1d26: Difference between revisions

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[[Image:1d26.gif|left|200px]]
{{Seed}}
[[Image:1d26.png|left|200px]]


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{{STRUCTURE_1d26|  PDB=1d26  |  SCENE=  }}  
{{STRUCTURE_1d26|  PDB=1d26  |  SCENE=  }}  


'''EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX'''
===EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX===




==Overview==
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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.
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{{ABSTRACT_PUBMED_2011517}}


==About this Structure==
==About this Structure==
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[[Category: Double helix]]
[[Category: Double helix]]
[[Category: Modified]]
[[Category: Modified]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:21:55 2008''
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:10:28 2008''

Revision as of 19:10, 30 June 2008

File:1d26.png

Template:STRUCTURE 1d26

EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX

Template:ABSTRACT PUBMED 2011517

About this Structure

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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