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

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...

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Bibliographic Details
Published in:Science China. Chemistry 1997-04, Vol.40 (2), p.113-121
Main Author: 白春礼 王琛 汪新文
Format: Article
Language:English
Subjects:
analysis
computational
DNA
effect
Oligonucleotides
Protonation
Screening
stability
Stability analysis
triplex
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Summary: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
ISSN:1674-7291
1869-1870
DOI:10.1007/BF02876401