The structures of 20 bimolecular triplexes have been built and simuleted by molecular mechanics. The sequence of pyrimidine strand is 5'-dTTCTTTC-L(1) TTTI-(3)CTTTTcTT-3, where the five nucleotides underlined cornpaw Ioop sequences. L(1) and L(5) 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.