1f69: Difference between revisions

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[[Image:1f69.gif|left|200px]]
{{Seed}}
[[Image:1f69.png|left|200px]]


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{{STRUCTURE_1f69|  PDB=1f69  |  SCENE=  }}  
{{STRUCTURE_1f69|  PDB=1f69  |  SCENE=  }}  


'''CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE'''
===CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE===




==Overview==
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Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3'-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs.
The line below this paragraph, {{ABSTRACT_PUBMED_10966645}}, adds the Publication Abstract to the page
(as it appears on PubMed at http://www.pubmed.gov), where 10966645 is the PubMed ID number.
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{{ABSTRACT_PUBMED_10966645}}


==About this Structure==
==About this Structure==
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[[Category: Double helix]]
[[Category: Double helix]]
[[Category: E-dna]]
[[Category: E-dna]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:57:13 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 02:46:06 2008''

Revision as of 23:46, 30 June 2008

File:1f69.png

Template:STRUCTURE 1f69

CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE

Template:ABSTRACT PUBMED 10966645

About this Structure

Full crystallographic information is available from OCA.

Reference

The extended and eccentric E-DNA structure induced by cytosine methylation or bromination., Vargason JM, Eichman BF, Ho PS, Nat Struct Biol. 2000 Sep;7(9):758-61. PMID:10966645

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