Spatial configuration of ordered polynucleotide chains: a novel double helix.

Abstract

Structural details are reported for a novel right-handed polynucleotide double helix stabilized by vertical base stacking and H-bonding. The primary difference between this duplex and the familiar Watson-Crick horizontally stabilized polynucleotide complex arises in the glycosyl rotation of the heterocyclic bases with respect to the sugar-phosphate backbone. In the vertical double helix the bases adopt a fairly unusual (although not sterically impossible) high-anti conformation, while in the horizontal models deduced from X-ray analyses the bases occur in the favored anti arrangement. The base pairing scheme in both duplexes is the standard Watson-Crick type. The vertical double helix is demonstrated to be a plausible model for the unusual complex formation observed between complementary synthetic polycyclonucleotides (the bases of which are fixed by a chemical linkage in the high-anti orientation) and also a potential alternative ordered structure available to naturally occurring nucleic acid systems that can adopt both anti and high-anti glycosyl arrangements.