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Coarse grained simulation of DNA-based hairpin force sensors

Nikhil Nmbiar
Department of Chemical & Biomolecular Engineering, University of Tennessee

This page shows visualizations of Langevin Dynamics simulation of coarse grained DNA hairpin molecule

DNA is a biopolymer that is made up of a sequence of 4 kinds of nucleotides, denine (A), cytosine (C), guanine (G), or thymine (T). These nucleotides are covalently linked together and they have very specific interactions with each other. Zhang et al. introduced DNA hairpins with tunable force response depending on the nucleotides in the DNA. These force at which these hairpins unwound were depended on the nucleotide make-up of the hairpins. In my work, I modelled these DNA hairpins using a Coarse-grained oxDNA model that can perform large time scale simulations that allow the relaxation of DNA molecules as well as maintains the chemical representability of the nucleotides in the DNA molecule. The molecule was first started out in a stretched out configuration and allowed to relax to its equilibriums structure using Langevin dynamics. I investigated the energy landscape of the unwinding process of the hairpin by calculating the potential of mean force as a function of distance between the ends of the hairpin. 1

Interactive Structures

Color Legend:

  • Different colours show the different nucleotides A,G,C,T


Zhang, Yun, et al. "DNA-based digital tension probes reveal integrin forces during early cell adhesion." Nature communications 5.1 (2014): 1-10.

posted: April 2020.
updated: April 2020.