Which base triplet stabilizes triple helix? Ab initio SCF and density functional methods of calculations on some base triplets

Abstract

Ab initio SCF and density functional methods of calculation have been performed for determining the stability of some experimentally observed base triplets of triple helix. The computed binding energies provide the importance of Hoogsteen hydrogen bonding in forming the stable triplets as observed in C +GC, TAT, GGC and AAT triplets while mismatched triplets GTA, C +AT and TTA show no such bonding. The Hoogsteen hydrogen bonding pattern that emerges in some triplets are contributed from the favorable binding between Watson Crick and single base, whereas the structure of less stable triplets do not show such hydrogen bonding. The substantial differences in the binding energies of triplets obtained from SCF and density functional methods explain the sequence specificity in triplet formation.