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A study of model energetics and conformational properties of polynucleotide triplexes
Author(s) -
Van Vlijmen Herman W. Th.,
Rameé Graciela L.,
Pettitt B. Montgomery
Publication year - 1990
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.360300505
Subject(s) - polynucleotide , chemistry , energetics , nucleic acid , molecular dynamics , electrostatics , molecular mechanics , base pair , molecular model , computational chemistry , dna , stereochemistry , thermodynamics , physics , biochemistry
The formation of triple‐stranded nucleic acid helices is studied by molecular mechanics and molecular dynamics calculations. Using standard TAT and CGG homopolymers, single, triple, and quintuple molecular replacements are made. Some of these replacements are expected to form Hoogsteen bonds and some are not. While the electrostatic and total energetic differences for base triplet mismatches were dependent on the electrostatic model chosen, clear trends in the local geometric distortions were apparent. Relationships between these model‐built strand geometries and chemical probe experiments are discussed.