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Effect of undulations on spontaneous braid formation.
1Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom.
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|September 17, 2013
Summary
Molecular braiding of DNA is explored, incorporating bending fluctuations. This analysis reveals that configurational entropy loss in braids increases attraction requirements for spontaneous DNA braiding, impacting molecular interactions.
Area of Science:
- Biophysics
- Molecular Biology
- Theoretical Chemistry
Background:
- Recent studies demonstrated that molecular helical structure forces can induce spontaneous DNA braiding.
- Understanding the mechanics of DNA interactions is crucial for molecular biology and nanotechnology.
Purpose of the Study:
- To extend existing DNA braiding theory by incorporating bending fluctuations.
- To recalculate the free energy of paired DNA molecules considering these undulations.
- To assess the impact of configurational entropy on spontaneous braiding.
Main Methods:
- Theoretical modeling of DNA braiding, extending previous work.
- Incorporation of bending fluctuations of molecular center lines into braiding theory.
- Recalculation and comparison of free energy with and without undulations.
Main Results:
- The loss of configurational entropy due to confinement in a braid is significant.
- This entropy loss increases the required attraction for spontaneous braiding driven by helix-dependent forces.
- The developed theory is generalizable to other helical molecules and interactions.
Conclusions:
- Bending fluctuations play a critical role in the thermodynamics of DNA braiding.
- High configurational entropy loss necessitates stronger attractive forces for spontaneous braiding.
- Further theoretical development is planned for plectonemes and braids under mechanical forces.
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