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PDBsum entry 1vj4
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DOI no:
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J Mol Biol
166:183-201
(1983)
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PubMed id:
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Sequence-dependent conformation of an A-DNA double helix. The crystal structure of the octamer d(G-G-T-A-T-A-C-C).
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Z.Shakked,
D.Rabinovich,
O.Kennard,
W.B.Cruse,
S.A.Salisbury,
M.A.Viswamitra.
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ABSTRACT
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The crystal structures of the synthetic self-complementary octamer
d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined
to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The
molecules adopt and A-DNA type double-helical conformation, which is minimally
affected by crystal forces. A detailed analysis of the structure shows a
considerable influence of the nucleotide sequence on the base-pair stacking
patterns. In particular, the electrostatic stacking interactions between
adjacent guanine and thymine bases produce symmetric bending of the double helix
and a major-groove widening. The sugar-phosphate backbone appears to be only
slightly affected by the base sequence. The local variations in the base-pair
orientation are brought about by correlated adjustments in the backbone torsion
angles and the glycosidic orientation. Sequence-dependent conformational
variations of the type observed here may contribute to the specificity of
certain protein-DNA interactions.
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Selected figure(s)
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Figure 1.
Fro. 1. Steeoscopic view of the octamer perpendicular the helix and pseudo 2-fold axes. Strand 1
begins with 1 t upper left and ends with C8 at lower right; strand 2 begins with G9 at lower left and
ends with Cl6 at upper right. The double helix is bent to the right in the plane of the paper.
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Figure 7.
Fro. 7. Schematic representation f (a) parallel and (b) antiparallel arrangements of the keto groups.
he view is ede-on to the 0 plane.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1983,
166,
183-201)
copyright 1983.
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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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T.Gruene,
and
G.M.Sheldrick
(2011).
Geometric properties of nucleic acids with potential for autobuilding.
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Acta Crystallogr A,
67,
1-8.
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R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
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Annu Rev Biochem,
79,
233-269.
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A.Marathe,
D.Karandur,
and
M.Bansal
(2009).
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs.
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BMC Struct Biol,
9,
24.
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R.Fourme,
E.Girard,
R.Kahn,
A.C.Dhaussy,
and
I.Ascone
(2009).
Advances in high-pressure biophysics: status and prospects of macromolecular crystallography.
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Annu Rev Biophys,
38,
153-171.
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D.Svozil,
J.Kalina,
M.Omelka,
and
B.Schneider
(2008).
DNA conformations and their sequence preferences.
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Nucleic Acids Res,
36,
3690-3706.
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E.Girard,
T.Prangé,
A.C.Dhaussy,
E.Migianu-Griffoni,
M.Lecouvey,
J.C.Chervin,
M.Mezouar,
R.Kahn,
and
R.Fourme
(2007).
Adaptation of the base-paired double-helix molecular architecture to extreme pressure.
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Nucleic Acids Res,
35,
4800-4808.
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PDB codes:
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R.E.Dickerson,
and
H.L.Ng
(2001).
DNA structure from A to B.
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Proc Natl Acad Sci U S A,
98,
6986-6988.
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M.C.Wahl,
and
M.Sundaralingam
(2000).
B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G).
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Nucleic Acids Res,
28,
4356-4363.
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PDB code:
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Y.G.Gao,
H.Robinson,
and
A.H.Wang
(1999).
High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC).
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Eur J Biochem,
261,
413-420.
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PDB codes:
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C.Mayer-Jung,
D.Moras,
and
Y.Timsit
(1998).
Hydration and recognition of methylated CpG steps in DNA.
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EMBO J,
17,
2709-2718.
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PDB codes:
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L.Pardo,
N.Pastor,
and
H.Weinstein
(1998).
Progressive DNA bending is made possible by gradual changes in the torsion angle of the glycosyl bond.
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Biophys J,
74,
2191-2198.
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A.Lebrun,
Z.Shakked,
and
R.Lavery
(1997).
Local DNA stretching mimics the distortion caused by the TATA box-binding protein.
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Proc Natl Acad Sci U S A,
94,
2993-2998.
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M.C.Wahl,
and
M.Sundaralingam
(1997).
Crystal structures of A-DNA duplexes.
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Biopolymers,
44,
45-63.
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M.Popenda,
E.Biala,
J.Milecki,
and
R.W.Adamiak
(1997).
Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions.
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Nucleic Acids Res,
25,
4589-4598.
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PDB codes:
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C.Ban,
and
M.Sundaralingam
(1996).
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II.
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Biophys J,
71,
1222-1227.
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PDB code:
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I.Berger,
M.Egli,
and
A.Rich
(1996).
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA.
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Proc Natl Acad Sci U S A,
93,
12116-12121.
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Y.G.Gao,
H.Robinson,
J.H.van Boom,
and
A.H.Wang
(1995).
Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.
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Biophys J,
69,
559-568.
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PDB codes:
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B.Langlois d'Estaintot,
A.Dautant,
C.Courseille,
and
G.Precigoux
(1993).
Orthorhombic crystal structure of the A-DNA octamer d(GTACGTAC). Comparison with the tetragonal structure.
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Eur J Biochem,
213,
673-682.
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PDB code:
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H.Fabian,
W.Hölzer,
U.Heinemann,
H.Sklenar,
and
H.Welfle
(1993).
Conformation of d(GGGATCCC)2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling.
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Nucleic Acids Res,
21,
569-576.
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H.Sfihi,
J.Liquier,
L.Urpi,
N.Verdaguer,
J.A.Subirana,
J.Igolen,
and
E.Taillandier
(1993).
A and Z canonical conformations in d(CnGCGn) crystals characterized by microFTIR and microRaman spectroscopies.
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Biopolymers,
33,
1715-1723.
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D.L.Milton,
M.L.Casper,
N.M.Wills,
and
R.F.Gesteland
(1990).
Guanine tracts enhance sequence directed DNA bends.
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Nucleic Acids Res,
18,
817-820.
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F.Han,
W.Watt,
D.J.Duchamp,
L.Callahan,
F.J.Kézdy,
and
K.Agarwal
(1990).
Molecular structure of deoxycytidyl-3'-methylphosphonate (RP) 5'-deoxyguanidine, d[Cp(CH3)G]. A neutral dinucleotide with Watson-Crick base pairing and a right handed helical twist.
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Nucleic Acids Res,
18,
2759-2767.
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M.Eisenstein,
F.Frolow,
Z.Shakked,
and
D.Rabinovich
(1990).
The structure and hydration of the A-DNA fragment d(GGGTACCC) at room temperature and low temperature.
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Nucleic Acids Res,
18,
3185-3194.
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PDB codes:
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B.E.Hingerty,
S.Figueroa,
T.L.Hayden,
and
S.Broyde
(1989).
Prediction of DNA structure from sequence: a build-up technique.
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Biopolymers,
28,
1195-1222.
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C.A.Frederick,
G.J.Quigley,
M.K.Teng,
M.Coll,
G.A.Van der Marel,
J.H.Van Boom,
A.Rich,
and
A.H.Wang
(1989).
Molecular structure of an A-DNA decamer d(ACCGGCCGGT).
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Eur J Biochem,
181,
295-307.
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PDB code:
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J.Mazur,
A.Sarai,
and
R.L.Jernigan
(1989).
Sequence dependence of the B-A conformational transition of DNA.
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Biopolymers,
28,
1223-1233.
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L.Fairall,
S.Martin,
and
D.Rhodes
(1989).
The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure.
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EMBO J,
8,
1809-1817.
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O.Kennard,
and
W.N.Hunter
(1989).
Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies.
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Q Rev Biophys,
22,
327-379.
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D.A.Pearlman,
and
S.H.Kim
(1988).
Conformational studies of nucleic acids. V. Sequence specificities in the conformational energetics of oligonucleotides: the homo-tetramers.
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Biopolymers,
27,
59-77.
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H.Lauble,
R.Frank,
H.Blöcker,
and
U.Heinemann
(1988).
Three-dimensional structure of d(GGGATCCC) in the crystalline state.
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Nucleic Acids Res,
16,
7799-7816.
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PDB code:
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R.C.Maroun,
and
W.K.Olson
(1988).
Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains.
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Biopolymers,
27,
561-584.
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R.C.Maroun,
and
W.K.Olson
(1988).
Base sequence effects in double-helical DNA. III. Average properties of curved DNA.
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Biopolymers,
27,
585-603.
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A.I.Murchie,
and
D.M.Lilley
(1987).
The mechanism of cruciform formation in supercoiled DNA: initial opening of central basepairs in salt-dependent extrusion.
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Nucleic Acids Res,
15,
9641-9654.
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L.J.Rinkel,
G.A.van der Marel,
J.H.van Boom,
and
C.Altona
(1987).
Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 1. The duplex form.
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Eur J Biochem,
163,
275-286.
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L.J.Rinkel,
G.A.van der Marel,
J.H.van Boom,
and
C.Altona
(1987).
Influence of the base sequence on the conformational behaviour of DNA polynucleotides in solution.
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Eur J Biochem,
166,
87.
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S.Broyde,
and
B.E.Hingerty
(1987).
Visualization of an AAF induced frameshift mutation: molecular views of base displacement in B-DNA from minimized potential energy calculations.
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Nucleic Acids Res,
15,
6539-6552.
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U.Heinemann,
H.Lauble,
R.Frank,
and
H.Blöcker
(1987).
Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC).
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Nucleic Acids Res,
15,
9531-9550.
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PDB code:
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D.J.Patel,
L.Shapiro,
and
D.Hare
(1986).
Sequence-dependent conformations of DNA duplexes: the TATA segment of the d(G-G-T-A-T-A-C-C) duplex in aqueous solution.
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Biopolymers,
25,
693-706.
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G.Yagil,
and
J.L.Sussman
(1986).
Structural models for non-helical DNA.
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EMBO J,
5,
1719-1725.
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M.McCall,
T.Brown,
W.N.Hunter,
and
O.Kennard
(1986).
The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA.
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Nature,
322,
661-664.
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PDB code:
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S.N.Rao,
and
V.Sasisekharan
(1986).
Conformations of dinucleoside monophosphates in relation to duplex DNA structures.
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Biopolymers,
25,
17-30.
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W.K.Olson,
and
J.Cicariello
(1986).
Computer simulation of DNA supercoiling.
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Ann N Y Acad Sci,
482,
69-81.
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Y.Nishimura,
C.Torigoe,
and
M.Tsuboi
(1986).
Salt induced B----A transition of poly(dG).poly(dC) and the stabilization of A form by its methylation.
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Nucleic Acids Res,
14,
2737-2748.
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G.M.Clore,
A.M.Gronenborn,
and
L.W.McLaughlin
(1985).
The structure of the double-stranded RNA pentamer 5'(CACAG) . 5'(CUGUG) determined by nuclear Overhauser enhancement measurements: interproton distance determination and structure refinement on the basis of X-ray coordinates.
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Eur J Biochem,
151,
153-165.
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J.W.Suggs,
and
D.A.Taylor
(1985).
Evidence for sequence-specific conformational changes in DNA from the melting temperatures of DNA phosphorothioate derivatives.
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Nucleic Acids Res,
13,
5707-5716.
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K.Kita,
N.Hiraoka,
F.Kimizuka,
A.Obayashi,
H.Kojima,
H.Takahashi,
and
H.Saito
(1985).
Interaction of the restriction endonuclease ScaI with its substrates.
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Nucleic Acids Res,
13,
7015-7024.
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N.Jamin,
T.L.James,
and
G.Zon
(1985).
Two-dimensional nuclear Overhauser enhancement investigation of the solution structure and dynamics of the DNA octamer [d(GGTATACC)]2.
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Eur J Biochem,
152,
157-166.
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P.P.Lankhorst,
C.A.Haasnoot,
C.Erkelens,
H.P.Westerink,
G.A.van der Marel,
J.H.van Boom,
and
C.Altona
(1985).
Carbon-13 NMR in conformational analysis of nucleic acid fragments. 4. The torsion angle distribution about the C3'-O3' bond in DNA constituents.
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Nucleic Acids Res,
13,
927-942.
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A.Aggarwal,
S.A.Islam,
R.Kuroda,
and
S.Neidle
(1984).
X-ray crystallographic analysis of a ternary intercalation complex between proflavine and the dinucleoside monophosphates CpA and UpG.
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Biopolymers,
23,
1025-1041.
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C.S.Tung,
and
S.C.Harvey
(1984).
A molecular mechanical model to predict the helix twist angles of B-DNA.
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Nucleic Acids Res,
12,
3343-3356.
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G.M.Clore,
and
A.M.Gronenborn
(1984).
A nuclear-Overhauser-enhancement study of the solution structure of a double-stranded DNA undecamer comprising a portion of the specific target site for the cyclic-AMP-receptor protein in the gal operon. Sequential resonance assignment.
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Eur J Biochem,
141,
119-129.
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G.M.Clore,
and
A.M.Gronenborn
(1984).
An investigation into the solution structure of the single-stranded DNA undecamer 5'd AAGTGTGATAT by means of nuclear Overhauser enhancement measurements.
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Eur Biophys J,
11,
95.
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G.M.Clore,
H.Lauble,
T.A.Frenkiel,
and
A.M.Gronenborn
(1984).
A two-dimensional NMR study of the solution structure of a DNA dodecamer comprising the concensus sequence for the specific DNA-binding sites of the glucocorticoid receptor protein.
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Eur J Biochem,
145,
629-636.
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J.R.Mellema,
A.K.Jellema,
C.A.Haasnoot,
J.H.Van Boom,
and
C.Altona
(1984).
Conformational analysis of the single-helical DNA fragment d(T-A-A-T) in aqueous solution. The combined use of NMR proton chemical shifts and coupling constants obtained at 300 MHz and 500 MHz.
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Eur J Biochem,
141,
165-175.
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J.R.Mellema,
J.M.Pieters,
G.A.van der Marel,
J.H.van Boom,
C.A.Haasnoot,
and
C.Altona
(1984).
Sequence-dependent structural variation in single-helical DNA. Proton NMR studies of d(T-A-T-A) and d(A-T-A-T) in aqueous solution.
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Eur J Biochem,
143,
285-301.
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G.M.Clore,
and
A.M.Gronenborn
(1983).
Sequence-dependent structural variations in two right-handed alternating pyrimidine-purine DNA oligomers in solution determined by nuclear Overhauser enhancement measurements.
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EMBO J,
2,
2109-2115.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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Where a reference describes a PDB structure, the PDB
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shown on the right.
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