LOOP AND WATER EFFECT ON STABILITY OF INTERTRIPLEX DNA

Stability of four intratriplexes and one intertriplex influenced by lo ops and water have been investigated by molecular mechanics calculatio n. The four intratriplexes are 5'-d(TC)(6)-d(T)(m)-d(CT)(6)-d(C)(n)-d( AG)(6)-3' (m, n = 3 or 4), the corresponding intertripler is d(TC)(6) d(AG)(6).d(CT)(6) (., Watson-Crick hydrogen bond; , Hoogsteen hydroge n band). We studied in detail how loops and water would effect intra-a nd interstrand interactions of the five triplexes, respectively. The r esults showed that the existence of loops may have limited impact on t he stability of the concerned triplex structures, regardless of water environment. In contrast, water molecules do have appreciable effects on tripler stability. Sugar conformations of the five triplexes were a lso discussed in this paper. The theoretical results are in good agree ment with the FT-IR experiments. (C) 1998 Elsevier Science B.V.