M.Evans,
and
P.E.Wright
(1994).
NMR assignments and secondary structure of the retinoid X receptor alpha DNA-binding domain. Evidence for the novel C-terminal helix.
|
| |
Eur J Biochem,
224,
639-650.
|
|
|
|
|
|
|
M.Suzuki,
M.Gerstein,
and
N.Yagi
(1994).
Stereochemical basis of DNA recognition by Zn fingers.
|
| |
Nucleic Acids Res,
22,
3397-3405.
|
|
|
|
|
|
|
M.Suzuki,
and
N.Yagi
(1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
|
| |
Proc Natl Acad Sci U S A,
91,
12357-12361.
|
|
|
|
|
|
|
M.Suzuki
(1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
|
| |
Structure,
2,
317-326.
|
|
|
|
|
|
|
M.Tanaka,
and
W.Herr
(1994).
Reconstitution of transcriptional activation domains by reiteration of short peptide segments reveals the modular organization of a glutamine-rich activation domain.
|
| |
Mol Cell Biol,
14,
6056-6067.
|
|
|
|
|
|
|
N.Koyano-Nakagawa,
J.Nishida,
D.Baldwin,
K.Arai,
and
T.Yokota
(1994).
Molecular cloning of a novel human cDNA encoding a zinc finger protein that binds to the interleukin-3 promoter.
|
| |
Mol Cell Biol,
14,
5099-5107.
|
|
|
|
|
|
|
N.L.Marky,
and
W.K.Olson
(1994).
Spatial translational motions of base pairs in DNA molecules: application of the extended matrix generator method.
|
| |
Biopolymers,
34,
121-142.
|
|
|
|
|
|
|
P.M.Sharma,
M.Bowman,
B.F.Yu,
and
S.Sukumar
(1994).
A rodent model for Wilms tumors: embryonal kidney neoplasms induced by N-nitroso-N'-methylurea.
|
| |
Proc Natl Acad Sci U S A,
91,
9931-9935.
|
|
|
|
|
|
|
Q.Zheng,
and
D.J.Kyle
(1994).
Multiple copy sampling: rigid versus flexible protein.
|
| |
Proteins,
19,
324-329.
|
|
|
|
|
|
|
R.P.Kühnlein,
G.Frommer,
M.Friedrich,
M.Gonzalez-Gaitan,
A.Weber,
J.F.Wagner-Bernholz,
W.J.Gehring,
H.Jäckle,
and
R.Schuh
(1994).
spalt encodes an evolutionarily conserved zinc finger protein of novel structure which provides homeotic gene function in the head and tail region of the Drosophila embryo.
|
| |
EMBO J,
13,
168-179.
|
|
|
|
|
|
|
R.Sekido,
K.Murai,
J.Funahashi,
Y.Kamachi,
A.Fujisawa-Sehara,
Y.Nabeshima,
and
H.Kondoh
(1994).
The delta-crystallin enhancer-binding protein delta EF1 is a repressor of E2-box-mediated gene activation.
|
| |
Mol Cell Biol,
14,
5692-5700.
|
|
|
|
|
|
|
R.Varanasi,
N.Bardeesy,
M.Ghahremani,
M.J.Petruzzi,
N.Nowak,
M.A.Adam,
P.Grundy,
T.B.Shows,
and
J.Pelletier
(1994).
Fine structure analysis of the WT1 gene in sporadic Wilms tumors.
|
| |
Proc Natl Acad Sci U S A,
91,
3554-3558.
|
|
|
|
|
|
|
R.Vignali,
S.De Lucchini,
B.Kablar,
and
G.Barsacchi
(1994).
Genetic control of development in Xenopus laevis.
|
| |
Genetica,
94,
235-248.
|
|
|
|
|
|
|
R.Witzgall,
E.O'Leary,
A.Leaf,
D.Onaldi,
and
J.V.Bonventre
(1994).
The Krüppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression.
|
| |
Proc Natl Acad Sci U S A,
91,
4514-4518.
|
|
|
|
|
|
|
T.Pieler,
and
E.Bellefroid
(1994).
Perspectives on zinc finger protein function and evolution--an update.
|
| |
Mol Biol Rep,
20,
1-8.
|
|
|
|
|
|
|
U.Schäfer,
O.Rausch,
T.Bouwmeester,
and
T.Pieler
(1994).
Sequence-specific recognition of a repetitive DNA element by a C2H2 zinc-finger protein in Xenopus.
|
| |
Eur J Biochem,
226,
567-576.
|
|
|
|
|
|
|
Y.Choo,
and
A.Klug
(1994).
Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage.
|
| |
Proc Natl Acad Sci U S A,
91,
11163-11167.
|
|
|
|
|
|
|
Y.Choo,
and
A.Klug
(1994).
Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions.
|
| |
Proc Natl Acad Sci U S A,
91,
11168-11172.
|
|
|
|
|
|
|
A.D.Sharrocks,
H.Gille,
and
P.E.Shaw
(1993).
Identification of amino acids essential for DNA binding and dimerization in p67SRF: implications for a novel DNA-binding motif.
|
| |
Mol Cell Biol,
13,
123-132.
|
|
|
|
|
|
|
A.L.Gashler,
S.Swaminathan,
and
V.P.Sukhatme
(1993).
A novel repression module, an extensive activation domain, and a bipartite nuclear localization signal defined in the immediate-early transcription factor Egr-1.
|
| |
Mol Cell Biol,
13,
4556-4571.
|
|
|
|
|
|
|
B.A.Krizek,
L.E.Zawadzke,
and
J.M.Berg
(1993).
Independence of metal binding between tandem Cys2His2 zinc finger domains.
|
| |
Protein Sci,
2,
1313-1319.
|
|
|
|
|
|
|
D.J.Whyatt,
E.deBoer,
and
F.Grosveld
(1993).
The two zinc finger-like domains of GATA-1 have different DNA binding specificities.
|
| |
EMBO J,
12,
4993-5005.
|
|
|
|
|
|
|
D.Zarkower,
and
J.Hodgkin
(1993).
Zinc fingers in sex determination: only one of the two C. elegans Tra-1 proteins binds DNA in vitro.
|
| |
Nucleic Acids Res,
21,
3691-3698.
|
|
|
|
|
|
|
E.J.Bellefroid,
J.C.Marine,
T.Ried,
P.J.Lecocq,
M.Rivière,
C.Amemiya,
D.A.Poncelet,
P.G.Coulie,
P.de Jong,
and
C.Szpirer
(1993).
Clustered organization of homologous KRAB zinc-finger genes with enhanced expression in human T lymphoid cells.
|
| |
EMBO J,
12,
1363-1374.
|
|
|
|
|
|
|
F.Estruch,
and
M.Carlson
(1993).
Two homologous zinc finger genes identified by multicopy suppression in a SNF1 protein kinase mutant of Saccharomyces cerevisiae.
|
| |
Mol Cell Biol,
13,
3872-3881.
|
|
|
|
|
|
|
H.J.Thiesen,
and
C.Bach
(1993).
DNA recognition of C2H2 zinc-finger proteins. Evidence for a zinc-finger-specific DNA recognition code.
|
| |
Ann N Y Acad Sci,
684,
246-249.
|
|
|
|
|
|
|
I.J.Miller,
and
J.J.Bieker
(1993).
A novel, erythroid cell-specific murine transcription factor that binds to the CACCC element and is related to the Krüppel family of nuclear proteins.
|
| |
Mol Cell Biol,
13,
2776-2786.
|
|
|
|
|
|
|
J.D.Puglisi,
L.Chen,
A.D.Frankel,
and
J.R.Williamson
(1993).
Role of RNA structure in arginine recognition of TAR RNA.
|
| |
Proc Natl Acad Sci U S A,
90,
3680-3684.
|
|
|
|
|
|
|
J.O.Bustamante
(1993).
Restricted ion flow at the nuclear envelope of cardiac myocytes.
|
| |
Biophys J,
64,
1735-1749.
|
|
|
|
|
|
|
J.R.Desjarlais,
and
J.M.Berg
(1993).
Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins.
|
| |
Proc Natl Acad Sci U S A,
90,
2256-2260.
|
|
|
|
|
|
|
J.Tanikawa,
T.Yasukawa,
M.Enari,
K.Ogata,
Y.Nishimura,
S.Ishii,
and
A.Sarai
(1993).
Recognition of specific DNA sequences by the c-myb protooncogene product: role of three repeat units in the DNA-binding domain.
|
| |
Proc Natl Acad Sci U S A,
90,
9320-9324.
|
|
|
|
|
|
|
J.W.Schwabe,
L.Chapman,
J.T.Finch,
and
D.Rhodes
(1993).
The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements.
|
| |
Cell,
75,
567-578.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Nagai
(1993).
Recent advances in RNA-protein interaction studies.
|
| |
Mol Biol Rep,
18,
105-112.
|
|
|
|
|
|
|
K.Satyamoorthy,
K.Park,
M.L.Atchison,
and
C.C.Howe
(1993).
The intracisternal A-particle upstream element interacts with transcription factor YY1 to activate transcription: pleiotropic effects of YY1 on distinct DNA promoter elements.
|
| |
Mol Cell Biol,
13,
6621-6628.
|
|
|
|
|
|
|
K.Sogawa,
H.Imataka,
Y.Yamasaki,
H.Kusume,
H.Abe,
and
Y.Fujii-Kuriyama
(1993).
cDNA cloning and transcriptional properties of a novel GC box-binding protein, BTEB2.
|
| |
Nucleic Acids Res,
21,
1527-1532.
|
|
|
|
|
|
|
M.B.Toledano,
D.Ghosh,
F.Trinh,
and
W.J.Leonard
(1993).
N-terminal DNA-binding domains contribute to differential DNA-binding specificities of NF-kappa B p50 and p65.
|
| |
Mol Cell Biol,
13,
852-860.
|
|
|
|
|
|
|
M.J.Coppes,
G.J.Liefers,
P.Paul,
H.Yeger,
and
B.R.Williams
(1993).
Homozygous somatic Wt1 point mutations in sporadic unilateral Wilms tumor.
|
| |
Proc Natl Acad Sci U S A,
90,
1416-1419.
|
|
|
|
|
|
|
M.K.Ogilvie,
J.F.Smith,
and
J.S.Hanas
(1993).
Sequence divergence of a TFIIIA-type zinc finger protein from fish ovarian tissue.
|
| |
Nucleic Acids Res,
21,
4152.
|
|
|
|
|
|
|
M.Kiessling,
and
P.Gass
(1993).
Immediate early gene expression in experimental epilepsy.
|
| |
Brain Pathol,
3,
381-393.
|
|
|
|
|
|
|
M.Marino,
N.Archidiacono,
A.Franzé,
M.Rosati,
M.Rocchi,
A.Ballabio,
and
G.Grimaldi
(1993).
A novel X-linked member of the human zinc finger protein gene family: isolation, mapping, and expression.
|
| |
Mamm Genome,
4,
252-257.
|
|
|
|
|
|
|
M.Molinete,
W.Vermeulen,
A.Bürkle,
J.Ménissier-de Murcia,
J.H.Küpper,
J.H.Hoeijmakers,
and
G.de Murcia
(1993).
Overproduction of the poly(ADP-ribose) polymerase DNA-binding domain blocks alkylation-induced DNA repair synthesis in mammalian cells.
|
| |
EMBO J,
12,
2109-2117.
|
|
|
|
|
|
|
M.Numoto,
O.Niwa,
J.Kaplan,
K.K.Wong,
K.Merrell,
K.Kamiya,
K.Yanagihara,
and
K.Calame
(1993).
Transcriptional repressor ZF5 identifies a new conserved domain in zinc finger proteins.
|
| |
Nucleic Acids Res,
21,
3767-3775.
|
|
|
|
|
|
|
M.Suzuki
(1993).
Common features in DNA recognition helices of eukaryotic transcription factors.
|
| |
EMBO J,
12,
3221-3226.
|
|
|
|
|
|
|
N.D.Hastie
(1993).
Wilms' tumour gene and function.
|
| |
Curr Opin Genet Dev,
3,
408-413.
|
|
|
|
|
|
|
P.Kulmburg,
M.Mathieu,
C.Dowzer,
J.Kelly,
and
B.Felenbok
(1993).
Specific binding sites in the alcR and alcA promoters of the ethanol regulon for the CREA repressor mediating carbon catabolite repression in Aspergillus nidulans.
|
| |
Mol Microbiol,
7,
847-857.
|
|
|
|
|
|
|
P.S.Freemont
(1993).
The RING finger. A novel protein sequence motif related to the zinc finger.
|
| |
Ann N Y Acad Sci,
684,
174-192.
|
|
|
|
|
|
|
Q.Xu,
R.K.Shoemaker,
and
W.H.Braunlin
(1993).
Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution.
|
| |
Biophys J,
65,
1039-1049.
|
|
|
|
|
|
|
R.Bosselut,
J.Levin,
E.Adjadj,
and
J.Ghysdael
(1993).
A single amino-acid substitution in the Ets domain alters core DNA binding specificity of Ets1 to that of the related transcription factors Elf1 and E74.
|
| |
Nucleic Acids Res,
21,
5184-5191.
|
|
|
|
|
|
|
R.C.Hoffman,
S.J.Horvath,
and
R.E.Klevit
(1993).
Structures of DNA-binding mutant zinc finger domains: implications for DNA binding.
|
| |
Protein Sci,
2,
951-965.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.Delwel,
T.Funabiki,
B.L.Kreider,
K.Morishita,
and
J.N.Ihle
(1993).
Four of the seven zinc fingers of the Evi-1 myeloid-transforming gene are required for sequence-specific binding to GA(C/T)AAGA(T/C)AAGATAA.
|
| |
Mol Cell Biol,
13,
4291-4300.
|
|
|
|
|
|
|
R.Lovering,
I.M.Hanson,
K.L.Borden,
S.Martin,
N.J.O'Reilly,
G.I.Evan,
D.Rahman,
D.J.Pappin,
J.Trowsdale,
and
P.S.Freemont
(1993).
Identification and preliminary characterization of a protein motif related to the zinc finger.
|
| |
Proc Natl Acad Sci U S A,
90,
2112-2116.
|
|
|
|
|
|
|
R.M.Brazas,
and
D.J.Stillman
(1993).
Identification and purification of a protein that binds DNA cooperatively with the yeast SWI5 protein.
|
| |
Mol Cell Biol,
13,
5524-5537.
|
|
|
|
|
|
|
R.P.Huang,
and
E.D.Adamson
(1993).
Characterization of the DNA-binding properties of the early growth response-1 (Egr-1) transcription factor: evidence for modulation by a redox mechanism.
|
| |
DNA Cell Biol,
12,
265-273.
|
|
|
|
|
|
|
R.Tan,
L.Chen,
J.A.Buettner,
D.Hudson,
and
A.D.Frankel
(1993).
RNA recognition by an isolated alpha helix.
|
| |
Cell,
73,
1031-1040.
|
|
|
|
|
|
|
S.L.Madden,
and
F.J.Rauscher
(1993).
Positive and negative regulation of transcription and cell growth mediated by the EGR family of zinc-finger gene products.
|
| |
Ann N Y Acad Sci,
684,
75-84.
|
|
|
|
|
|
|
T.E.Wilson,
K.A.Padgett,
M.Johnston,
and
J.Milbrandt
(1993).
A genetic method for defining DNA-binding domains: application to the nuclear receptor NGFI-B.
|
| |
Proc Natl Acad Sci U S A,
90,
9186-9190.
|
|
|
|
|
|
|
T.Feldmann,
R.Alex,
J.Suckow,
R.Dildrop,
B.Kisters-Woike,
and
B.Müller-Hill
(1993).
Single exchanges of amino acids in the basic region change the specificity of N-Myc.
|
| |
Nucleic Acids Res,
21,
5050-5058.
|
|
|
|
|
|
|
T.Pieler,
and
O.Theunissen
(1993).
TFIIIA: nine fingers--three hands?
|
| |
Trends Biochem Sci,
18,
226-230.
|
|
|
|
|
|
|
Y.Choo,
and
A.Klug
(1993).
A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA.
|
| |
Nucleic Acids Res,
21,
3341-3346.
|
|
|
|
|
|
|
Y.L.Chan,
K.Suzuki,
J.Olvera,
and
I.G.Wool
(1993).
Zinc finger-like motifs in rat ribosomal proteins S27 and S29.
|
| |
Nucleic Acids Res,
21,
649-655.
|
|
|
|
|
|
|
A.D.Frankel
(1992).
Peptide models of the Tat-TAR protein-RNA interaction.
|
| |
Protein Sci,
1,
1539-1542.
|
|
|
|
|
|
|
A.D.Keller,
and
T.Maniatis
(1992).
Only two of the five zinc fingers of the eukaryotic transcriptional repressor PRDI-BF1 are required for sequence-specific DNA binding.
|
| |
Mol Cell Biol,
12,
1940-1949.
|
|
|
|
|
|
|
A.V.Kajava
(1992).
Left-handed topology of super-secondary structure formed by aligned alpha-helix and beta-hairpin.
|
| |
FEBS Lett,
302,
8.
|
|
|
|
|
|
|
C.Vesque,
and
P.Charnay
(1992).
Mapping functional regions of the segment-specific transcription factor Krox-20.
|
| |
Nucleic Acids Res,
20,
2485-2492.
|
|
|
|
|
|
|
D.F.Bogenhagen,
and
M.S.Sands
(1992).
Binding of TFIIIA to derivatives of 5S RNA containing sequence substitutions or deletions defines a minimal TFIIIA binding site.
|
| |
Nucleic Acids Res,
20,
2639-2645.
|
|
|
|
|
|
|
D.Zarkower,
and
J.Hodgkin
(1992).
Molecular analysis of the C. elegans sex-determining gene tra-1: a gene encoding two zinc finger proteins.
|
| |
Cell,
70,
237-249.
|
|
|
|
|
|
|
G.H.Jacobs
(1992).
Determination of the base recognition positions of zinc fingers from sequence analysis.
|
| |
EMBO J,
11,
4507-4517.
|
|
|
|
|
|
|
G.Hagen,
S.Müller,
M.Beato,
and
G.Suske
(1992).
Cloning by recognition site screening of two novel GT box binding proteins: a family of Sp1 related genes.
|
| |
Nucleic Acids Res,
20,
5519-5525.
|
|
|
|
|
|
|
H.Takatsuji,
M.Mori,
P.N.Benfey,
L.Ren,
and
N.H.Chua
(1992).
Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings.
|
| |
EMBO J,
11,
241-249.
|
|
|
|
|
|
|
H.Tseng,
and
H.Green
(1992).
Basonuclin: a keratinocyte protein with multiple paired zinc fingers.
|
| |
Proc Natl Acad Sci U S A,
89,
10311-10315.
|
|
|
|
|
|
|
J.A.Tainer,
V.A.Roberts,
and
E.D.Getzoff
(1992).
Protein metal-binding sites.
|
| |
Curr Opin Biotechnol,
3,
378-387.
|
|
|
|
|
|
|
J.C.Lacey,
N.S.Wickramasinghe,
G.W.Cook,
and
J.C.Lacey
(1992).
Experimental studies on the origin of the genetic code and the process of protein synthesis: a review update.
|
| |
Orig Life Evol Biosph,
22,
243-275.
|
|
|
|
|
|
|
J.G.Kim,
and
L.D.Hudson
(1992).
Novel member of the zinc finger superfamily: A C2-HC finger that recognizes a glia-specific gene.
|
| |
Mol Cell Biol,
12,
5632-5639.
|
|
|
|
|
|
|
J.J.Hayes,
and
A.P.Wolffe
(1992).
The interaction of transcription factors with nucleosomal DNA.
|
| |
Bioessays,
14,
597-603.
|
|
|
|
|
|
|
J.M.Berg
(1992).
Sp1 and the subfamily of zinc finger proteins with guanine-rich binding sites.
|
| |
Proc Natl Acad Sci U S A,
89,
11109-11110.
|
|
|
|
|
|
|
J.Mohler,
N.Weiss,
S.Murli,
S.Mohammadi,
K.Vani,
G.Vasilakis,
C.H.Song,
A.Epstein,
T.Kuang,
and
J.English
(1992).
The embryonically active gene, unkempt, of Drosophila encodes a Cys3His finger protein.
|
| |
Genetics,
131,
377-388.
|
|
|
|
|
|
|
J.Nardelli,
T.Gibson,
and
P.Charnay
(1992).
Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis.
|
| |
Nucleic Acids Res,
20,
4137-4144.
|
|
|
|
|
|
|
J.R.Desjarlais,
and
J.M.Berg
(1992).
Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach.
|
| |
Proteins,
12,
101-104.
|
|
|
|
|
|
|
J.R.Desjarlais,
and
J.M.Berg
(1992).
Toward rules relating zinc finger protein sequences and DNA binding site preferences.
|
| |
Proc Natl Acad Sci U S A,
89,
7345-7349.
|
|
|
|
|
|
|
J.W.Schwabe
(1992).
DNA between the sheets.
|
| |
Curr Biol,
2,
661-663.
|
|
|
|
|
|
|
K.L.Knight,
and
R.T.Sauer
(1992).
Biochemical and genetic analysis of operator contacts made by residues within the beta-sheet DNA binding motif of Mnt repressor.
|
| |
EMBO J,
11,
215-223.
|
|
|
|
|
|
|
K.R.Clemens,
X.Liao,
V.Wolf,
P.E.Wright,
and
J.M.Gottesfeld
(1992).
Definition of the binding sites of individual zinc fingers in the transcription factor IIIA-5S RNA gene complex.
|
| |
Proc Natl Acad Sci U S A,
89,
10822-10826.
|
|
|
|
|
|
|
L.Fairall,
and
D.Rhodes
(1992).
A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex.
|
| |
Nucleic Acids Res,
20,
4727-4731.
|
|
|
|
|
|
|
M.Crozatier,
K.Kongsuwan,
P.Ferrer,
J.R.Merriam,
J.A.Lengyel,
and
A.Vincent
(1992).
Single amino acid exchanges in separate domains of the Drosophila serendipity delta zinc finger protein cause embryonic and sex biased lethality.
|
| |
Genetics,
131,
905-916.
|
|
|
|
|
|
|
M.F.Summers,
L.E.Henderson,
M.R.Chance,
J.W.Bess,
T.L.South,
P.R.Blake,
I.Sagi,
G.Perez-Alvarado,
R.C.Sowder,
and
D.R.Hare
(1992).
Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1.
|
| |
Protein Sci,
1,
563-574.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.H.Little,
J.Prosser,
A.Condie,
P.J.Smith,
V.Van Heyningen,
and
N.D.Hastie
(1992).
Zinc finger point mutations within the WT1 gene in Wilms tumor patients.
|
| |
Proc Natl Acad Sci U S A,
89,
4791-4795.
|
|
|
|
|
|
|
M.K.Darby,
and
K.E.Joho
(1992).
Differential binding of zinc fingers from Xenopus TFIIIA and p43 to 5S RNA and the 5S RNA gene.
|
| |
Mol Cell Biol,
12,
3155-3164.
|
|
|
|
|
|
|
M.Kiledjian,
and
G.Dreyfuss
(1992).
Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box.
|
| |
EMBO J,
11,
2655-2664.
|
|
|
|
|
|
|
M.S.Lee,
R.J.Mortishire-Smith,
and
P.E.Wright
(1992).
The zinc finger motif. Conservation of chemical shifts and correlation with structure.
|
| |
FEBS Lett,
309,
29-32.
|
|
|
|
|
|
|
M.Suzuki
(1992).
DNA-bridging by a palindromic alpha-helix.
|
| |
Proc Natl Acad Sci U S A,
89,
8726-8730.
|
|
|
|
|
|
|
N.A.Woychik,
and
R.A.Young
(1992).
Genes encoding transcription factor IIIA and the RNA polymerase common subunit RPB6 are divergently transcribed in Saccharomyces cerevisiae.
|
| |
Proc Natl Acad Sci U S A,
89,
3999-4003.
|
|
|
|
|
|
|
O.Theunissen,
F.Rudt,
U.Guddat,
H.Mentzel,
and
T.Pieler
(1992).
RNA and DNA binding zinc fingers in Xenopus TFIIIA.
|
| |
Cell,
71,
679-690.
|
|
|
|
|
|
|
P.Kulmburg,
D.Sequeval,
F.Lenouvel,
M.Mathieu,
and
B.Felenbok
(1992).
Identification of the promoter region involved in the autoregulation of the transcriptional activator ALCR in Aspergillus nidulans.
|
| |
Mol Cell Biol,
12,
1932-1939.
|
|
|
|
|
|
|
P.S.Burke,
and
D.J.Wolgemuth
(1992).
Zfp-37, a new murine zinc finger encoding gene, is expressed in a developmentally regulated pattern in the male germ line.
|
| |
Nucleic Acids Res,
20,
2827-2834.
|
|
|
|
|
|
|
R.E.Harrington
(1992).
DNA curving and bending in protein-DNA recognition.
|
| |
Mol Microbiol,
6,
2549-2555.
|
|
|
|
|
|
|
R.Hromas,
L.Zon,
and
A.D.Friedman
(1992).
Hematopoietic transcription regulators and the origins of leukemia.
|
| |
Crit Rev Oncol Hematol,
12,
167-190.
|
|
|
|
|
|
|
R.J.Sommer,
M.Retzlaff,
K.Goerlich,
K.Sander,
and
D.Tautz
(1992).
Evolutionary conservation pattern of zinc-finger domains of Drosophila segmentation genes.
|
| |
Proc Natl Acad Sci U S A,
89,
10782-10786.
|
|
|
|
|
|
|
R.M.Attar,
and
M.Z.Gilman
(1992).
Expression cloning of a novel zinc finger protein that binds to the c-fos serum response element.
|
| |
Mol Cell Biol,
12,
2432-2443.
|
|
|
|
|
|
|
R.P.Sheridan,
and
R.Venkataraghavan
(1992).
A systematic search for protein signature sequences.
|
| |
Proteins,
14,
16-28.
|
|
|
|
|
|
|
R.W.Kriwacki,
S.C.Schultz,
T.A.Steitz,
and
J.P.Caradonna
(1992).
Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1.
|
| |
Proc Natl Acad Sci U S A,
89,
9759-9763.
|
|
|
|
|
|
|
S.Camier,
N.Kacherovsky,
and
E.T.Young
(1992).
A mutation outside the two zinc fingers of ADR1 can suppress defects in either finger.
|
| |
Mol Cell Biol,
12,
5758-5767.
|
|
|
|
|
|
|
S.K.Thukral,
M.L.Morrison,
and
E.T.Young
(1992).
Mutations in the zinc fingers of ADR1 that change the specificity of DNA binding and transactivation.
|
| |
Mol Cell Biol,
12,
2784-2792.
|
|
|
|
|
|
|
S.Noselli,
F.Payre,
and
A.Vincent
(1992).
Zinc fingers and other domains cooperate in binding of Drosophila sry beta and delta proteins at specific chromosomal sites.
|
| |
Mol Cell Biol,
12,
724-733.
|
|
|
|
|
|
|
T.E.Ellenberger,
C.J.Brandl,
K.Struhl,
and
S.C.Harrison
(1992).
The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex.
|
| |
Cell,
71,
1223-1237.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
U.Heinemann,
C.Alings,
and
M.Bansal
(1992).
Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA.
|
| |
EMBO J,
11,
1931-1939.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Van Heyningen,
and
N.D.Hastie
(1992).
Wilms' tumour: reconciling genetics and biology.
|
| |
Trends Genet,
8,
16-21.
|
|
|
|
|
|
|
W.Bruening,
N.Bardeesy,
B.L.Silverman,
R.A.Cohn,
G.A.Machin,
A.J.Aronson,
D.Housman,
and
J.Pelletier
(1992).
Germline intronic and exonic mutations in the Wilms' tumour gene (WT1) affecting urogenital development.
|
| |
Nat Genet,
1,
144-148.
|
|
|
|
|
|
|
W.T.Miller,
and
P.Schimmel
(1992).
A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene product.
|
| |
Mol Microbiol,
6,
1259-1262.
|
|
|
|
|
|
|
W.T.Miller,
and
P.Schimmel
(1992).
A retroviral-like metal binding motif in an aminoacyl-tRNA synthetase is important for tRNA recognition.
|
| |
Proc Natl Acad Sci U S A,
89,
2032-2035.
|
|
|
|
|
|
|
Y.Kasai,
J.R.Nambu,
P.M.Lieberman,
and
S.T.Crews
(1992).
Dorsal-ventral patterning in Drosophila: DNA binding of snail protein to the single-minded gene.
|
| |
Proc Natl Acad Sci U S A,
89,
3414-3418.
|
|
|
|
|
|
|
D.Neuhaus,
and
D.Rhodes
(1991).
Putting the finger on DNA.
|
| |
Curr Biol,
1,
268-270.
|
|
|
|
|
|
|
H.J.Müller,
C.Skerka,
A.Bialonski,
and
P.F.Zipfel
(1991).
Clone pAT 133 identifies a gene that encodes another human member of a class of growth factor-induced genes with almost identical zinc-finger domains.
|
| |
Proc Natl Acad Sci U S A,
88,
10079-10083.
|
|
|
|
|
|
|
J.F.Smith,
J.Hawkins,
R.E.Leonard,
and
J.S.Hanas
(1991).
Structural elements in the N-terminal half of transcription factor IIIA required for factor binding to the 5S RNA gene internal control region.
|
| |
Nucleic Acids Res,
19,
6871-6876.
|
|
|
|
|
|
|
J.G.Omichinski,
G.M.Clore,
K.Sakaguchi,
E.Appella,
and
A.M.Gronenborn
(1991).
Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy.
|
| |
FEBS Lett,
292,
25-30.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.R.Coggins
(1991).
Deletions, fusions and domain rearrangements.
|
| |
Curr Opin Biotechnol,
2,
576-581.
|
|
|
|
|
|
|
J.W.Schwabe,
and
D.Rhodes
(1991).
Beyond zinc fingers: steroid hormone receptors have a novel structural motif for DNA recognition.
|
| |
Trends Biochem Sci,
16,
291-296.
|
|
|
|
|
|
|
M.Kochoyan,
H.T.Keutmann,
and
M.A.Weiss
(1991).
Architectural rules of the zinc-finger motif: comparative two-dimensional NMR studies of native and "aromatic-swap" domains define a "weakly polar switch".
|
| |
Proc Natl Acad Sci U S A,
88,
8455-8459.
|
|
|
|
|
|
|
N.Hariharan,
D.E.Kelley,
and
R.P.Perry
(1991).
Delta, a transcription factor that binds to downstream elements in several polymerase II promoters, is a functionally versatile zinc finger protein.
|
| |
Proc Natl Acad Sci U S A,
88,
9799-9803.
|
|
|
|
|
|
|
P.W.Huber,
T.Morii,
H.Y.Mei,
and
J.K.Barton
(1991).
Structural polymorphism in the major groove of a 5S RNA gene complements the zinc finger domains of transcription factor IIIA.
|
| |
Proc Natl Acad Sci U S A,
88,
10801-10805.
|
|
|
|
|
|
|
R.Kaptein
(1991).
Distinguishing features.
|
| |
Curr Biol,
1,
336-338.
|
|
|
|
|
|
|
S.K.Thukral,
M.L.Morrison,
and
E.T.Young
(1991).
Alanine scanning site-directed mutagenesis of the zinc fingers of transcription factor ADR1: residues that contact DNA and that transactivate.
|
| |
Proc Natl Acad Sci U S A,
88,
9188-9192.
|
|
|
|
|
|
|
T.R.Bürglin
(1991).
The TEA domain: a novel, highly conserved DNA-binding motif.
|
| |
Cell,
66,
11-12.
|
|
|
|
|
|
|
W.C.Abraham,
M.Dragunow,
and
W.P.Tate
(1991).
The role of immediate early genes in the stabilization of long-term potentiation.
|
| |
Mol Neurobiol,
5,
297-314.
|
|
|
|
|
|
|
X.He,
and
M.G.Rosenfeld
(1991).
Mechanisms of complex transcriptional regulation: implications for brain development.
|
| |
Neuron,
7,
183-196.
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
Links
