Theoretical calculations of base-base interactions in nucleic acids: II stacking interactions in polynucleotides

Abstract

Base-base interactions were computed for single-nd double-stranded polynucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interaction energies of a regular duplex and the alternative structures³ were compared. It was found that the type II model³ is energetically more favourable than the rest.