1D26

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

Summary for 1D26

• Entry DOI: 10.2210/pdb1d26/pdb
• Descriptor: DNA (5'-D(*GP*CP*CP*CP*(G31)P*GP*GP*C)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, modified, dna
• Total number of polymer chains: 1
• Total formula weight: 2426.62

Authors

Heinemann, U. (deposition date: 1990-09-17, release date: 1992-04-07, Last modification date: 2024-02-07)

Primary citation

Heinemann, U.,Rudolph, L.N.,Alings, C.,Morr, M.,Heikens, W.,Frank, R.,Blocker, H.
Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix.
Nucleic Acids Res., 19:427-433, 1991

PubMed 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.

PubMed: 2011517
DOI: 10.1093/nar/19.3.427

Experimental method

X-RAY DIFFRACTION (2.12 Å)