Mesoscopic models for DNA stretching under force: New results and comparison with experiments

Area of Science:

• Biophysics
• Molecular Biology
• Genetics

Background:

• Single-molecule experiments reveal DNA structural transitions under force.
• These transitions involve changes in DNA length and rigidity, influenced by sequence, salt, and temperature.
• Existing models struggle to explain the variety of observed DNA force-induced transitions.

Purpose of the Study:

• To develop a unified analytical model for DNA structural transitions under force.
• To provide a coherent picture explaining B-DNA to S-DNA and S-DNA to single-stranded DNA (ssDNA) transitions.
• To connect force-induced transitions with thermal DNA denaturation models.

Main Methods:

• Derivation of an analytical formula using a coupled discrete worm-like chain-Ising model.
• Incorporation of bending rigidity, chain discreteness, and linear/non-linear bond stretching.
• Validation against experimental data for various DNA sequences and conditions.

Main Results:

• An analytical formula accurately fits ssDNA over a nano-Newton range with three parameters.
• A novel formula for B-DNA to S-DNA transitions shows excellent agreement with transfer matrix calculations.
• The model reveals S-DNA to ssDNA transitions are more sequence-dependent than B-DNA to S-DNA transitions.

Conclusions:

• The developed model provides a coherent framework for understanding DNA force-induced transitions.
• It accurately predicts force-extension curves for different DNA types.
• The model facilitates quantitative studies on the influence of salt and base-pairing on DNA mechanics.