1d26
From Proteopedia
(New page: 200px<br /><applet load="1d26" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d26, resolution 2.120Å" /> '''EFFECT OF A SINGLE ...) |
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| - | [[Image:1d26.gif|left|200px]]<br /><applet load="1d26" size=" | + | [[Image:1d26.gif|left|200px]]<br /><applet load="1d26" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1d26, resolution 2.120Å" /> | caption="1d26, resolution 2.120Å" /> | ||
'''EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX'''<br /> | '''EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional structure of the self-complementary DNA octamer | + | The three-dimensional structure of the self-complementary DNA octamer d(GCCCGpGGC) has been determined in the crystalline state using X-ray diffraction data to a nominal resolutoin of 2.12 measured from a very small crystal at DESY, Hamburg. The structure was refined with stereochemical restraints to an R value of 17.1%. d(GCCCGpGGC), containing one single 3'-methylene phosphonate linkage (denoted p), forms an A-DNA double helix with strict dyad symmetry, that is distinct from canonical A-DNA by a wide open major groove and a small average base-pair inclination against the helix axis. The conformation of the unmodified control d(GCCCGGGC) is known from an X-ray analysis of isomorphous crystals (Heinemann et al. (1987) Nucleic Acids Res. 15, 9531-9550). Comparison of the two structures reveals only minor conformational differences, most notably in the pucker of the reduced deoxyribose. It is suggested that oligonucleotides with charged 3'-methylene phosphonate groups may form stable duplexes with complementary DNA or RNA strands rendering them candidates for use as gene-regulatory antisense probes. |
==About this Structure== | ==About this Structure== | ||
| - | 1D26 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:// | + | 1D26 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=1D26 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: modified]] | [[Category: modified]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:08 2008'' |
Revision as of 10:12, 21 February 2008
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EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX
Overview
The three-dimensional structure of the self-complementary DNA octamer d(GCCCGpGGC) has been determined in the crystalline state using X-ray diffraction data to a nominal resolutoin of 2.12 measured from a very small crystal at DESY, Hamburg. The structure was refined with stereochemical restraints to an R value of 17.1%. d(GCCCGpGGC), containing one single 3'-methylene phosphonate linkage (denoted p), forms an A-DNA double helix with strict dyad symmetry, that is distinct from canonical A-DNA by a wide open major groove and a small average base-pair inclination against the helix axis. The conformation of the unmodified control d(GCCCGGGC) is known from an X-ray analysis of isomorphous crystals (Heinemann et al. (1987) Nucleic Acids Res. 15, 9531-9550). Comparison of the two structures reveals only minor conformational differences, most notably in the pucker of the reduced deoxyribose. It is suggested that oligonucleotides with charged 3'-methylene phosphonate groups may form stable duplexes with complementary DNA or RNA strands rendering them candidates for use as gene-regulatory antisense probes.
About this Structure
1D26 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix., Heinemann U, Rudolph LN, Alings C, Morr M, Heikens W, Frank R, Blocker H, Nucleic Acids Res. 1991 Feb 11;19(3):427-33. PMID:2011517
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