Virtual bond probe to study ordered and random coil conformations of nucleic acids

Abstract

Recognition of the stereochemical features inherent to a nucleotide, viz., the preferred trans character of the two C[BOND]O bonds and the approximate chemical and conformational symmetry, has facilitated the representation of a nucleotide in terms of two nearly equal blocks or two virtual bonds spanning the atoms P to C4' on the 5' side and C4' to P on the 3' side. The scheme, by virtue of its unique ability to account for the main sources of flexibility and to incorporate their interdependence, could be effectively applied to probe ordered, as well as random coil conformations of polynucleotide chains. Using this scheme, conformations of nucleotide, dinucleotides, helices, and yeast tRNA^Phe have been characterized by virtual bond parameters. The two blocks of nucleotide have also been described in terms of two approximate planes similar to peptides. Unperturbed end-to-end dimensions and persistence lengths of random coil polynucleotides have been computed by considering short-range as well as near-neighbor bond long-range correlations and are in excellent agreement with the experimentally determined values. A striking finding of these studies is the relevation that random coils comprise of a large proportion of stacked A-type helical segments in sharp contrast to earlier interpretations which invoked a high fraction of unstacked extended conformations.