The End Restraint Method for Mechanically Perturbing Nucleic Acids In Silico

Area of Science:

• Biophysics
• Computational Biology
• Molecular Biology

Background:

• The genome is a mechanically dynamic system where DNA torsion and tension regulate gene expression.
• Molecular machines like topoisomerases introduce mechanical stress during DNA repair and replication.
• Current imaging techniques lack the resolution to study DNA mechanics at the single base pair level.

Purpose of the Study:

• To present a flexible and extensible umbrella-sampling protocol for in silico twisting and stretching of nucleic acids.
• To provide a method for analyzing structural motif formation in DNA under mechanical stress.
• To enable base pair resolution interrogation of experimental data from optical and magnetic tweezers.

Main Methods:

• Developed a straightforward umbrella-sampling protocol using the Amber simulation package.
• Defined fixed translations of specified atoms between umbrella-sampling steps, avoiding force or pseudoatom definitions.
• Included guidance on system setup, force field and solvation model selection, and equilibration.
• Presented analysis techniques for characterizing structural motif formation.

Main Results:

• The protocol allows for in silico twisting and stretching of nucleic acids.
• Structural motif formation under mechanical stress can be characterized.
• The method provides a metric (fractional end-to-end displacement) for comparison with experimental data without force estimation.

Conclusions:

• The developed protocol offers an accessible solution for studying nucleic acid mechanics at base pair resolution.
• This method can be valuable for interpreting optical and magnetic tweezers data.
• The principles are applicable to other simulation packages like GROMACS.