Dynamics of a DNA minicircle: Poloidal rotation and in‐plane circular vibration. (25th January 2022)

• Record Type: Journal Article
• Authors: Kim, Minjung; Hong, Chi Cheng; Lee, Saeyeon; Kim, Jun Soo
• Is Part Of: Bulletin of the Korean Chemical Society. Volume 43:Number 4(2022)
• Page Start: 523
• Page End: 528
• Publication Date: 2022-01-25
• Subjects: DNA dynamics -- DNA minicircle -- internal DNA dynamics -- molecular dynamics simulation; Chemistry -- Periodicals; 540.5
• DOI: 10.1002/bkcs.12492
• Languages: English
• ISSNs: 0253-2964

Abstract

Abstract: 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. Abstract : The internal dynamics of a DNA minicircle with the sequence of (AT)45 /(AT)45 quantified by the poloidal rotation and the radial fluctuation.