@article {Pyne863423, author = {Alice L. B. Pyne and Agnes Noy and Kavit Main and Victor Velasco-Berrelleza and Michael M. Piperakis and Lesley A. Mitchenall and Fiorella M. Cugliandolo and Joseph G. Beton and Clare E.M. Stevenson and Bart W. Hoogenboom and Andrew D. Bates and Anthony Maxwell and Sarah A. Harris}, title = {Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and recognition}, elocation-id = {863423}, year = {2020}, doi = {10.1101/863423}, publisher = {Cold Spring Harbor Laboratory}, abstract = {In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition.Competing Interest StatementThe authors have declared no competing interest.}, URL = {https://www.biorxiv.org/content/early/2020/05/04/863423}, eprint = {https://www.biorxiv.org/content/early/2020/05/04/863423.full.pdf}, journal = {bioRxiv} }