In vivo, mismatched or damaged bases introduce defects into the DNA, which must be efficiently repaired. A common motif in defect recognition is the imposition of a sharp bend in the DNA at the defect. DNA supercoiling could potentially facilitate defect recognition by pinning defects at the ends of plectonemes where DNA is sharply bent. We use a single-molecule rotor bead assay to study the effect of mismatches on DNA supercoiling. Magnetic tweezers studies have shown that under conditions of high salt and high force on the DNA, a single mismatch can localize a positively supercoiled plectoneme at a mismatch. Under physiological salt conditions, lower forces, and under negative supercoiling, theoretical and computational studies predict plectoneme localization becomes probabilistic. However, technical limitations prevented experimental validation of these predictions. Here, we describe a new rotor-bead magnetic-tweezers based assay to directly measure plectoneme buckling and pinning at base-pair mismatches. This assay extends previous measurements into the probabilistic pinning regime for both positive and negative supercoiling in physiological salt and force conditions.
Fineberg et al. (Sun,) studied this question.