Effect of loop on the stability of intramolecular triplex DNA

Conformation stabilities of intramolecular triple-helical DNAs (intra-tnplex DNAs: 5-d(TC)6-d(T)m-d(CT)6-d(C)n-d(AG)6-3',where m and n are chosen to be 4 and 3) have been examined by molecular mechanics.The four intra-triplexes (H-DNAs) are compared with the mtermolecular triplexes d(TC)6 * d ( AG)6 d(CT)6.The results revealed that loops do not significantly influence the mtratriplex conformations,loop conformations,however,depend partly on its length.Loop also makes strand Ⅱ of every intra-triplex DNA longer than that of the inter-triplex DNA.Most of residue sugar conformations of triple-helical DNAs are S-type,there aiso exist,however,N-type conformation and the conformations between S-type and N-type Possible models of the five triplex DNAs are presented.

Effect of loop on the stability of intramolecular triplex DNA

Conformation stabilities of intramolecular triple-helical DNAs (intra-triplex DNAs: 5′-d(TC)_6- d(T)_m-d(CT)₆-d(C)_n-d(AG)₆-3′, wherem andn are chosen to be 4 and 3) have been examined by molecular mechanics. The four intra-triplexes (H-DNAs) are compared with the intermolecular triplexes d(TC)6 * d(AG)₆ · d(CT)6. The results revealed that loops do not significantly influence the intratriplex conformations, loop conformations, however, depend partly on its length. Loop also makes strand II of every intra-triplex DNA longer than that of the inter-triplex DNA. Most of residue sugar conformations of triple-helical DNAs are S-type, there also exist, however, N-type conformation and the conformations between S-type and N-type. Possible models of the five triplex DNAs are presented. Project supported by the Chinese Academy of Sciences.