Accommodation of R-TFO in major groove of DNA deviates its conformation from natural B-DNA towards the A-DNA

The natural DNA triplexes form at the initiation of replication, transcription, or homologous recombination in cells, for a very short interval of time. A conformational change of DNA from B-DNA to A-DNA for the recommendation of Hoogsteen triplexes may not be possible but for R-triplexes may be possible because it doesn’t need complete A-DNA to form triplexes. To examine this we made a computational study to observe the conformation of duplex for a recommendation of R-triplexes. To study this, we designed an R-triplex in a mixed sequence of DNA and run molecular dynamics for 150 ns to observe the stability of the triplex and conformational analysis during dynamics. The same dynamics provide us with trajectories for the study of the conformation of the duplex in the R-triplex. In this study we found that the accommodation of R-TFO only requires a little deviation of B-DNA to A-DNA, the conformational parameters are evident.