Abstract
The relative stability of three intratriplex DNAs with substitution of 5-bromocytosines for cytosines in different strands and the corresponding unsubstituted intratriplex have been respectively investigated by molecular mechanics calculation. The results showed that intratriplex YTC with substitution occurring in strand III is the most stable and YTCY with substitution occurring in both strand I and III is the most unstable. Sugar conformations of the four intratriplexes are mainly C3’-endo. However, there are more C2’-endo sugar conformations in YTCY than in other intratriplexes, especially in strand I and III. Thus intratriplex YTCY is the combination of A-DNA and B-DNA, the other three intratriplexes are classical A-type DNA.
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