1f6c
From Proteopedia
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[[Image:1f6c.gif|left|200px]] | [[Image:1f6c.gif|left|200px]] | ||
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| - | + | {{STRUCTURE_1f6c| PDB=1f6c | SCENE= }} | |
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'''CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE''' | '''CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6C OCA]. | |
==Reference== | ==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:[http://www.ncbi.nlm.nih.gov/pubmed/10966645 10966645] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/10966645 10966645] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Eichman, B F.]] | [[Category: Eichman, B F.]] | ||
[[Category: Ho, P S.]] | [[Category: Ho, P S.]] | ||
[[Category: Vargason, J M.]] | [[Category: Vargason, J M.]] | ||
| - | [[Category: | + | [[Category: B-dna]] |
| - | [[Category: | + | [[Category: Double helix]] |
| - | [[Category: | + | [[Category: E-dna]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:57:25 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 12:57, 2 May 2008
CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE
Overview
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.
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 Page seeded by OCA on Fri May 2 15:57:25 2008
Categories: Eichman, B F. | Ho, P S. | Vargason, J M. | B-dna | Double helix | E-dna
