C n d G i2 triple helices

When the first crystal structure for the B-DNA was reported [53], it was observed that the relative orientation of two basepairs was non planar and there existed a sequence dependent variation in this local structural 

G18 in CGGP and C9 in CGGA) or between e and (between t,g — g, t conformations for G29 in CGGP and almost throughout the third strand in CGGA) in the same nucleotide. The (s, Q transitions are also accompanied by correlated changes in P(i+I) of the next nucleotide, to a more eclipsed conformation, within the same strand. 

Distribution of sugar puckers (%). in the different ranges of pseudorotation phase angle T , for all three strands in the CGGP and CGGA MD structures, in the 20-200 ps interval. In the 

3 Effect of explicit water and counterions on the energetics of the structures An energy minimization analysis of the M.D. average structures indicates that the C.G G parallel triplex is energetically more favourable than the antiparallel structure, if the hydrogen bonds are to be retained. Free energy calculations on C.G G triplexes had also indicated that the antiparallel structure becomes 

Total energy of the system, including solvent, suggests that both the antiparallel structures are marginally better eompared to the parallel structure, as seen from Table 3. However, since the number of water molecules present in each system is different (listed in first row of Table 3), a meaningful energy comparison, between the three structures, requires correction due to this factor. 

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