Computational modelling and single-molecule rotor bead study of DNA plectoneme pinning in the presence of base-pair mismatches

In vivo, mismatched or damaged bases introduce defects into the DNA, these must be efficiently repaired. A common motif in defect recognition is the imposition of a sharp bend in the DNA. DNA supercoiling could potentially facilitate defect recognition by pinning defects at the ends of the plectonemes where DNA is sharply bent. We use MD simulations and single-molecule rotor bead assay to study the effect of mismatches on DNA supercoiling. Magnetic tweezers studies have shown that in 1M NaCl a single mismatch can localize a plectoneme at a mismatch. In physiological salt condition theoretical studies predict plectoneme localization becomes probabilistic. However, approaches were limited to positively supercoiled DNA. We developed a mismatch model in the OxDNA framework and study the effect of mismatches on positively and negatively supercoiled DNA. The simulations reproduce the experimental and theoretical results for positive supercoiling. The probability of plectoneme pinning is greatly enhanced by negative supercoiling. We validate the simulation predictions experimentally with a single-molecule rotor bead assay that extends previous measurements into the probabilistic localization regime for both positive and negative supercoiling in physiological salt conditions.