Intercalation conformations in single- and double-stranded nucleic acids

Abstract

Two regions in the crystal structure of yeast phenylalanine tRNA, where single-stranded loops interact by intercalation, have been examined in detail. There are four examples of a nucleotide base from one loop intercalating between two sequential bases of another loop in these two regions. These four dinucleoside phosphate conformations serve as models for intercalation in single-stranded nucleic acids. Double-stranded DNA and RNA polymers were constructed by computer model building methods, which incorporated the dinucleoside phosphate conformations found in these single-stranded, intercalation regions in otherwise standard double-helices. The results suggest that it is unlikely that there is a unique intercalation geometry for either single- or double-stranded nucleic acids, but that nucleic acids may assume one of a variety of intercalation geometries which will best accommodate a particular intercalating agent for a particular base sequence.