Simulations of the B‐DNA molecular dynamics of d(CGCGAATTCGCG)₂ and d(GCGCGCGCGC)₂: An analysis of the role of initial geometry and a comparison of united and all‐atom models

Molecular dynamics simulations on the sequence d(CGCGAATTCGCG)2 have been carried out using both united atom and all-atom representations, and starting the simulations both from a regular repeating B-DNA structure and from the x-ray single crystal B-DNA structure. An all-atom B-DNA simulation on the sequence d(GCGCGCGCGC)2 has also been carried out, in order to compare it with a previous united atom simulation. The helix repeats, H-bonding, sugar pucker profiles, and average torsional angles are all in the range observed in crystallographic and nmr studies for B-DNA helices. In some of the sequences, there is a significant bend in the DNA helices. The individual helix repeats, with focus on 3'CpG5' and 3'GpC5' units, show the opposite helix repeat to that suggested by Calladine's rules.