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PDBsum entry 1dnh
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Nucleic Acids Res
16:2671-2690
(1988)
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PubMed id:
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The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG).
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M.K.Teng,
N.Usman,
C.A.Frederick,
A.H.Wang.
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ABSTRACT
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The crystal structure of the complex between the dodecamer d(CGCGAATTCGCG) and a
synthetic dye molecule Hoechst 33258 was solved by X-ray diffraction analysis
and refined to an R-factor of 15.7% at 2.25 A resolution. The crescent-shaped
Hoechst compound is found to bind to the central four AATT base pairs in the
narrow minor groove of the B-DNA double helix. The piperazine ring of the drug
has its flat face almost parallel to the aromatic bisbenzimidazole ring and lies
sideways in the minor groove. No evidence of disordered structure of the drug is
seen in the complex. The binding of Hoechst to DNA is stabilized by a
combination of hydrogen bonding, van der Waals interaction and electrostatic
interactions. The binding preference for AT base pairs by the drug is the result
of the close contact between the Hoechst molecule and the C2 hydrogen atoms of
adenine. The nature of these contacts precludes the binding of the drug to G-C
base pairs due to the presence of N2 amino groups of guanines. The present
crystal structural information agrees well with the data obtained from chemical
footprinting experiments.
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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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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
(2011).
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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R.Prado-Gotor,
and
E.Grueso
(2011).
A kinetic study of the interaction of DNA with gold nanoparticles: mechanistic aspects of the interaction.
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| |
Phys Chem Chem Phys,
13,
1479-1489.
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E.C.Magat Juan,
S.Shimizu,
X.Ma,
T.Kurose,
T.Haraguchi,
F.Zhang,
M.Tsunoda,
A.Ohkubo,
M.Sekine,
T.Shibata,
C.L.Millington,
D.M.Williams,
and
A.Takénaka
(2010).
Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
|
| |
Nucleic Acids Res,
38,
6737-6745.
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PDB codes:
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M.Tsunoda,
T.Sakaue,
S.Naito,
T.Sunami,
N.Abe,
Y.Ueno,
A.Matsuda,
and
A.Takénaka
(2010).
Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil.
|
| |
J Nucleic Acids,
2010,
107289.
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PDB codes:
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N.A.Cherepanova,
A.L.Zhuze,
and
E.S.Gromova
(2010).
Inhibition of murine DNA methyltransferase Dnmt3a by DNA duplexes containing pyrimidine-2(1H)-one.
|
| |
Biochemistry (Mosc),
75,
1115-1125.
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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.
|
| |
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.
|
| |
Biotech Histochem,
85,
247-256.
|
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|
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|
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R.Ruiz,
B.García,
J.Garcia-Tojal,
N.Busto,
S.Ibeas,
J.M.Leal,
C.Martins,
J.Gaspar,
J.Borrás,
R.Gil-García,
and
M.González-Alvarez
(2010).
Biological assays and noncovalent interactions of pyridine-2-carbaldehyde thiosemicarbazonecopper(II) drugs with [poly(dA-dT)](2), [poly(dG-dC)] (2), and calf thymus DNA.
|
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J Biol Inorg Chem,
15,
515-532.
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G.D.McEwen,
F.Chen,
and
A.Zhou
(2009).
Immobilization, hybridization, and oxidation of synthetic DNA on gold surface: electron transfer investigated by electrochemistry and scanning tunneling microscopy.
|
| |
Anal Chim Acta,
643,
26-37.
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M.U.Ahmed,
M.Saito,
M.M.Hossain,
S.R.Rao,
S.Furui,
A.Hino,
Y.Takamura,
M.Takagi,
and
E.Tamiya
(2009).
Electrochemical genosensor for the rapid detection of GMO using loop-mediated isothermal amplification.
|
| |
Analyst,
134,
966-972.
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S.Takiya,
S.Saito,
T.Yokoyama,
D.Matsumoto,
T.Aizawa,
M.Kamiya,
M.Demura,
and
K.Kawano
(2009).
DNA-binding property of the novel DNA-binding domain STPR in FMBP-1 of the silkworm Bombyx mori.
|
| |
J Biochem,
146,
103-111.
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Y.Zhu,
Z.Chen,
Z.Guo,
Y.Wang,
and
G.Chen
(2009).
Systematic characterization on electronic structures and spectra for a series of complexes, M(IDB)Cl2 (M = Mn, Fe, Co, Ni, Cu and Zn): a theoretical study.
|
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J Mol Model,
15,
469-479.
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J.Wang,
and
C.R.Martin
(2008).
A new drug-sensing paradigm based on ion-current rectification in a conically shaped nanopore.
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Nanomed,
3,
13-20.
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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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A.V.Gromyko,
K.V.Popov,
A.P.Mozoleva,
S.A.Strel'tsov,
S.L.Grokhovskiĭ,
V.A.Oleĭnikov,
and
A.L.Zhuze
(2005).
[Ligands with affinity to specific sequence of DNA base pairs. XII. The synthesis and cytological studies of dimeric Hoechst 33258 molecules]
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Bioorg Khim,
31,
385-393.
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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.
|
| |
Biosens Bioelectron,
20,
1358-1365.
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H.Zipper,
H.Brunner,
J.Bernhagen,
and
F.Vitzthum
(2004).
Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications.
|
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Nucleic Acids Res,
32,
e103.
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M.D.Disney,
J.L.Childs,
and
D.H.Turner
(2004).
Hoechst 33258 selectively inhibits group I intron self-splicing by affecting RNA folding.
|
| |
Chembiochem,
5,
1647-1652.
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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.
|
| |
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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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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S.K.Pal,
L.Zhao,
and
A.H.Zewail
(2003).
Water at DNA surfaces: ultrafast dynamics in minor groove recognition.
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Proc Natl Acad Sci U S A,
100,
8113-8118.
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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.Shi,
S.N.Mitra,
and
M.Sundaralingam
(2002).
Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin.
|
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Acta Crystallogr D Biol Crystallogr,
58,
601-606.
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PDB code:
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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).
|
| |
Eur J Biochem,
269,
2868-2877.
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PDB codes:
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R.E.Speight,
D.J.Hart,
and
J.M.Blackburn
(2002).
Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner.
|
| |
J Mol Recognit,
15,
19-26.
|
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B.Wellenzohn,
W.Flader,
R.H.Winger,
A.Hallbrucker,
E.Mayer,
and
K.R.Liedl
(2001).
Significance of ligand tails for interaction with the minor groove of B-DNA.
|
| |
Biophys J,
81,
1588-1599.
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C.E.Bostock-Smith,
S.A.Harris,
C.A.Laughton,
and
M.A.Searle
(2001).
Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations.
|
| |
Nucleic Acids Res,
29,
693-702.
|
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C.J.Squire,
L.J.Baker,
G.R.Clark,
R.F.Martin,
and
J.White
(2000).
Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design.
|
| |
Nucleic Acids Res,
28,
1252-1258.
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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).
|
| |
Nucleic Acids Res,
28,
728-735.
|
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PDB code:
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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.
|
| |
Biopolymers,
57,
306-315.
|
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|
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X.Li,
and
A.L.Lu
(2000).
Intact MutY and its catalytic domain differentially contact with A/8-oxoG-containing DNA.
|
| |
Nucleic Acids Res,
28,
4593-4603.
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B.S.Reddy,
S.M.Sondhi,
and
J.W.Lown
(1999).
Synthetic DNA minor groove-binding drugs.
|
| |
Pharmacol Ther,
84,
1.
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K.H.Lee
(1999).
Anticancer drug design based on plant-derived natural products.
|
| |
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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H.Robinson,
Y.G.Gao,
C.Bauer,
C.Roberts,
C.Switzer,
and
A.H.Wang
(1998).
2'-Deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis.
|
| |
Biochemistry,
37,
10897-10905.
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PDB codes:
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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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|
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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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|
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|
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G.R.Clark,
D.W.Boykin,
A.Czarny,
and
S.Neidle
(1997).
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition.
|
| |
Nucleic Acids Res,
25,
1510-1515.
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PDB code:
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J.B.Chaires
(1997).
Energetics of drug-DNA interactions.
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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.
|
| |
Eur J Biochem,
250,
184-196.
|
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|
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|
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M.A.Young,
G.Ravishanker,
and
D.L.Beveridge
(1997).
A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation.
|
| |
Biophys J,
73,
2313-2336.
|
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|
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D.Sengupta,
A.Blaskó,
and
T.C.Bruice
(1996).
A microgonotropen pentaaza pentabutylamine and its interactions with DNA.
|
| |
Bioorg Med Chem,
4,
803-813.
|
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|
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|
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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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|
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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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|
|
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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.
|
|
|
|
|
|
|
M.Durand,
and
J.C.Maurizot
(1996).
Distamycin A complexation with a nucleic acid triple helix.
|
| |
Biochemistry,
35,
9133-9139.
|
|
|
|
|
|
|
R.F.Martin,
S.Broadhurst,
S.D'Abrew,
R.Budd,
R.Sephton,
M.Reum,
and
D.P.Kelly
(1996).
Radioprotection by DNA ligands.
|
| |
Br J Cancer Suppl,
27,
S99-101.
|
|
|
|
|
|
|
S.Bevers,
G.Xiang,
and
L.W.McLaughlin
(1996).
Importance of specific adenosine N3-nitrogens for efficient cleavage by a hammerhead ribozyme.
|
| |
Biochemistry,
35,
6483-6490.
|
|
|
|
|
|
|
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.
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
D.G.Stokes,
and
R.P.Perry
(1995).
DNA-binding and chromatin localization properties of CHD1.
|
| |
Mol Cell Biol,
15,
2745-2753.
|
|
|
|
|
|
|
D.Suh,
and
J.B.Chaires
(1995).
Criteria for the mode of binding of DNA binding agents.
|
| |
Bioorg Med Chem,
3,
723-728.
|
|
|
|
|
|
|
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.Egli,
and
R.V.Gessner
(1995).
Stereoelectronic effects of deoxyribose O4' on DNA conformation.
|
| |
Proc Natl Acad Sci U S A,
92,
180-184.
|
|
|
|
|
|
|
M.J.O'Donnell,
S.B.Rajur,
and
L.W.McLaughlin
(1995).
Synthesis and properties of a Hoechst-like minor-groove binding agent tethered to an oligodeoxynucleotide.
|
| |
Bioorg Med Chem,
3,
743-750.
|
|
|
|
|
|
|
C.M.Nunn,
T.C.Jenkins,
and
S.Neidle
(1994).
Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition.
|
| |
Eur J Biochem,
226,
953-961.
|
|
|
PDB code:
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|
|
E.Stofer,
and
R.Lavery
(1994).
Measuring the geometry of DNA grooves.
|
| |
Biopolymers,
34,
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