Theoretical micromechanics of DNA and DNA-protein complexes

We theoretically analyze three problems in single-molecule micromechanics. These are: (1) the elastic response of torsionally constrained DNA, (2) the effect of applied torque on the stability of binding of proteins to DNA and (3) the force response of DNA with designed sequence inhomogeneities or bound proteins undergoing mechanical strand separation. Statistical mechanics and polymer physics are the main tools in our study. We find that the high-force elasticity of topologically-constrained DNA can be explained in terms of transitions between novel DNA structural states. We find static torques of a few kBT are sufficient to disrupt the binding of proteins to DNA. Dynamical torque generation through transient twist distortions in the DNA are found to propagate up to 100 bp with sufficient strength to dislodge bound proteins. Unzipping DNA with sequence variations or bound proteins is found to generate distinct force signals with large amplitude. We discuss the biological relevance of our work and point to future experiments that may be able to test our predictions.