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1p54

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{{STRUCTURE_1p54| PDB=1p54 | SCENE= }}
{{STRUCTURE_1p54| PDB=1p54 | SCENE= }}
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'''Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions'''
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===Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions===
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==Overview==
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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) (&gt;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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{{ABSTRACT_PUBMED_12911300}}
==About this Structure==
==About this Structure==
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[[Category: Four-way junction]]
[[Category: Four-way junction]]
[[Category: Stacked-x junction]]
[[Category: Stacked-x junction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:41:54 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 15:22:00 2008''

Revision as of 12:22, 27 July 2008

Image:1p54.png

Template:STRUCTURE 1p54

Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions

Template:ABSTRACT PUBMED 12911300

About this Structure

Full crystallographic information is available from OCA.

Reference

Effect of sequence on the conformation of DNA holliday junctions., Hays FA, Vargason JM, Ho PS, Biochemistry. 2003 Aug 19;42(32):9586-97. PMID:12911300

Page seeded by OCA on Sun Jul 27 15:22:00 2008

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