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Bubble Relaxation Dynamics in Homopolymer DNA Sequences.

Malcolm Hillebrand1, George Kalosakas2, Alan R Bishop3

  • 1Nonlinear Dynamics and Chaos Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa.

Molecules (Basel, Switzerland)
|February 11, 2023
PubMed
Summary
This summary is machine-generated.

Large bubbles in DNA dynamics relax over extended periods, with guanine-cytosine sequences showing significantly longer relaxation times than adenine-thymine sequences. These bubble dynamics impact DNA

Keywords:
DNAbase pair stretchingbubblesmolecular dynamicsrelaxation

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Understanding DNA bubble dynamics is crucial for comprehending DNA physicochemical properties and biological functions.
  • Large bubbles can influence DNA helix opening and overall molecular behavior.

Purpose of the Study:

  • To investigate the relaxation dynamics of large bubbles in homopolymer DNA using simulations.
  • To determine characteristic relaxation times for adenine-thymine (AT) and guanine-cytosine (GC) sequences.

Main Methods:

  • Employed the coarse-grained Peyrard-Bishop-Dauxois model for DNA simulations.
  • Utilized microsecond timescale simulations to study bubble relaxation.
  • Analyzed energy autocorrelation functions and fitted relaxation processes for various bubble shapes and sizes.

Main Results:

  • Characteristic relaxation times increase with bubble amplitude and width.
  • Relaxation times in GC sequences are approximately two orders of magnitude longer than in AT sequences.
  • Large bubbles impact DNA dynamics for durations ranging from 0.5 to 500 ns.

Conclusions:

  • Large DNA bubbles significantly influence long-time molecular dynamics.
  • The type of homopolymer (AT vs. GC) and bubble geometry critically affect relaxation timescales.
  • These findings provide insights into DNA stability and conformational changes.