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Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
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Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models
Enrico Skoruppa1, Aderik Voorspoels1, Jocelyne Vreede2
1Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium.
Physical Review. E
|May 19, 2021
Summary
Nonlocal couplings significantly impact DNA elasticity, affecting torsional and bending properties. These off-site interactions create length-scale-dependent elasticity, influencing DNA mechanics across various scales.
Area of Science:
- Biophysics
- Molecular Biology
- Computational Biology
Background:
- DNA elasticity is crucial for its biological functions.
- Previous simulations suggested nonlocal couplings influence DNA structure.
- Understanding these couplings is key to predicting DNA behavior.
Purpose of the Study:
- To investigate the impact of nonlocal couplings on DNA's torsional and bending elasticities.
- To analyze DNA conformations using tilt, roll, and twist variables.
- To develop a theoretical framework for nonlocal DNA elasticity.
Main Methods:
- Analysis of coarse-grained (oxDNA) and all-atom molecular dynamics simulations.
- Utilizing tilt, roll, and twist variables to describe DNA conformations.
- Developing an analytical framework to estimate persistence lengths in nonlocal DNA models.
Main Results:
- Strong off-site couplings observed for tilt-tilt and twist-twist interactions.
- Weaker off-site couplings found for roll-roll interactions.
- Predicted significant length-scale-dependent effects on torsional fluctuations and modest effects on bending fluctuations.
Conclusions:
- Nonlocal interactions introduce length-scale-dependent elasticity in DNA.
- The findings align with experimental observations across different length scales.
- This study provides a theoretical basis for understanding DNA mechanics influenced by nonlocal couplings.
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