title: Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix.
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.
authors.affiliation: Abteilung Saenger, Freie Universität Berlin, FRG.
authors.forename: U
authors.initials: U
authors.lastname: Heinemann
authors.forename: L N
authors.initials: LN
authors.lastname: Rudolph
authors.forename: C
authors.initials: C
authors.lastname: Alings
authors.forename: M
authors.initials: M
authors.lastname: Morr
authors.forename: W
authors.initials: W
authors.lastname: Heikens
authors.forename: R
authors.initials: R
authors.lastname: Frank
authors.forename: H
authors.initials: H
authors.lastname: Blöcker
mesh_terms: D003461:Crystallography; D004247:DNA / Q000737:chemistry / Q000648:ultrastructure*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D063065:Organophosphonates; D013329:Structure-Activity Relationship; D014867:Water
chemical_list: D009841:Oligonucleotides; D063065:Organophosphonates; D014867:Water; D004247:DNA