The structures of 20 bimolecular triplexes have been built and simulated by molecular mechanics. The sequence of pyrimidine strand is 5′ dTTCTTTC L\-1TTTL\-5 CTTTTCTT 3′, where the five nucleotides underlined compos...The structures of 20 bimolecular triplexes have been built and simulated by molecular mechanics. The sequence of pyrimidine strand is 5′ dTTCTTTC L\-1TTTL\-5 CTTTTCTT 3′, where the five nucleotides underlined compose loop 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 composition on the relative stability of twenty triplexes have been 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 bases are stronger than that of pyrimidines. The stability of triplexes is mainly determined by the first and last nucleotides in the loop.展开更多
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 intr...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.展开更多
文摘The structures of 20 bimolecular triplexes have been built and simulated by molecular mechanics. The sequence of pyrimidine strand is 5′ dTTCTTTC L\-1TTTL\-5 CTTTTCTT 3′, where the five nucleotides underlined compose loop 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 composition on the relative stability of twenty triplexes have been 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 bases are stronger than that of pyrimidines. The stability of triplexes is mainly determined by the first and last nucleotides in the loop.
基金Project supported by the Chinese Academy of Sciences
文摘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.
