1d41: Difference between revisions

Revision as of 13:12, 21 February 2008

STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)

OverviewOverview

Methylation of cytosine bases at the C5 position has been known to stabilize Z-DNA. We had previously predicted from calculations of solvent-accessible surfaces that the methyl group at the same position of thymine has a destabilizing effect on Z-DNA. In the current studies, the sequence d(m5CGUAm5CG) has been crystallized and its structure solved as Z-DNA to 1.3-A resolution. A well-defined octahedral hexaaquomagnesium complex was observed to bridge the O4 oxygens of the adjacent uridine bases at the major groove surface, and four well-structured water molecules were found in the minor groove crevice at the d(UA) dinucleotide. These solvent interactions were not observed in the previously published Z-DNA structure of the analogous d(m5CGTAm5CG) sequence. A comparison of the thymine and uridine structures supports our prediction that demethylation of thymine bases helps to stabilize Z-DNA. A comparison of this d(UA)-containing Z-DNA structure with the analogous d(TA) structure shows that access of the O4 position is hindered by the C5 methyl of thymine due to steric and hydrophobic inhibition. In the absence of the methyl group, a magnesium-water complex binds to and slightly affects the structure of the Z-DNA major groove surface. This perturbation of the solvent structure at the major groove surface is translated into a much larger 1.41-A widening of the minor groove crevice, thereby allowing the specific binding of two water molecules at well-defined sites of each internal d(UA) base pair. Possible mechanisms by which modifications at the major groove surface of Z-DNA can affect the solvent properties of the minor groove crevice are discussed.

About this StructureAbout this Structure

1D41 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG)., Zhou GW, Ho PS, Biochemistry. 1990 Aug 7;29(31):7229-36. PMID:2207101

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-[[Image:1d41.jpg|left|200px]]<br /><applet load="1d41" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1d41.jpg|left|200px]]<br /><applet load="1d41" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1d41, resolution 1.300&Aring;" />
 '''STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)'''<br />
 ==Overview==
-Methylation of cytosine bases at the C5 position has been known to, stabilize Z-DNA. We had previously predicted from calculations of, solvent-accessible surfaces that the methyl group at the same position of, thymine has a destabilizing effect on Z-DNA. In the current studies, the, sequence d(m5CGUAm5CG) has been crystallized and its structure solved as, Z-DNA to 1.3-A resolution. A well-defined octahedral hexaaquomagnesium, complex was observed to bridge the O4 oxygens of the adjacent uridine, bases at the major groove surface, and four well-structured water, molecules were found in the minor groove crevice at the d(UA), dinucleotide. These solvent interactions were not observed in the, previously published Z-DNA structure of the analogous d(m5CGTAm5CG), sequence. A comparison of the thymine and uridine structures supports our, prediction that demethylation of thymine bases helps to stabilize Z-DNA. A, comparison of this d(UA)-containing Z-DNA structure with the analogous, d(TA) structure shows that access of the O4 position is hindered by the C5, methyl of thymine due to steric and hydrophobic inhibition. In the absence, of the methyl group, a magnesium-water complex binds to and slightly, affects the structure of the Z-DNA major groove surface. This perturbation, of the solvent structure at the major groove surface is translated into a, much larger 1.41-A widening of the minor groove crevice, thereby allowing, the specific binding of two water molecules at well-defined sites of each, internal d(UA) base pair. Possible mechanisms by which modifications at, the major groove surface of Z-DNA can affect the solvent properties of the, minor groove crevice are discussed.
+Methylation of cytosine bases at the C5 position has been known to stabilize Z-DNA. We had previously predicted from calculations of solvent-accessible surfaces that the methyl group at the same position of thymine has a destabilizing effect on Z-DNA. In the current studies, the sequence d(m5CGUAm5CG) has been crystallized and its structure solved as Z-DNA to 1.3-A resolution. A well-defined octahedral hexaaquomagnesium complex was observed to bridge the O4 oxygens of the adjacent uridine bases at the major groove surface, and four well-structured water molecules were found in the minor groove crevice at the d(UA) dinucleotide. These solvent interactions were not observed in the previously published Z-DNA structure of the analogous d(m5CGTAm5CG) sequence. A comparison of the thymine and uridine structures supports our prediction that demethylation of thymine bases helps to stabilize Z-DNA. A comparison of this d(UA)-containing Z-DNA structure with the analogous d(TA) structure shows that access of the O4 position is hindered by the C5 methyl of thymine due to steric and hydrophobic inhibition. In the absence of the methyl group, a magnesium-water complex binds to and slightly affects the structure of the Z-DNA major groove surface. This perturbation of the solvent structure at the major groove surface is translated into a much larger 1.41-A widening of the minor groove crevice, thereby allowing the specific binding of two water molecules at well-defined sites of each internal d(UA) base pair. Possible mechanisms by which modifications at the major groove surface of Z-DNA can affect the solvent properties of the minor groove crevice are discussed.
 ==About this Structure==
-D41 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D41 OCA].
+D41 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D41 OCA].
 ==Reference==
 Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG)., Zhou GW, Ho PS, Biochemistry. 1990 Aug 7;29(31):7229-36. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2207101 2207101]
 [[Category: Protein complex]]
-[[Category: Ho, P.S.]]
+[[Category: Ho, P S.]]
 [[Category: Zhou, G.]]
 [[Category: MG]]
@@ Line 19: / Line 19: @@
 [[Category: z-dna]]
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