RT Journal Article
SR Electronic
T1 Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2019.12.20.885533
DO 10.1101/2019.12.20.885533
A1 Parth Rakesh Desai
A1 Sumitabha Brahmachari
A1 John F. Marko
A1 Siddhartha Das
A1 Keir C. Neuman
YR 2020
UL http://biorxiv.org/content/early/2020/10/04/2019.12.20.885533.abstract
AB Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (> 2 pN) and high salt concentration (> 0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.Competing Interest StatementThe authors have declared no competing interest.