RT Journal Article SR Electronic T1 Supercoiling DNA locates mismatches JF bioRxiv FD Cold Spring Harbor Laboratory SP 130567 DO 10.1101/130567 A1 Dittmore, Andrew A1 Brahmachari, Sumitabha A1 Takagi, Yasuhara A1 Marko, John F. A1 Neuman, Keir C. YR 2017 UL http://biorxiv.org/content/early/2017/04/25/130567.abstract AB We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules with 0 to 16 adjacent mismatches at 1 M monovalent salt and 3.5 pN force and show that, under these conditions, a single plectoneme forms and is stably pinned at the defect. We use these measurements to estimate the energy and degree of end-loop kinking at defects. From this, we calculate the relative probability of plectoneme pinning at the mismatch under physiologically relevant conditions. Based on this estimate, we propose that DNA supercoiling could contribute to mismatch and damage sensing in vivo.