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Measuring internal forces in single-stranded DNA: Applications to a DNA force clamp
Megan C. Engel, Flavio Romano, Ard A. Louis and Jonathan P.K. Doye
J. Chem. Theor. Comput. 16, 7764–7775 (2020)
Abstract
We present a new method for calculating internal forces in DNA structures using thecoarse-grained oxDNA model. The instantaneous forces on individual nucleotides areexplored and related to model potentials, and using our framework, internal forces arecalculated for two simple DNA systems and for a recently-published nanoscopic forceclamp. Our results highlight some pitfalls associated with conventional methods forestimating internal forces, which are based on elastic polymer models, and emphasisethe importance of carefully considering secondary structure and ionic conditions whenmodelling the elastic behaviour of single-stranded DNA.The full paper is available from J. Chem. Theor. Comput. and arXiv.org.