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Dynamics of force-induced DNA slippage
Richard A Neher1, Ulrich Gerland
1Department of Physics and CENS, LMU München, Theresienstrasse 37, 80333 München, Germany. Richard.Neher@physik.lmu.de
Physical Review Letters
|December 17, 2004
Summary
We investigated DNA base pairing dynamics in repetitive sequences, revealing distinct behaviors like reptation and strand separation under shear force. These findings suggest DNA sequence can program its viscoelastic properties.
Area of Science:
- Biophysics
- Molecular Biology
- Theoretical Chemistry
Background:
- DNA's repetitive sequences can exhibit complex dynamics, including strand slippage.
- Bulge loops are critical intermediates in DNA replication and repair, influencing DNA stability.
Purpose of the Study:
- To investigate the dynamics of DNA base pairing in repetitive sequences under shear force.
- To model the behavior of bulge loops (creation, annihilation, movement) during DNA strand slippage.
- To predict the viscoelastic properties of periodic DNA sequences.
Main Methods:
- Development of an explicit theoretical model for DNA base pairing dynamics.
- Analysis of DNA behavior as a function of applied shear force (f).
- Characterization of dynamics including reptation, drift-diffusion, and strand separation.
Main Results:
- Identified distinct dynamical regimes: reptation-like dynamics at a critical force (f=f(c)) with rupture time scaling as N^3.
- Observed drift-diffusion dynamics in an intermediate force range (f(c)
- Discovered a dynamical transition to strand separation (unraveling) at a critical force (f=f(*)).
Conclusions:
- DNA with repetitive sequences exhibits rich, force-dependent dynamics.
- The study predicts a viscoelastic behavior for periodic DNA.
- These viscoelastic properties, including time and force scales, can be programmed by the DNA sequence itself.