1l6b

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{{STRUCTURE_1l6b| PDB=1l6b | SCENE= }}
{{STRUCTURE_1l6b| PDB=1l6b | SCENE= }}
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'''CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG'''
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===CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG===
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==Overview==
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The single crystal structure of the methylated sequence d(CCGGTACm(5)CGG) has been solved as an antiparallel stacked X Holliday junction to 1.5 A resolution. When compared with the parent nonmethylated d(CCGGTACCGG) structure, the duplexes are translated by 3.4 A along the helix axis and rotated by 10.8 degrees relative to each other, rendering the major grooves more accessible overall. A Ca(2+) complex is seen in the minor groove opposite the junction but is related to the B conformation of the stacked arms. At the junction itself, the hydrogen bond from the N4 nitrogen of cytosine C8 to the C7 phosphate at the crossover in the parent structure has been replaced by a water bridge. Thus, this direct interaction is not absolutely required to stabilize the junction at the previously defined ACC trinucleotide core. The more compact methylated junction forces the Na(+) of the protected central cavity of the nonmethylated junction into a solvent cluster that spans the space between the junction crossover and the stacked arms. A series of void volumes within the methylated and the nonmethylated structures suggests that small monovalent cations can fill and vacate this central cavity without the need to unfold the four-stranded Holliday junction completely.
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(as it appears on PubMed at http://www.pubmed.gov), where 11919197 is the PubMed ID number.
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{{ABSTRACT_PUBMED_11919197}}
==About this Structure==
==About this Structure==
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[[Category: Dna four-way junction]]
[[Category: Dna four-way junction]]
[[Category: Holliday junction]]
[[Category: Holliday junction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:35:23 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 11:48:06 2008''

Revision as of 08:48, 2 July 2008

Image:1l6b.png

Template:STRUCTURE 1l6b

CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG

Template:ABSTRACT PUBMED 11919197

About this Structure

Full crystallographic information is available from OCA.

Reference

The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution., Vargason JM, Ho PS, J Biol Chem. 2002 Jun 7;277(23):21041-9. Epub 2002 Mar 27. PMID:11919197

Page seeded by OCA on Wed Jul 2 11:48:06 2008

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