Brownian ratchet for directional nanoparticle transport by repetitive stretch-relaxation of DNA

Inrok Oh, Jeongeun Song, Hye Ree Hyun, Sang Hak Lee, Jun Soo Kim

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Brownian motion subject to a periodic and asymmetric potential can be biased by external, nonequilibrium fluctuations, leading to directional movement of Brownian particles. Sequence-dependent flexibility variation along double-stranded DNA has been proposed as a tool to develop periodic and asymmetric potentials for DNA binding of cationic nanoparticles with sizes below tens of nanometers. Here, we propose that repetitive stretching and relaxation of a long, double-stranded DNA molecule with periodic flexibility gradient can induce nonequilibrium fluctuations that tune the amplitude of asymmetric potentials for DNA-nanoparticle binding to result in directional transport of nanometer-sized particles along DNA. Realization of the proposed Brownian ratchet was proven by Brownian dynamics simulations of coarse-grained models of a single, long DNA molecule with flexibility variation and a cationic nanoparticle.

Original languageEnglish
Article number054117
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume106
Issue number5
DOIs
StatePublished - Nov 2022

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© 2022 American Physical Society.

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