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PDBsum entry 1zig
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DOI no:
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J Mol Biol
264:968-980
(1996)
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PubMed id:
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A network of heterogeneous hydrogen bonds in GNRA tetraloops.
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F.M.Jucker,
H.A.Heus,
P.F.Yip,
E.H.Moors,
A.Pardi.
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ABSTRACT
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RNA hairpin loops containing a GNRA consensus sequence are the most frequently
occurring hairpins in a variety of prokaryotic and eukaryotic RNAs. These
tetraloops play important functional roles in RNA folding, in RNA-RNA tertiary
interactions and as protein binding sites. Homo and heteronuclear NMR
spectroscopy have been used to determine the structures of the most abundant
members of the GNRA tetraloop family: the GAGA, GCAA and GAAA loops closed by a
C-G base pair. Analysis of the structures of these three hairpin loops reveals a
network of heterogeneous hydrogen bonds. The loops contain a G-A base pair, a G
base-phosphate hydrogen bond and several 2' OH-base hydrogen bonds. These
intramolecular interactions and the extensive base stacking in the loop help
explain the high thermodynamic stability and give insight into the diverse
biological roles of the GNRA RNA hairpins.
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Selected figure(s)
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Figure 6.
Figure 6. Schematic drawing of the hydrogen bonding
network proposed for GNRA tetraloops. The following
hydrogen bonds are indicated: G5 H2 to A8 N7, G5 N3
to A8 H6, G5 O2' to A8 H6, G5 2'OH to the six and seven
positions of nucleotide 7, G5 H2 to A8 OP and G5 H1 to
A8 OP.
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Figure 7.
Figure 7. Comparison of the
GCAA and GAGA loops, illustrates
small differences in hydrogen bond-
ing patterns. The hydrogen bonding
between -G5 2'OH and the third
base of the loops are shown. No
hydrogen atoms are displayed ex-
cept the G5 2'OH and the protons of
the third base, which are shown in
dark circles. (a) In the GCAA loop
the 2' hydroxyl group of G5 can
interact with the N7 of A7 and the
amino group of A7. (b) In the
GAGA loop the 2' hydroxyl group
of G5 can interact with the N7 of G7
or with the O6 of G7.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
264,
968-980)
copyright 1996.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.J.DePaul,
E.J.Thompson,
S.S.Patel,
K.Haldeman,
and
E.J.Sorin
(2010).
Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics.
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Nucleic Acids Res,
38,
4856-4867.
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J.P.Sheehy,
A.R.Davis,
and
B.M.Znosko
(2010).
Thermodynamic characterization of naturally occurring RNA tetraloops.
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RNA,
16,
417-429.
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M.Cevec,
C.Thibaudeau,
and
J.Plavec
(2010).
NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans.
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Nucleic Acids Res,
38,
7814-7821.
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PDB code:
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O.Taxilaga-Zetina,
P.Pliego-Pastrana,
and
M.D.Carbajal-Tinoco
(2010).
Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials.
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Phys Rev E Stat Nonlin Soft Matter Phys,
81,
041914.
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J.A.Dupont,
and
K.Snoussi
(2009).
Mg(2+ ) modulation of EMCV IRES key activity fragment equilibria and r(G.C) base-pair kinetics.
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| |
J Biol Phys,
35,
231-243.
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M.B.Sturm,
P.C.Tyler,
G.B.Evans,
and
V.L.Schramm
(2009).
Transition state analogues rescue ribosomes from saporin-L1 ribosome inactivating protein.
|
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Biochemistry,
48,
9941-9948.
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M.C.Ho,
M.B.Sturm,
S.C.Almo,
and
V.L.Schramm
(2009).
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
|
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Proc Natl Acad Sci U S A,
106,
20276-20281.
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PDB codes:
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M.de la Peña,
D.Dufour,
and
J.Gallego
(2009).
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold.
|
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RNA,
15,
1949-1964.
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T.J.Tavares,
A.V.Beribisky,
and
P.E.Johnson
(2009).
Structure of the cytosine-cytosine mismatch in the thymidylate synthase mRNA binding site and analysis of its interaction with the aminoglycoside paromomycin.
|
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RNA,
15,
911-922.
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PDB code:
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A.Bacolla,
J.E.Larson,
J.R.Collins,
J.Li,
A.Milosavljevic,
P.D.Stenson,
D.N.Cooper,
and
R.D.Wells
(2008).
Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties.
|
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Genome Res,
18,
1545-1553.
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G.R.Bowman,
X.Huang,
Y.Yao,
J.Sun,
G.Carlsson,
L.J.Guibas,
and
V.S.Pande
(2008).
Structural insight into RNA hairpin folding intermediates.
|
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J Am Chem Soc,
130,
9676-9678.
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J.E.Johnson,
and
C.G.Hoogstraten
(2008).
Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling.
|
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J Am Chem Soc,
130,
16757-16769.
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J.M.Hart,
S.D.Kennedy,
D.H.Mathews,
and
D.H.Turner
(2008).
NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.
|
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J Am Chem Soc,
130,
10233-10239.
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K.A.Vander Meulen,
J.H.Davis,
T.R.Foster,
M.T.Record,
and
S.E.Butcher
(2008).
Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing.
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J Mol Biol,
384,
702-717.
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M.Cevec,
C.Thibaudeau,
and
J.Plavec
(2008).
Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans.
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Nucleic Acids Res,
36,
2330-2337.
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PDB code:
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M.Schwalbe,
O.Ohlenschläger,
A.Marchanka,
R.Ramachandran,
S.Häfner,
T.Heise,
and
M.Görlach
(2008).
Solution structure of stem-loop alpha of the hepatitis B virus post-transcriptional regulatory element.
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Nucleic Acids Res,
36,
1681-1689.
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PDB code:
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N.J.Reiter,
L.J.Maher,
and
S.E.Butcher
(2008).
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.
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Nucleic Acids Res,
36,
1227-1236.
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PDB code:
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N.V.Prabhu,
M.Panda,
Q.Yang,
and
K.A.Sharp
(2008).
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules.
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J Comput Chem,
29,
1113-1130.
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P.C.Bevilacqua,
and
J.M.Blose
(2008).
Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.
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Annu Rev Phys Chem,
59,
79.
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S.Fulle,
and
H.Gohlke
(2008).
Analyzing the flexibility of RNA structures by constraint counting.
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Biophys J,
94,
4202-4219.
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T.Xia
(2008).
Taking femtosecond snapshots of RNA conformational dynamics and complexity.
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Curr Opin Chem Biol,
12,
604-611.
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Y.Zhao,
J.L.Knee,
and
A.M.Baranger
(2008).
Characterization of two adenosine analogs as fluorescence probes in RNA.
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Bioorg Chem,
36,
271-277.
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F.Y.Siu,
R.J.Spanggord,
and
J.A.Doudna
(2007).
SRP RNA provides the physiologically essential GTPase activation function in cotranslational protein targeting.
|
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RNA,
13,
240-250.
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H.Jin,
J.P.Loria,
and
P.B.Moore
(2007).
Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA.
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Mol Cell,
26,
205-215.
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PDB codes:
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M.B.Sturm,
S.Roday,
and
V.L.Schramm
(2007).
Circular DNA and DNA/RNA hybrid molecules as scaffolds for ricin inhibitor design.
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J Am Chem Soc,
129,
5544-5550.
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M.Kimoto,
T.Mitsui,
Y.Harada,
A.Sato,
S.Yokoyama,
and
I.Hirao
(2007).
Fluorescent probing for RNA molecules by an unnatural base-pair system.
|
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Nucleic Acids Res,
35,
5360-5369.
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R.Das,
and
D.Baker
(2007).
Automated de novo prediction of native-like RNA tertiary structures.
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Proc Natl Acad Sci U S A,
104,
14664-14669.
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S.Roday,
S.Saen-oon,
and
V.L.Schramm
(2007).
Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin a-chain.
|
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Biochemistry,
46,
6169-6182.
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V.Lisi,
and
F.Major
(2007).
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships.
|
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RNA,
13,
1537-1545.
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Z.Zhuang,
L.Jaeger,
and
J.E.Shea
(2007).
Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.
|
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Nucleic Acids Res,
35,
6995-7002.
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A.V.Pertzev,
and
A.W.Nicholson
(2006).
Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III.
|
| |
Nucleic Acids Res,
34,
3708-3721.
|
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C.Hsiao,
S.Mohan,
E.Hershkovitz,
A.Tannenbaum,
and
L.D.Williams
(2006).
Single nucleotide RNA choreography.
|
| |
Nucleic Acids Res,
34,
1481-1491.
|
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E.Lescrinier,
K.Nauwelaerts,
K.Zanier,
K.Poesen,
M.Sattler,
and
P.Herdewijn
(2006).
The naturally occurring N6-threonyl adenine in anticodon loop of Schizosaccharomyces pombe tRNAi causes formation of a unique U-turn motif.
|
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Nucleic Acids Res,
34,
2878-2886.
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PDB code:
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L.Grajcar,
C.El Amri,
M.Ghomi,
S.Fermandjian,
V.Huteau,
R.Mandel,
S.Lecomte,
and
M.H.Baron
(2006).
Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy.
|
| |
Biopolymers,
82,
6.
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M.Seetharaman,
N.V.Eldho,
R.A.Padgett,
and
K.T.Dayie
(2006).
Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA.
|
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RNA,
12,
235-247.
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PDB code:
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N.Spacková,
and
J.Sponer
(2006).
Molecular dynamics simulations of sarcin-ricin rRNA motif.
|
| |
Nucleic Acids Res,
34,
697-708.
|
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S.Lemieux,
and
F.Major
(2006).
Automated extraction and classification of RNA tertiary structure cyclic motifs.
|
| |
Nucleic Acids Res,
34,
2340-2346.
|
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W.J.Melchers,
J.Zoll,
M.Tessari,
D.V.Bakhmutov,
A.P.Gmyl,
V.I.Agol,
and
H.A.Heus
(2006).
A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA.
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RNA,
12,
1671-1682.
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PDB code:
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J.Koplin,
Y.Mu,
C.Richter,
H.Schwalbe,
and
G.Stock
(2005).
Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study.
|
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Structure,
13,
1255-1267.
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R.Stefl,
and
F.H.Allain
(2005).
A novel RNA pentaloop fold involved in targeting ADAR2.
|
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RNA,
11,
592-597.
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PDB code:
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T.Hainzl,
S.Huang,
and
A.E.Sauer-Eriksson
(2005).
Structural insights into SRP RNA: an induced fit mechanism for SRP assembly.
|
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RNA,
11,
1043-1050.
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PDB code:
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T.Lönnberg,
and
H.Lönnberg
(2005).
Chemical models for ribozyme action.
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| |
Curr Opin Chem Biol,
9,
665-673.
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T.Xia,
C.Wan,
R.W.Roberts,
and
A.H.Zewail
(2005).
RNA-protein recognition: single-residue ultrafast dynamical control of structural specificity and function.
|
| |
Proc Natl Acad Sci U S A,
102,
13013-13018.
|
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Y.Ihle,
O.Ohlenschläger,
S.Häfner,
E.Duchardt,
M.Zacharias,
S.Seitz,
R.Zell,
R.Ramachandran,
and
M.Görlach
(2005).
A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA.
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| |
Nucleic Acids Res,
33,
2003-2011.
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PDB code:
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J.Cabello-Villegas,
K.E.Giles,
A.M.Soto,
P.Yu,
A.Mougin,
K.L.Beemon,
and
Y.X.Wang
(2004).
Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor.
|
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RNA,
10,
1388-1398.
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PDB codes:
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M.Phelan,
R.J.Banks,
G.Conn,
and
V.Ramesh
(2004).
NMR studies of the structure and Mg2+ binding properties of a conserved RNA motif of EMCV picornavirus IRES element.
|
| |
Nucleic Acids Res,
32,
4715-4724.
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M.R.Fabian,
and
K.A.White
(2004).
5'-3' RNA-RNA interaction facilitates cap- and poly(A) tail-independent translation of tomato bushy stunt virus mrna: a potential common mechanism for tombusviridae.
|
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J Biol Chem,
279,
28862-28872.
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S.Baba,
M.Kajikawa,
N.Okada,
and
G.Kawai
(2004).
Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2.
|
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RNA,
10,
1380-1387.
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PDB code:
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A.E.Sauer-Eriksson,
and
T.Hainzl
(2003).
S-domain assembly of the signal recognition particle.
|
| |
Curr Opin Struct Biol,
13,
64-70.
|
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B.Fürtig,
C.Richter,
J.Wöhnert,
and
H.Schwalbe
(2003).
NMR spectroscopy of RNA.
|
| |
Chembiochem,
4,
936-962.
|
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C.C.Correll,
and
K.Swinger
(2003).
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.
|
| |
RNA,
9,
355-363.
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PDB code:
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E.J.Sorin,
Y.M.Rhee,
B.J.Nakatani,
and
V.S.Pande
(2003).
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations.
|
| |
Biophys J,
85,
790-803.
|
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J.E.Barrick,
and
R.W.Roberts
(2003).
Achieving specificity in selected and wild-type N peptide-RNA complexes: the importance of discrimination against noncognate RNA targets.
|
| |
Biochemistry,
42,
12998-13007.
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J.Sarzynska,
L.Nilsson,
and
T.Kulinski
(2003).
Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations.
|
| |
Biophys J,
85,
3445-3459.
|
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N.J.Reiter,
L.J.Nikstad,
A.M.Allmann,
R.J.Johnson,
and
S.E.Butcher
(2003).
Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
|
| |
RNA,
9,
533-542.
|
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PDB codes:
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R.J.Austin,
T.Xia,
J.Ren,
T.T.Takahashi,
and
R.W.Roberts
(2003).
Differential modes of recognition in N peptide-boxB complexes.
|
| |
Biochemistry,
42,
14957-14967.
|
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S.J.Schroeder,
M.A.Fountain,
S.D.Kennedy,
P.J.Lukavsky,
J.D.Puglisi,
T.R.Krugh,
and
D.H.Turner
(2003).
Thermodynamic stability and structural features of the J4/5 loop in a Pneumocystis carinii group I intron.
|
| |
Biochemistry,
42,
14184-14196.
|
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T.Leeper,
N.Leulliot,
and
G.Varani
(2003).
The solution structure of an essential stem-loop of human telomerase RNA.
|
| |
Nucleic Acids Res,
31,
2614-2621.
|
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PDB code:
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T.Xia,
A.Frankel,
T.T.Takahashi,
J.Ren,
and
R.W.Roberts
(2003).
Context and conformation dictate function of a transcription antitermination switch.
|
| |
Nat Struct Biol,
10,
812-819.
|
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T.Xia,
H.C.Becker,
C.Wan,
A.Frankel,
R.W.Roberts,
and
A.H.Zewail
(2003).
The RNA-protein complex: direct probing of the interfacial recognition dynamics and its correlation with biological functions.
|
| |
Proc Natl Acad Sci U S A,
100,
8119-8123.
|
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A.Huppler,
L.J.Nikstad,
A.M.Allmann,
D.A.Brow,
and
S.E.Butcher
(2002).
Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure.
|
| |
Nat Struct Biol,
9,
431-435.
|
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PDB code:
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A.Kitamura,
Y.Muto,
S.Watanabe,
I.Kim,
T.Ito,
Y.Nishiya,
K.Sakamoto,
T.Ohtsuki,
G.Kawai,
K.Watanabe,
K.Hosono,
H.Takaku,
E.Katoh,
T.Yamazaki,
T.Inoue,
and
S.Yokoyama
(2002).
Solution structure of an RNA fragment with the P7/P9.0 region and the 3'-terminal guanosine of the tetrahymena group I intron.
|
| |
RNA,
8,
440-451.
|
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PDB code:
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|
C.Oubridge,
A.Kuglstatter,
L.Jovine,
and
K.Nagai
(2002).
Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle.
|
| |
Mol Cell,
9,
1251-1261.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.Schuster,
C.Isel,
I.Imbert,
C.Ehresmann,
R.Marquet,
and
M.P.Kieny
(2002).
Secondary structure of the 3' terminus of hepatitis C virus minus-strand RNA.
|
| |
J Virol,
76,
8058-8068.
|
|
|
|
|
|
|
L.R.Comolli,
N.B.Ulyanov,
A.M.Soto,
L.A.Marky,
T.L.James,
and
W.H.Gmeiner
(2002).
NMR structure of the 3' stem-loop from human U4 snRNA.
|
| |
Nucleic Acids Res,
30,
4371-4379.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.I.Newby,
and
N.L.Greenbaum
(2002).
Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine.
|
| |
Nat Struct Biol,
9,
958-965.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.C.Leeper,
M.B.Martin,
H.Kim,
S.Cox,
V.Semenchenko,
F.J.Schmidt,
and
S.R.Van Doren
(2002).
Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
|
| |
Nat Struct Biol,
9,
397-403.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
T.Hainzl,
S.Huang,
and
A.E.Sauer-Eriksson
(2002).
Structure of the SRP19 RNA complex and implications for signal recognition particle assembly.
|
| |
Nature,
417,
767-771.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.Juneau,
E.Podell,
D.J.Harrington,
and
T.R.Cech
(2001).
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
|
| |
Structure,
9,
221-231.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
K.S.Tanaka,
X.Y.Chen,
Y.Ichikawa,
P.C.Tyler,
R.H.Furneaux,
and
V.L.Schramm
(2001).
Ricin A-chain inhibitors resembling the oxacarbenium ion transition state.
|
| |
Biochemistry,
40,
6845-6851.
|
|
|
|
|
|
|
K.Wild,
I.Sinning,
and
S.Cusack
(2001).
Crystal structure of an early protein-RNA assembly complex of the signal recognition particle.
|
| |
Science,
294,
598-601.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.E.Burkard,
T.Xia,
and
D.H.Turner
(2001).
Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair.
|
| |
Biochemistry,
40,
2478-2483.
|
|
|
|
|
|
|
M.Zheng,
M.Wu,
and
I.Tinoco
(2001).
Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme.
|
| |
Proc Natl Acad Sci U S A,
98,
3695-3700.
|
|
|
|
|
|
|
N.L.Greenbaum,
C.Mundoma,
and
D.R.Peterman
(2001).
Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence.
|
| |
Biochemistry,
40,
1124-1134.
|
|
|
|
|
|
|
P.Z.Qin,
S.E.Butcher,
J.Feigon,
and
W.L.Hubbell
(2001).
Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study.
|
| |
Biochemistry,
40,
6929-6936.
|
|
|
|
|
|
|
Q.Zhang,
K.Harada,
H.S.Cho,
A.D.Frankel,
and
D.E.Wemmer
(2001).
Structural characterization of the complex of the Rev response element RNA with a selected peptide.
|
| |
Chem Biol,
8,
511-520.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.J.Carter,
I.Dubchak,
and
S.R.Holbrook
(2001).
A computational approach to identify genes for functional RNAs in genomic sequences.
|
| |
Nucleic Acids Res,
29,
3928-3938.
|
|
|
|
|
|
|
V.Baumruk,
C.Gouyette,
T.Huynh-Dinh,
J.S.Sun,
and
M.Ghomi
(2001).
Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy.
|
| |
Nucleic Acids Res,
29,
4089-4096.
|
|
|
|
|
|
|
C.G.Hoogstraten,
J.R.Wank,
and
A.Pardi
(2000).
Active site dynamics in the lead-dependent ribozyme.
|
| |
Biochemistry,
39,
9951-9958.
|
|
|
|
|
|
|
G.R.Zimmermann,
C.L.Wick,
T.P.Shields,
R.D.Jenison,
and
A.Pardi
(2000).
Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer.
|
| |
RNA,
6,
659-667.
|
|
|
|
|
|
|
J.L.Diener,
and
C.Wilson
(2000).
Role of SRP19 in assembly of the Archaeoglobus fulgidus signal recognition particle.
|
| |
Biochemistry,
39,
12862-12874.
|
|
|
|
|
|
|
J.Sarzynska,
T.Kulinski,
and
L.Nilsson
(2000).
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
|
| |
Biophys J,
79,
1213-1227.
|
|
|
|
|
|
|
M.E.Burkard,
and
D.H.Turner
(2000).
NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.
|
| |
Biochemistry,
39,
11748-11762.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Maderia,
T.E.Horton,
and
V.J.DeRose
(2000).
Metal interactions with a GAAA RNA tetraloop characterized by (31)P NMR and phosphorothioate substitutions.
|
| |
Biochemistry,
39,
8193-8200.
|
|
|
|
|
|
|
M.Menger,
F.Eckstein,
and
D.Porschke
(2000).
Dynamics of the RNA hairpin GNRA tetraloop.
|
| |
Biochemistry,
39,
4500-4507.
|
|
|
|
|
|
|
M.Schärpf,
H.Sticht,
K.Schweimer,
M.Boehm,
S.Hoffmann,
and
P.Rösch
(2000).
Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex.
|
| |
Eur J Biochem,
267,
2397-2408.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.J.Michiels,
C.H.Schouten,
C.W.Hilbers,
and
H.A.Heus
(2000).
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.
|
| |
RNA,
6,
1821-1832.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.E.Horton,
M.Maderia,
and
V.J.DeRose
(2000).
Impact of phosphorothioate substitutions on the thermodynamic stability of an RNA GAAA tetraloop: an unexpected stabilization.
|
| |
Biochemistry,
39,
8201-8207.
|
|
|
|
|
|
|
X.Chen,
J.A.McDowell,
R.Kierzek,
T.R.Krugh,
and
D.H.Turner
(2000).
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).
|
| |
Biochemistry,
39,
8970-8982.
|
|
|
PDB codes:
|
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|
|
|
|
|
D.Scarabino,
A.Crisari,
S.Lorenzini,
K.Williams,
and
G.P.Tocchini-Valentini
(1999).
tRNA prefers to kiss.
|
| |
EMBO J,
18,
4571-4578.
|
|
|
|
|
|
|
F.Jiang,
A.Gorin,
W.Hu,
A.Majumdar,
S.Baskerville,
W.Xu,
A.Ellington,
and
D.J.Patel
(1999).
Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples.
|
| |
Structure,
7,
1461-1472.
|
|
|
PDB codes:
|
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|
|
|
|
|
G.A.Soukup,
and
R.R.Breaker
(1999).
Relationship between internucleotide linkage geometry and the stability of RNA.
|
| |
RNA,
5,
1308-1325.
|
|
|
|
|
|
|
K.Juneau,
and
T.R.Cech
(1999).
In vitro selection of RNAs with increased tertiary structure stability.
|
| |
RNA,
5,
1119-1129.
|
|
|
|
|
|
|
K.Nakamura,
S.Yahagi,
T.Yamazaki,
and
K.Yamane
(1999).
Bacillus subtilis histone-like protein, HBsu, is an integral component of a SRP-like particle that can bind the Alu domain of small cytoplasmic RNA.
|
| |
J Biol Chem,
274,
13569-13576.
|
|
|
|
|
|
|
K.Wild,
O.Weichenrieder,
G.A.Leonard,
and
S.Cusack
(1999).
The 2 A structure of helix 6 of the human signal recognition particle RNA.
|
| |
Structure,
7,
1345-1352.
|
|
|
PDB code:
|
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|
|
|
|
|
L.Jiang,
A.Majumdar,
W.Hu,
T.J.Jaishree,
W.Xu,
and
D.J.Patel
(1999).
Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer.
|
| |
Structure,
7,
817-827.
|
|
|
PDB code:
|
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|
|
|
|
|
M.de la Peña,
B.Navarro,
and
R.Flores
(1999).
Mapping the molecular determinant of pathogenicity in a hammerhead viroid: a tetraloop within the in vivo branched RNA conformation.
|
| |
Proc Natl Acad Sci U S A,
96,
9960-9965.
|
|
|
|
|
|
|
P.B.Moore
(1999).
Structural motifs in RNA.
|
| |
Annu Rev Biochem,
68,
287-300.
|
|
|
|
|
|
|
S.K.Silverman,
and
T.R.Cech
(1999).
Energetics and cooperativity of tertiary hydrogen bonds in RNA structure.
|
| |
Biochemistry,
38,
8691-8702.
|
|
|
|
|
|
|
U.Schmitz,
S.Behrens,
D.M.Freymann,
R.J.Keenan,
P.Lukavsky,
P.Walter,
and
T.L.James
(1999).
Structure of the phylogenetically most conserved domain of SRP RNA.
|
| |
RNA,
5,
1419-1429.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
X.Ye,
A.Gorin,
R.Frederick,
W.Hu,
A.Majumdar,
W.Xu,
G.McLendon,
A.Ellington,
and
D.J.Patel
(1999).
RNA architecture dictates the conformations of a bound peptide.
|
| |
Chem Biol,
6,
657-669.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
B.L.Golden,
A.R.Gooding,
E.R.Podell,
and
T.R.Cech
(1998).
A preorganized active site in the crystal structure of the Tetrahymena ribozyme.
|
| |
Science,
282,
259-264.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.C.Correll,
A.Munishkin,
Y.L.Chan,
Z.Ren,
I.G.Wool,
and
T.A.Steitz
(1998).
Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
|
| |
Proc Natl Acad Sci U S A,
95,
13436-13441.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.E.Johansson,
D.Dertinger,
K.A.LeCuyer,
L.S.Behlen,
C.H.Greef,
and
O.C.Uhlenbeck
(1998).
A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein.
|
| |
Proc Natl Acad Sci U S A,
95,
9244-9249.
|
|
|
|
|
|
|
J.L.Diener,
and
P.B.Moore
(1998).
Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif.
|
| |
Mol Cell,
1,
883-894.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Mogridge,
P.Legault,
J.Li,
M.D.Van Oene,
L.E.Kay,
and
J.Greenblatt
(1998).
Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage lambda N protein.
|
| |
Mol Cell,
1,
265-275.
|
|
|
|
|
|
|
M.Boudvillain,
and
A.M.Pyle
(1998).
Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis.
|
| |
EMBO J,
17,
7091-7104.
|
|
|
|
|
|
|
M.R.Giese,
K.Betschart,
T.Dale,
C.K.Riley,
C.Rowan,
K.J.Sprouse,
and
M.J.Serra
(1998).
Stability of RNA hairpins closed by wobble base pairs.
|
| |
Biochemistry,
37,
1094-1100.
|
|
|
|
|
|
|
P.B.Moore
(1998).
The three-dimensional structure of the ribosome and its components.
|
| |
Annu Rev Biophys Biomol Struct,
27,
35-58.
|
|
|
|
|
|
|
P.Legault,
J.Li,
J.Mogridge,
L.E.Kay,
and
J.Greenblatt
(1998).
NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif.
|
| |
Cell,
93,
289-299.
|
|
|
|
|
|
|
P.Zheng,
C.J.Burrows,
and
S.E.Rokita
(1998).
Nickel- and cobalt-dependent reagents identify structural features of RNA that are not detected by dimethyl sulfate or RNase T1.
|
| |
Biochemistry,
37,
2207-2214.
|
|
|
|
|
|
|
W.Shepard,
W.B.Cruse,
R.Fourme,
E.de la Fortelle,
and
T.Prangé
(1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
|
| |
Structure,
6,
849-861.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
X.Y.Chen,
T.M.Link,
and
V.L.Schramm
(1998).
Ricin A-chain: kinetics, mechanism, and RNA stem-loop inhibitors.
|
| |
Biochemistry,
37,
11605-11613.
|
|
|
|
|
|
|
Z.Cai,
A.Gorin,
R.Frederick,
X.Ye,
W.Hu,
A.Majumdar,
A.Kettani,
and
D.J.Patel
(1998).
Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex.
|
| |
Nat Struct Biol,
5,
203-212.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.R.Zimmermann,
R.D.Jenison,
C.L.Wick,
J.P.Simorre,
and
A.Pardi
(1997).
Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA.
|
| |
Nat Struct Biol,
4,
644-649.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.P.Simorre,
P.Legault,
A.B.Hangar,
P.Michiels,
and
A.Pardi
(1997).
A conformational change in the catalytic core of the hammerhead ribozyme upon cleavage of an RNA substrate.
|
| |
Biochemistry,
36,
518-525.
|
|
|
|
|
|
|
L.Su,
J.T.Radek,
L.A.Labeots,
K.Hallenga,
P.Hermanto,
H.Chen,
S.Nakagawa,
M.Zhao,
S.Kates,
and
M.A.Weiss
(1997).
An RNA enhancer in a phage transcriptional antitermination complex functions as a structural switch.
|
| |
Genes Dev,
11,
2214-2226.
|
|
|
|
|
|
|
M.J.van Dongen,
M.M.Mooren,
E.F.Willems,
G.A.van der Marel,
J.H.van Boom,
S.S.Wijmenga,
and
C.W.Hilbers
(1997).
Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.
|
| |
Nucleic Acids Res,
25,
1537-1547.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.B.Moore
(1997).
The conformation of ribosomes and rRNA.
|
| |
Curr Opin Struct Biol,
7,
343-347.
|
|
|
|
|
|
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
