DSSR-PyMOL cartoon-block schematics: PDB entry 1d26

PDB-id

1d26; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.12 Å)

Summary

Effect of a single 3'-methylene phosphonate linkage on the conformation of an a-DNA octamer double helix

Reference

Heinemann U, Rudolph LN, Alings C, Morr M, Heikens W, Frank R, Blocker H (1991): "Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix." Nucleic Acids Res., 19, 427-433. doi: 10.1093/nar/19.3.427.

Abstract

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.