Mechanically Unzipping Double-Stranded DNA with Built-In Sequence Inhomogeneities and Bound Proteins

Abstract

We theoretically analyze the force signal expected during unzipping of DNA with a) bound proteins and b) when the DNA is more strongly base-paired over certain regions. We consider the case of a single bound protein, multiple isolated bound proteins, bound proteins with cooperative interactions that result in collective force-induced unbinding events, and the case of a very large number of bound proteins. In addition, we also analyze the case where the unzipping proceeds through multiple, isolated DNA regions which are more strongly bound than the surrounding DNA. Our calculations are done in the fixed-extension ensemble. In both cases we find two different types of force traces which we label sawtooth profile and ramp-plateau profile.. In the former, the force extension curve has a series of sawtooth peaks superposed on the usual constant force of ∼15pN found unzipping bare DNA, while in the ramp-plateau case, the force near an unzipping constraint increases roughly linearly and then levels off and then returns to its baseline value (∼15pN) after the protein in unbound or the strongly base-paired region is disrupted allowing the unzipping fork to pass through. These shapes are correlated with the positions of bound proteins or sequence inhomogeneities. We calculate how the force-extension profile depends on the protein or sequence parameters. Our results compare well with observed in unzipping of natural-sequence DNA and DNA with bound proteins. These results point the way toward inferring sequence-related information and protein binding enthalpies from single molecule unzipping experiments.