Conformational studies of (2′-5′) polynucleotides: Theorotical computations of energy, base morphology helical structure, and duplex formation

A. R. Srinivasan, W. K. Olson

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

A detailed theoretical analysis has been carried out to probe the conformational chacteristics of (2′-5′) polynucleotide chains. Semi-empirical energy calculations are used to estimate the preferred torsional combinations of the monomeric repeating unit. The resulting morphology of adjacent bases and the tendency to form regular single-stranded structures are determined by standard computational procedures. The torsional pref erences are in agreement with available nmr measurements on model compounds. The tendencies to adopt base stacked and intercalative geometries are markedly depressed compared to those in (3′-5′) chains. Very limited families of regular monomerically repeating single-stranded (2′-5′) helices are found. Base stacking, however, can be enhanced but helix formation is at the same time depressed) in mixed puckered chains. Constrained (2′-5′) duplex structures have been constructed from a search of all intervening glycosyl and sugar conformations that form geometrically feasible phosphodiester linkages. Both A- and B-type base stacking are found to generate non-standard backbone torsions and mixed glycosyl/sugar combinations. The 2′- and 5′-residues are locked in totally different arrangements and are thereby prevented from generating long helical structures.

Original languageEnglish (US)
Pages (from-to)5461-5479
Number of pages19
JournalNucleic acids research
Volume14
Issue number13
DOIs
StatePublished - Jul 11 1986

All Science Journal Classification (ASJC) codes

  • Genetics

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