'A' forms of RNAs in single strands, duplexes and RNA-DNA hybrids

S. Broyde, B. Hingerty

Research output: Contribution to journalArticlepeer-review

Abstract

Helical parameters have been calculated for the 'A' form minimum energy conformations of ApA, CpC, GpG, UpU, GpC and UpA. The helix geometries are base sequence dependent. The single strands are narrower and more tightly wound than the duplex RNA-11 form. 9-12 kcal./mole are needed to convert these single strands to the RNA-11 conformation. However, in some sequences other 'A' type conformers capable of complementary base pairing may be formed at lower energetic cost. There is substantially more base stacking in the calculated single strands than in the RNA-11 conformation. Calculated intrastrand base stacking energies reflect these differences, and also are sequence dependent. The 'A' form RNA subunits differ from the analogous DNAs in possessing a larger rise per residue, needed to accommodate the 2′-OH. RNA-DNA hybrids are consequently more likely to be in the 'A'-RNA than in the 'A'-DNA conformation, although the base sequence determines the extent of the preference.

Original languageEnglish (US)
Pages (from-to)2729-2742
Number of pages14
JournalNucleic acids research
Volume5
Issue number8
DOIs
StatePublished - Aug 1978

ASJC Scopus subject areas

  • Genetics

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