Comparative Studies on Parallel and Antiparallel Duplex and Triplex DNA

Parallel strand models for base sequences d(A)10·d(T)10, d(AT)5·d(TA)5, d(G5C5)d(C5G5), d(GC)5·d(CG)5and d(CTATAGGGAT)·d(GATATCCCTA), where reverse Watson–Crick A–T pairing with two H-bonds and reverse Watson–Crick G–C pairing with one H-bond or with two H-bonds were adopted, and three models of d(T)14·d(A)14·d(T)14triple helix with different strand orientations were built up by molecular architecture and energy minimization. Comparisons of parallel duplex models with their corresponding B-DNA models and comparisons among the three triple helices showed: (i) conformational energies of parallel AT duplex models were a little lower, while for GC duplex models they were about 8% higher than that of their corresponding B-DNA models; (ii) the energy differences between parallel and B-type duplex models and among the three triple helices arose mainly from base stacking energies, especially for GC base pairing; (iii) the parallel duplexes with one H-bond G–C pairs were less stable than those with two H-bonds G–C pairs. The present paper includes a brief discussion about the effect of base stacking and base sequences on DNA conformations.