Helix geometry of single stranded DNA 'A' and 'B' forms from minimum energy conformations of dimeric subunits

B. Hingerty, S. Broyde

Research output: Contribution to journalArticlepeer-review

Abstract

Low energy conformations with dihedral angles similar to those occurring in fibers of the 'A'and 'B' forms of DNAs have been calculated for the deoxydinucleoside phosphates dApdA, dCpdC, dTpdT, dGpdG and dGpdC (1-3). These conformers have been used as building blocks for generating larger single stranded polymers, whose helical parameters we have calculated. We find that single stranded 'A' and 'B' form helices tend to be narrower and more tightly wound than the duplexes obtained in fibers (4,5). This is consistent with experimental observations on single stranded fibers of poly (rC) (6). We also find that the different sequences have different helix geometries. In addition, it is observed that large variations in helix geometry for a given sequence are achievable at little energetic cost.

Original languageEnglish (US)
Pages (from-to)127-137
Number of pages11
JournalNucleic acids research
Volume5
Issue number1
DOIs
StatePublished - Jan 1978

ASJC Scopus subject areas

  • Genetics

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