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PDBsum entry 1dc0
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DOI no:
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Proc Natl Acad Sci U S A
97:2035-2039
(2000)
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PubMed id:
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The structure of a stable intermediate in the A <--> B DNA helix transition.
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H.L.Ng,
M.L.Kopka,
R.E.Dickerson.
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ABSTRACT
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The DNA dodecamer CATGGGCCCATG in a crystal structure of resolution 1.3 A has a
conformation intermediate between A and B DNA. This trapping of a stable
intermediate suggests that the A and B DNA families are not discrete, as
previously believed. The structure supports a base-centered rather than a
backbone-centered mechanism for the A <--> B transition mediated by guanine
tracts. Interconversion between A and B DNA provides another means for
regulating protein-DNA recognition.
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Selected figure(s)
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Figure 2.
Fig. 2. Side and top views to the same scale of ideal A
DNA (a and d), G[3]C[3] or CATGGGCCCATG (b and e), and ideal B
DNA (c and f). Ideal structures are taken from fiber diffraction
data (10).
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Figure 5.
Fig. 5. Calladine-Drew base-centered mechanism for the
B-to-A helix transition. (a) B DNA with neither slide nor roll.
(b) B DNA with addition of a  1.5-Å
slide. (c) B DNA with addition of a +12° roll. (d) A DNA,
resulting from addition of both slide and roll to B DNA. The
G[3]C[3] helix corresponds to the helix in b and can be regarded
as a B DNA helix to which slide has been added but not roll.
Conversely, it can be thought of as A DNA from which roll has
been removed. Figures were created with NUSTAR (X.-J. Lu and W.
K. Olson, unpublished work).
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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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H.E.Peckham,
and
W.K.Olson
(2011).
Nucleic-acid structural deformability deduced from anisotropic displacement parameters.
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Biopolymers,
95,
254-269.
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S.Venkadesh,
P.K.Mandal,
and
N.Gautham
(2011).
The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)₂.
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Biochem Biophys Res Commun,
407,
307-312.
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PDB code:
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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.G.Tsai,
A.E.Engelhart,
M.M.Hatmal,
S.I.Houston,
N.V.Hud,
I.S.Haworth,
and
M.R.Lieber
(2009).
Conformational variants of duplex DNA correlated with cytosine-rich chromosomal fragile sites.
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J Biol Chem,
284,
7157-7164.
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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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J.W.Locasale,
A.A.Napoli,
S.Chen,
H.M.Berman,
and
C.L.Lawson
(2009).
Signatures of protein-DNA recognition in free DNA binding sites.
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J Mol Biol,
386,
1054-1065.
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PDB codes:
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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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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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A.Noy,
A.Pérez,
C.A.Laughton,
and
M.Orozco
(2007).
Theoretical study of large conformational transitions in DNA: the B<-->A conformational change in water and ethanol/water.
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Nucleic Acids Res,
35,
3330-3338.
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C.Lee,
K.H.Park,
J.A.Kim,
S.Hahn,
and
M.Cho
(2006).
Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra.
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J Chem Phys,
125,
114510.
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J.Zhou,
S.Krueger,
and
S.K.Gregurick
(2005).
A coarse graining approach to determine nucleic acid structures from small angle neutron scattering profiles in solution.
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Nucleic Acids Res,
33,
6361-6371.
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N.Pastor
(2005).
The B- to A-DNA transition and the reorganization of solvent at the DNA surface.
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Biophys J,
88,
3262-3275.
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S.B.Dixit,
D.L.Beveridge,
D.A.Case,
T.E.Cheatham,
E.Giudice,
F.Lankas,
R.Lavery,
J.H.Maddocks,
R.Osman,
H.Sklenar,
K.M.Thayer,
and
P.Varnai
(2005).
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.
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Biophys J,
89,
3721-3740.
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T.A.Soares,
P.H.Hünenberger,
M.A.Kastenholz,
V.Kräutler,
T.Lenz,
R.D.Lins,
C.Oostenbrink,
and
W.F.van Gunsteren
(2005).
An improved nucleic acid parameter set for the GROMOS force field.
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J Comput Chem,
26,
725-737.
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A.Paz,
D.Mester,
I.Baca,
E.Nevo,
and
A.Korol
(2004).
Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes.
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Proc Natl Acad Sci U S A,
101,
2951-2956.
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A.Ghosh,
and
M.Bansal
(2003).
A glossary of DNA structures from A to Z.
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Acta Crystallogr D Biol Crystallogr,
59,
620-626.
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M.Kaushik,
R.Kukreti,
D.Grover,
S.K.Brahmachari,
and
S.Kukreti
(2003).
Hairpin-duplex equilibrium reflected in the A-->B transition in an undecamer quasi-palindrome present in the locus control region of the human beta-globin gene cluster.
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Nucleic Acids Res,
31,
6904-6915.
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X.J.Lu,
and
W.K.Olson
(2003).
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.
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Nucleic Acids Res,
31,
5108-5121.
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A.E.Maris,
M.R.Sawaya,
M.Kaczor-Grzeskowiak,
M.R.Jarvis,
S.M.Bearson,
M.L.Kopka,
I.Schröder,
R.P.Gunsalus,
and
R.E.Dickerson
(2002).
Dimerization allows DNA target site recognition by the NarL response regulator.
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Nat Struct Biol,
9,
771-778.
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PDB code:
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F.Lankas,
T.E.Cheatham,
N.Spacková,
P.Hobza,
J.Langowski,
and
J.Sponer
(2002).
Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts.
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Biophys J,
82,
2592-2609.
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H.L.Ng,
and
R.E.Dickerson
(2002).
Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.
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Nucleic Acids Res,
30,
4061-4067.
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Y.Umezawa,
and
M.Nishio
(2002).
Thymine-methyl/pi interaction implicated in the sequence-dependent deformability of DNA.
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Nucleic Acids Res,
30,
2183-2192.
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J.M.Vargason,
K.Henderson,
and
P.S.Ho
(2001).
A crystallographic map of the transition from B-DNA to A-DNA.
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Proc Natl Acad Sci U S A,
98,
7265-7270.
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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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T.Lan,
and
L.W.McLaughlin
(2001).
Minor groove functional groups are critical for the B-form conformation of duplex DNA.
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Biochemistry,
40,
968-976.
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J.Poner,
J.Florián,
H.L.Ng,
J.E.Poner,
and
N.Packová
(2000).
Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure.
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Nucleic Acids Res,
28,
4893-4902.
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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
code is
shown on the right.
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Links
