Computational analysis of triplex formation of oligonucleotides:protonated and 5-methylated py-pu-py motif

• Published in: Science China. Chemistry Vol. 40; no. 2; pp. 113 - 121
• Main Author: 白春礼 王琛 汪新文
• Format: Journal Article
• Language: English
• Published: Heidelberg Springer Nature B.V 01.04.1997
• Subjects: analysis; computational; DNA; effect; Oligonucleotides; Protonation; Screening; stability; Stability analysis; triplex
• ISSN: 1674-7291; 1006-9291; 1869-1870; 1862-2771
• DOI: 10.1007/BF02876401

A triple helix composed of three dodecanucleotides,5’-d(TC)6,5-(AG)6 and 3’-d(TC)6 with each containing a methylcytosme or a protonated-cylosine,was examined in terms of various interactions Computational malvsis of the stability of triplex formation was consistent with the experimental observations.The Hoogsleen hase among interaction was increased through substitution of 5-methylcytosme for cytosme and/or protonation The inter-woon between water molecules and DNA triplex was visualized in terms,of the end-to-end distance change of each trand The chain length was reduced by about 7 5%-16 2% due to the screening effect In addition,as the screening fleer nerenises,Hoogsteen base pairs appear to be stable in triplex formation.Our computational results also show this the effect of protonated- and methylated cytosme on the stability of triplex formation was due to the change of the beerostanis mteractions rather than the surface stacking interaction