1f6j: Difference between revisions

Revision as of 13:35, 21 February 2008

CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGBR5CC

OverviewOverview

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 StructureAbout this Structure

1F6J is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

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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-[[Image:1f6j.gif|left|200px]]<br /><applet load="1f6j" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1f6j.gif|left|200px]]<br /><applet load="1f6j" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1f6j, resolution 2.25&Aring;" />
 '''CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGBR5CC'''<br />
 ==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.
+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==
-F6J is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F6J OCA].
+F6J is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6J 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=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: double helix]]
 [[Category: e-dna]]
 [[Category: methylation]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:22:30 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:35:23 2008''