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PDBsum entry 151c
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Electron transport 2
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PDB id
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151c
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J Mol Biol
197:257-271
(1987)
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PubMed id:
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Binding of Hoechst 33258 to the minor groove of B-DNA.
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P.E.Pjura,
K.Grzeskowiak,
R.E.Dickerson.
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ABSTRACT
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An X-ray crystallographic structure analysis has been carried out on the complex
between the antibiotic and DNA fluorochrome Hoechst 33258 and a synthetic B-DNA
dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G. The drug molecule, which can be
schematized as: phenol-benzimidazole-benzimidazole-piperazine, sits within the
minor groove in the A-T-T-C region of the DNA double helix, displacing the spine
of hydration that is found in drug-free DNA. The NH groups of the benzimidazoles
make bridging three-center hydrogen bonds between adenine N-3 and thymine O-2
atoms on the edges of base-pairs, in a manner both mimicking the spine of
hydration and calling to mind the binding of the auti-tumor drug netropsin. Two
conformers of Hoechst are seen in roughly equal populations, related by 180
degrees rotation about the central benzimidazole-benzimidazole bond: one form in
which the piperazine ring extends out from the surface of the double helix, and
another in which it is buried deep within the minor groove. Steric clash between
the drug and DNA dictates that the phenol-benzimidazole-benzimidazole portion of
Hoechst 33258 binds only to A.T regions of DNA, whereas the piperazine ring
demands the wider groove characteristic of G.C regions. Hence, the piperazine
ring suggests a possible G.C-reading element for synthetic DNA sequence-reading
drug analogs.
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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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J.C.Stockert,
and
M.I.Abasolo
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Inaccurate chemical structures of dyes and fluorochromes found in the literature can be problematic for teaching and research.
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Biotech Histochem,
86,
52-60.
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N.A.Cherepanova,
A.A.Ivanov,
D.V.Maltseva,
A.S.Minero,
A.V.Gromyko,
S.A.Streltsov,
A.L.Zhuze,
and
E.S.Gromova
(2011).
Dimeric bisbenzimidazoles inhibit the DNA methylation catalyzed by the murine Dnmt3a catalytic domain.
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J Enzyme Inhib Med Chem,
26,
295-300.
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P.Peñalver,
F.Marcelo,
J.Jiménez-Barbero,
and
C.Vicent
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Carbohydrate recognition at the minor-groove of the self-complementary duplex d(CGCGAATTCGCG)2 by a synthetic glyco-oligoamide.
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Chemistry,
17,
4561-4570.
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O.Y.Susova,
A.A.Ivanov,
S.S.Morales Ruiz,
E.A.Lesovaya,
A.V.Gromyko,
S.A.Streltsov,
and
A.L.Zhuze
(2010).
Minor groove dimeric bisbenzimidazoles inhibit in vitro DNA binding to eukaryotic DNA topoisomerase I.
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| |
Biochemistry (Mosc),
75,
695-701.
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P.Del Castillo,
R.W.Horobin,
A.Blázquez-Castro,
and
J.C.Stockert
(2010).
Binding of cationic dyes to DNA: distinguishing intercalation and groove binding mechanisms using simple experimental and numerical models.
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Biotech Histochem,
85,
247-256.
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A.K.Jain,
S.K.Gupta,
and
V.Tandon
(2009).
Evaluation of electronic effect of phenyl ring substituents on the DNA minor groove binding properties of novel bis and terbenzimidazoles: synthesis and spectroscopic studies of ligand-DNA interaction.
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Oligonucleotides,
19,
329-340.
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D.Banerjee,
A.Makhal,
and
S.K.Pal
(2009).
Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes.
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J Fluoresc,
19,
1111-1118.
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G.D.McEwen,
F.Chen,
and
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Immobilization, hybridization, and oxidation of synthetic DNA on gold surface: electron transfer investigated by electrochemistry and scanning tunneling microscopy.
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Anal Chim Acta,
643,
26-37.
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H.Mojzisova,
J.Olesiak,
M.Zielinski,
K.Matczyszyn,
D.Chauvat,
and
J.Zyss
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Polarization-sensitive two-photon microscopy study of the organization of liquid-crystalline DNA.
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Biophys J,
97,
2348-2357.
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K.Mishra,
R.Bhardwaj,
and
N.K.Chaudhury
(2009).
Netropsin, a minor groove binding ligand: a potential radioprotective agent.
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| |
Radiat Res,
172,
698-705.
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M.U.Ahmed,
M.Saito,
M.M.Hossain,
S.R.Rao,
S.Furui,
A.Hino,
Y.Takamura,
M.Takagi,
and
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Electrochemical genosensor for the rapid detection of GMO using loop-mediated isothermal amplification.
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Analyst,
134,
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A.V.Vargiu,
P.Ruggerone,
A.Magistrato,
and
P.Carloni
(2008).
Dissociation of minor groove binders from DNA: insights from metadynamics simulations.
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Nucleic Acids Res,
36,
5910-5921.
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K.M.Knee,
S.B.Dixit,
C.E.Aitken,
S.Ponomarev,
D.L.Beveridge,
and
I.Mukerji
(2008).
Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA.
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Biophys J,
95,
257-272.
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N.N.Degtyareva,
B.D.Wallace,
A.R.Bryant,
K.M.Loo,
and
J.T.Petty
(2007).
Hydration changes accompanying the binding of minor groove ligands with DNA.
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Biophys J,
92,
959-965.
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Q.A.Khan,
and
D.S.Pilch
(2007).
Topoisomerase I-mediated DNA cleavage induced by the minor groove-directed binding of bibenzimidazoles to a distal site.
|
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J Mol Biol,
365,
561-569.
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S.Bhattacharya,
and
P.Chaudhuri
(2007).
Metal-ion-mediated tuning of duplex DNA binding by bis(2-(2-pyridyl)-1H-benzimidazole).
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Chem Asian J,
2,
648-655.
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V.S.Sibirtsev
(2007).
Fluorescent DNA probes: study of mechanisms of changes in spectral properties and features of practical application.
|
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Biochemistry (Mosc),
72,
887-900.
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V.S.Sibirtsev,
and
A.V.Garabadzhiu
(2007).
Spectral study of the interaction of DNA with benzothiazolyl-benz-alpha-chromene.
|
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Biochemistry (Mosc),
72,
901-909.
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L.Grant,
J.Sun,
H.Xu,
S.H.Subramony,
J.B.Chaires,
and
M.D.Hebert
(2006).
Rational selection of small molecules that increase transcription through the GAA repeats found in Friedreich's ataxia.
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FEBS Lett,
580,
5399-5405.
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P.Balagurumoorthy,
K.Chen,
R.C.Bash,
S.J.Adelstein,
and
A.I.Kassis
(2006).
Mechanisms underlying production of double-strand breaks in plasmid DNA after decay of 125I-Hoechst.
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| |
Radiat Res,
166,
333-344.
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A.Adams,
C.Leong,
W.A.Denny,
and
J.M.Guss
(2005).
Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)(2) at 1.6 and 1.8 Angstrom resolution.
|
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Acta Crystallogr D Biol Crystallogr,
61,
1348-1353.
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PDB codes:
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M.D.Disney,
R.Stephenson,
T.W.Wright,
C.G.Haidaris,
D.H.Turner,
and
F.Gigliotti
(2005).
Activity of Hoechst 33258 against Pneumocystis carinii f. sp. muris, Candida albicans, and Candida dubliniensis.
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Antimicrob Agents Chemother,
49,
1326-1330.
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M.Takahashi,
J.Okada,
K.Ito,
M.Hashimoto,
K.Hashimoto,
Y.Yoshida,
Y.Furuichi,
Y.Ohta,
S.Mishiro,
and
N.Gemma
(2005).
Construction of an electrochemical DNA chip for simultaneous genotyping of single nucleotide polymorphisms.
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Analyst,
130,
687-693.
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R.Gupta,
S.Mozumdar,
and
N.K.Chaudhury
(2005).
Fluorescence spectroscopic studies to characterize the internal environment of tetraethyl-orthosilicate derived sol-gel bulk and thin films with aging.
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Biosens Bioelectron,
20,
1358-1365.
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V.S.Sibirtsev
(2005).
Study of applicability of the bifunctional system "ethidium bromide + Hoechst-33258" for DNA analysis.
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Biochemistry (Mosc),
70,
449-457.
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V.S.Sibirtsev,
A.Y.Tolmachev,
M.V.Kovaleva,
A.V.Garabadzhiu,
and
V.F.Traven
(2005).
Spectral study of interactions of 4,8,4'-trimethylpsoralen and 4,4'-dimethylangelicin dyes with DNA.
|
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Biochemistry (Mosc),
70,
822-832.
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A.Adhikary,
V.Buschmann,
C.Müller,
and
M.Sauer
(2003).
Ensemble and single-molecule fluorescence spectroscopic study of the binding modes of the bis-benzimidazole derivative Hoechst 33258 with DNA.
|
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Nucleic Acids Res,
31,
2178-2186.
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C.A.Briehn,
P.Weyermann,
and
P.B.Dervan
(2003).
Alternative heterocycles for DNA recognition: the benzimidazole/imidazole pair.
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| |
Chemistry,
9,
2110-2122.
|
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C.Bailly,
G.Chessari,
C.Carrasco,
A.Joubert,
J.Mann,
W.D.Wilson,
and
S.Neidle
(2003).
Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition.
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Nucleic Acids Res,
31,
1514-1524.
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G.L.Olsen,
E.A.Louie,
G.P.Drobny,
and
S.T.Sigurdsson
(2003).
Determination of DNA minor groove width in distamycin-DNA complexes by solid-state NMR.
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| |
Nucleic Acids Res,
31,
5084-5089.
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H.J.Karlsson,
M.Eriksson,
E.Perzon,
B.Akerman,
P.Lincoln,
and
G.Westman
(2003).
Groove-binding unsymmetrical cyanine dyes for staining of DNA: syntheses and characterization of the DNA-binding.
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Nucleic Acids Res,
31,
6227-6234.
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S.B.Howerton,
A.Nagpal,
and
L.D.Williams
(2003).
Surprising roles of electrostatic interactions in DNA-ligand complexes.
|
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Biopolymers,
69,
87-99.
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PDB code:
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K.D.Leslie,
and
K.R.Fox
(2002).
Interaction of Hoechst 33258 and echinomycin with nucleosomal DNA fragments containing isolated ligand binding sites.
|
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Biochemistry,
41,
3484-3497.
|
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K.Uytterhoeven,
J.Sponer,
and
L.Van Meervelt
(2002).
Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG).
|
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Eur J Biochem,
269,
2868-2877.
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PDB codes:
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C.A.Hawkins,
C.Watson,
Y.Yan,
B.Gong,
and
D.E.Wemmer
(2001).
Structural analysis of the binding modes of minor groove ligands comprised of disubstituted benzenes.
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Nucleic Acids Res,
29,
936-942.
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H.Görner
(2001).
Direct and sensitized photoprocesses of bis-benzimidazole dyes and the effects of surfactants and DNA.
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Photochem Photobiol,
73,
339-348.
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M.Tsunoda,
N.Karino,
Y.Ueno,
A.Matsuda,
and
A.Takenaka
(2001).
Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?
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Acta Crystallogr D Biol Crystallogr,
57,
345-348.
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PDB codes:
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E.Gavathiotis,
G.J.Sharman,
and
M.S.Searle
(2000).
Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2).
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Nucleic Acids Res,
28,
728-735.
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PDB code:
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R.M.Brosh,
J.K.Karow,
E.J.White,
N.D.Shaw,
I.D.Hickson,
and
V.A.Bohr
(2000).
Potent inhibition of werner and bloom helicases by DNA minor groove binding drugs.
|
| |
Nucleic Acids Res,
28,
2420-2430.
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S.I.Murata,
J.Kuśba,
G.Piszczek,
I.Gryczynski,
and
J.R.Lakowicz
(2000).
Donor fluorescence decay analysis for energy transfer in double-helical DNA with various acceptor concentrations.
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Biopolymers,
57,
306-315.
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S.Murata,
P.Herman,
H.J.Lin,
and
J.R.Lakowicz
(2000).
Fluorescence lifetime imaging of nuclear DNA: effect of fluorescence resonance energy transfer.
|
| |
Cytometry,
41,
178-185.
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B.S.Reddy,
S.M.Sondhi,
and
J.W.Lown
(1999).
Synthetic DNA minor groove-binding drugs.
|
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Pharmacol Ther,
84,
1.
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F.J.Alba,
and
J.R.Daban
(1999).
Inhibition of peroxyoxalate chemiluminescence by intercalation of fluorescent acceptors between DNA bases.
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Photochem Photobiol,
69,
405-409.
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K.H.Lee
(1999).
Anticancer drug design based on plant-derived natural products.
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J Biomed Sci,
6,
236-250.
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R.M.Romero,
M.Mitas,
and
I.S.Haworth
(1999).
Anomalous cross-linking by mechlorethamine of DNA duplexes containing C-C mismatch pairs.
|
| |
Biochemistry,
38,
3641-3648.
|
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Z.Xu,
T.K.Li,
J.S.Kim,
E.J.LaVoie,
K.J.Breslauer,
L.F.Liu,
and
D.S.Pilch
(1998).
DNA minor groove binding-directed poisoning of human DNA topoisomerase I by terbenzimidazoles.
|
| |
Biochemistry,
37,
3558-3566.
|
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C.J.Squire,
G.R.Clark,
and
W.A.Denny
(1997).
Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.
|
| |
Nucleic Acids Res,
25,
4072-4078.
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PDB code:
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D.S.Pilch,
Z.Xu,
Q.Sun,
E.J.LaVoie,
L.F.Liu,
and
K.J.Breslauer
(1997).
A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning.
|
| |
Proc Natl Acad Sci U S A,
94,
13565-13570.
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J.B.Chaires
(1997).
Energetics of drug-DNA interactions.
|
| |
Biopolymers,
44,
201-215.
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L.Trieschmann,
E.Schulze,
B.Schulze,
and
U.Grossbach
(1997).
The histone H1 genes of the dipteran insect, Chironomus thummi, fall under two divergent classes and encode proteins with distinct intranuclear distribution and potentially different functions.
|
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Eur J Biochem,
250,
184-196.
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B.Jollès,
A.Laigle,
W.Priebe,
and
A.Garnier-Suillerot
(1996).
Comparison of DNA sequence selectivity of anthracycline antibiotics and their 3'-hydroxylated analogs.
|
| |
Chem Biol Interact,
100,
165-176.
|
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G.R.Clark,
C.J.Squire,
E.J.Gray,
W.Leupin,
and
S.Neidle
(1996).
Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.
|
| |
Nucleic Acids Res,
24,
4882-4889.
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PDB codes:
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G.R.Clark,
E.J.Gray,
S.Neidle,
Y.H.Li,
and
W.Leupin
(1996).
Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex.
|
| |
Biochemistry,
35,
13745-13752.
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PDB code:
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J.H.Moon,
S.K.Kim,
U.Sehlstedt,
A.Rodger,
and
B.Nordén
(1996).
DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258.
|
| |
Biopolymers,
38,
593-606.
|
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J.M.Rydzewski,
W.Leupin,
and
W.Chazin
(1996).
The width of the minor groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA.
|
| |
Nucleic Acids Res,
24,
1287-1293.
|
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L.Tabernero,
J.Bella,
and
C.Alemán
(1996).
Hydrogen bond geometry in DNA-minor groove binding drug complexes.
|
| |
Nucleic Acids Res,
24,
3458-3466.
|
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M.C.Vega,
M.Coll,
and
C.Alemán
(1996).
Intrinsic conformational preferences of the Hoechst dye family and their influence of DNA binding.
|
| |
Eur J Biochem,
239,
376-383.
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M.Durand,
and
J.C.Maurizot
(1996).
Distamycin A complexation with a nucleic acid triple helix.
|
| |
Biochemistry,
35,
9133-9139.
|
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S.J.Adelstein,
and
A.I.Kassis
(1996).
Strand breaks in plasmid DNA following positional changes of Auger-electron-emitting radionuclides.
|
| |
Acta Oncol,
35,
797-801.
|
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A.A.Wood,
C.M.Nunn,
A.Czarny,
D.W.Boykin,
and
S.Neidle
(1995).
Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.
|
| |
Nucleic Acids Res,
23,
3678-3684.
|
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|
PDB code:
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A.Abu-Daya,
P.M.Brown,
and
K.R.Fox
(1995).
DNA sequence preferences of several AT-selective minor groove binding ligands.
|
| |
Nucleic Acids Res,
23,
3385-3392.
|
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|
|
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,
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PDB code:
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PDB code:
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PDB codes:
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PDB code:
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PDB codes:
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PDB code:
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N.B.Ramsing,
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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
codes are
shown on the right.
|
|
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