Influence of loop sequence on relative stability of bimolecular triplex DNA

The structures of 20 bimolecular triplexes have been built and simuleted by molecular mechanics. The sequence of pyrimidine strand is 5’-dTTCTTTC-L₁ TTTI-₃CTTTTcTT-3, where the five nucleotides underlined cornpaw Ioop sequences. L₁ and L₅ represent varied residues. The sequences of purine strands are 5′-dGAAAAGAA-3′ and the reversed orientation 5′-dAAGAAAG-3′. The influence of different loop sequences and compositicm on the relative stability of twenty triplexes have bem energetically analyzed. The results indicate that 5′-loop triplexes are more stable than 3′-loop ones and the stacking interaction of purines with their adjacent basw are stronger than that of pyrimidines. The stability of triplexes is mainly determined by the first and last nucleotides in the loop. Project supported by the National Natural Science Foundation of China (Grant No. 29525304).