Mechanically unzipping dsDNA with built-in sequence inhomogeneities and bound proteins

We theoretically analyze the force signal from unzipping dsDNA with bound proteins and sequence inhomogeneties. Two different force traces are obtained determined by binding and sequence parameters. Sawtooth force curves, as observed in experiments, are found for short enough designed sequences and binding sites. Longer inhomogeneities lead to force plateaus which correspond to gradual, piece-meal, unzipping of the variant stretch of DNA. We generalize our model to allow comparisons to recent experiments on unzipping decorated DNAs.