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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
Summary
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
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.
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