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PDBsum entry 1dn9
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References listed in PDB file
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Key reference
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Title
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Structure of an alternating-B DNA helix and its relationship to a-Tract DNA.
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Authors
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C.Yoon,
G.G.Privé,
D.S.Goodsell,
R.E.Dickerson.
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Ref.
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Proc Natl Acad Sci U S A, 1988,
85,
6332-6336.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the synthetic DNA dodecamer CGCATATATGCG has been
solved at 2.2-A resolution. Its central 6 base pairs adopt the alternating-B-DNA
helix structure proposed nearly a decade ago. This alternating poly(AT)
structure contrasts with the four known examples of what can be termed a poly(A)
subfamily of B-DNA structures: CGCAAAAAAGCG, CGCAAATTTGCG, CGCGAATTCGCG, and
CGCGAATTbrCGCG, their defining characteristic being a succession of two or more
adenines along one strand, in a region of 4 or more A.T base pairs. All five
helices show a characteristically narrow minor groove in their AT centers, but
the mean propeller twist at A.T base pairs is lower in the alternating poly(AT)
helix than in the poly(A) subfamily of helices. Three general principles emerge
from x-ray analyses of B-DNA oligonucleotides: (i) GC and mixed-sequence B-DNA
have a wide minor groove, whereas the minor groove is narrow in heteropolymer or
homopolymer AT sequences. (ii) G.C base pairs have low propeller twist; A.T
pairs can adopt a high propeller twist but need not do so. A high propeller
twist can be stabilized by cross-strand hydrogen bonds in the major or minor
groove, examples being the minor groove bonds seen in CCAAGATTGG and the major
groove bonds that can accompany AA sequences in the poly(A) family. (iii)
Homopolymer poly(A) tracts may be stiffer than are alternating AT or
general-sequence DNA because of these cross-strand major groove hydrogen bonds.
Poly(A) tracts appear internally unbent, but bends may occur at junctions with
mixed-sequence DNA because of differences in propeller twist, base pair
inclination, and base stacking on the two sides of the junction. Bending occurs
most easily via base roll, favoring compression of the broad major groove.
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Headers
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