Random coil conformations of polynucleotides: a study incorporating long-range correlations due to dynamics of the sugar residue

Abstract

A novel virtual bond scheme joining the atoms P-C4' and C4'-P of a nucleotide repeat, consistent with the stereochemistry of polynucleotide chains, has been developed. The scheme, with its inherent feature to account for all the major sources of flexibility, could also consider effectively the short range and long range interactions, thereby simplifying the analysis of random coil and ordered structures. Using this scheme, unperturbed end-to-end dimensions and persistence lengths of polynucleotide chains have been computed incorporating the dynamical aspects of the sugar ring as well as the C4' C5' bond and the correlated changes in phosphodiester conformations. Calculated unperturbed dimensions are in excellent agreement with experimental values. Results show that the random coil is characterized by a large proportion of helical segments of the A-form.