Dynamics of a DNA minicircle: Poloidal rotation and in‐plane circular vibration

We investigated the dynamics of a 90‐base pair‐long DNA minicircle with the sequence of (AT)45/(AT)45 using the all‐atom molecular dynamics (MD) simulation. The simulation was run for a duration of 5 μs and the internal dynamics was analyzed in terms of the poloidal rotation and the in‐plane circula...

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Bibliographic Details
Published in:Bulletin of the Korean Chemical Society 2022, 43(4), , pp.523-528
Main Authors: Kim, Minjung, Hong, Chi Cheng, Lee, Saeyeon, Kim, Jun Soo
Format: Article
Language:English
Subjects:
DNA dynamics
DNA minicircle
internal DNA dynamics
molecular dynamics simulation
화학
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Summary:We investigated the dynamics of a 90‐base pair‐long DNA minicircle with the sequence of (AT)45/(AT)45 using the all‐atom molecular dynamics (MD) simulation. The simulation was run for a duration of 5 μs and the internal dynamics was analyzed in terms of the poloidal rotation and the in‐plane circular vibration. The poloidal rotation was defined by the directional variation of each base pair relative to the plane of the DNA minicircle, and its correlation time was estimated to be 61 ns. The in‐plane circular vibration was measured as the radial distance variation of each base pair from the center‐of‐mass of the DNA, and the correlation time was 6.3 ns. The characteristic time scales determined for the poloidal rotation and the radial fluctuation suggest that the internal motion of a small DNA minicircle is highly dynamic. This work provides a new set of dynamic information for small DNA minicircles, available for future applications. The internal dynamics of a DNA minicircle with the sequence of (AT)45/(AT)45 quantified by the poloidal rotation and the radial fluctuation.
ISSN:1229-5949
0253-2964
1229-5949
DOI:10.1002/bkcs.12492