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Abstract
Abstract Effective sequence-specific recognition of duplex DNA is possible by triplex formation with natural oligonucleotides via Hoogsteen H-bonding. However, triplex formation is in practice limited to pyrimidine oligonucleotides binding duplex A-T or G-C base pair DNA sequences specifically at homopurine sites in the major groove as T·A-T and C+ ·G-C triplets. Here we report the successful molecular dynamics modelling of novel unnatural nucleosides that recognize the T-A DNA base pair by Hoogsteen interaction. These X·T-A triplets were placed within (T·A-T)11 triplexes of A-type or B-type starting configuration. These triplex structures underwent energy minimization and 300 ps molecular dynamics simulation with counter-ions and solvent. The same procedures were applied to unmodified (T·A-T)11 triplexes and their trajectories compared to those of the central triplet modified triplexes of similar starting configuration. The phosphodiester backbone dihedrals, χ-dihedrals, and H-bonding distances of the ce...
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