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PDBsum entry 1p4z
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References listed in PDB file
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Key reference
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Title
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Effect of sequence on the conformation of DNA holliday junctions.
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Authors
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F.A.Hays,
J.M.Vargason,
P.S.Ho.
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Ref.
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Biochemistry, 2003,
42,
9586-9597.
[DOI no: ]
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PubMed id
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Abstract
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Structures of the DNA sequences d(CCGGCGCCGG) and d(CCAGTACbr(5)UGG) are
presented here as four-way Holliday junctions in their compact stacked-X forms,
with antiparallel alignment of the DNA strands. Thus, the ACC-trinucleotide
motif, previously identified as important for stabilizing the junction, is now
extended to PuCPy, where Pu is either an adenine or guanine, and Py is either a
cytosine, 5-methylcytosine, or 5-bromouracil but not thymine nucleotide. We see
that both sequence and base substituents affect the geometry of the junction in
terms of the interduplex angle as well as the previously defined conformational
variables, J(roll) (the rotation of the stacked duplexes about their respective
helical axis) and J(slide) (the translational displacement of the stacked
duplexes along their respective helical axis). The structures of the GCC and
parent ACC containing junctions fall into a distinct conformational class that
is relatively undistorted in terms of J(slide) and J(roll), with interduplex
angles of 40-43 degrees. The substituted ACbr(5)U structure, however, is more
akin to that of the distorted methylated ACm(5)C containing junction, with
J(slide) (>or=2.3 A) and a similar J(roll) (164 degrees) opening the major
groove-side of the junction, but shows a reduced interduplex angle. In contrast,
the analogous d(CCAGTACTGG) sequence has to date been crystallized only as
resolved B-DNA duplexes. This suggests that there is an electronic effect of
substituents at the pyrimidine Py position on the stability of four-stranded
junctions. The single-crystal structures presented here, therefore, show how
sequence affects the detailed geometry, and subsequently, the associated
stability and conformational dynamics of the Holliday junction.
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Headers
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