Backbone conformations in nucleic acids: the occurrence of g⁺g⁺ internucleotide phosphodiester conformation

Abstract

Semiempirical conformational energy calculations have been performed on dinucleoside triphosphate models with and without base interactions to investigate the conformational requirement for the stereochemical and energetic feasibility of (gauche⁺,gauche⁺) phosphodiester conformation in a polynucleotide chain. Results show that the trans conformation of the C4' - C5' bond on the 5'-sugar (either C3'-endo or C2'-endo) of a dinucleoside triphosphate renders the g⁺g⁺ phosphodiester energetically favorable. The degree of energetic preference shows a dependence on the C3' - O3' bond torsions (φ '); higher g⁺g⁺ conformation populations are correlated with higher values of φ ' = 270° due to increased van der Waals interactions between adjacent sugar residues. For similar reasons, the g⁺g⁺ phosphodiester displays an energetic dependence on the nature and sequence of bases and their orientations. Other conformational combinations that also stereochemically permit the g⁺g⁺ phosphodiester are discussed along with base effects.