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Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGA T TCGCG)
Author(s) -
Venable Richard M.,
Widmalm Göran,
Brooks Bernard R.,
Egan William,
Pastor Richard W.
Publication year - 1992
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360320707
Subject(s) - chemistry , molecular dynamics , hydrogen bond , duplex (building) , crystallography , speed wobble , computational chemistry , molecule , stereochemistry , dna , physics , organic chemistry , classical mechanics , biochemistry
The TT mismatch region in duplex d(CGCGA T TCGCG) was studied using a 500‐ps molecular dynamics (MD) simulation in water, and a series of 1‐ps MD simulations and energy minimizations in vacuum. The DNA maintained its duplex structure, although the mismatch region showed significantly higher flexibility than the GC regions. The predominant conformation in the 500‐ps MD simulation involved an average −42° propeller twist between T 6 and T′ 6 , and a −22° buckle between A 5 and T′ 7 , One hydrogen bond was formed between T 6 and T′ 6 , and another between T 6 and the O2 of T′ 7 with both Watson‐Crick hydrogen bonds between A 5 and T′ 7 remaining intact. The minimizations resulted in conformations with the equivalent hydrogen‐bonding pattern, as well as ones with “wobble pair” hydrogen bonds between T 6 and T′ 6 . However, the wobble pair conformation was found to be unstable in the water simulation.