Dynamics of B-DNA on the microsecond time scale.

  title={Dynamics of B-DNA on the microsecond time scale.},
  author={Alberto P{\'e}rez and F. Javier Luque and Modesto Orozco},
  journal={Journal of the American Chemical Society},
  volume={129 47},
We present the first microsecond MD simulation of B-DNA. Trajectory shows good agreement with available data and clarifies the mus dynamics of DNA. The duplex is sampling the B-conformation, but many relevant local transitions are found, including S --> N repuckers (up to 7 N-sugars are found simultaneously), local BII transitions (15% of the dinucleotides are in BII-form; some of these forms are stable for up to 7 ns), and sequence-dependent alpha/gamma transitions (happening in the 7-50 ns… CONTINUE READING

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