In silico construction of a flexibility-based DNA Brownian ratchet for directional nanoparticle delivery

Suehyun Park, Jeongeun Song, Jun Soo Kim

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Brownian particles confined in a system with periodic and asymmetric potential can be transported in a specific direction along the potential by repetitively switching the potential on and off. Here, we propose a DNA-based Brownian ratchet for directional transport of positively charged nanoparticles in which nanoparticle delivery follows the path dictated by a single, long, double-stranded DNA. We performed Brownian dynamics simulations to prove its realization using coarse-grained models. A periodic and asymmetric potential for nanoparticle binding is constructed along a single, long, double-stranded DNA molecule by a novel strategy that uses variation in sequence-dependent DNA flexibility. Directional and processive motion of nanoparticles is achieved by changing salt concentration repetitively over several cycles to switch the asymmetric potential on and off. This work suggests that double-stranded DNA molecules with elaborately designed flexibility variation can be used as a molecule-scale guide for spatial and dynamic control of nanoparticles for future applications.

Original languageEnglish
Article numbereaav4943
JournalScience Advances
Issue number4
StatePublished - 2019

Bibliographical note

Funding Information:
This research was supported by the National Research Foundation of Korea (NRF) under grant nos. NRF-2015R1D1A1A01059005 and NRF-2018R1D1A1B07043246.

Publisher Copyright:
© 2019 The Authors, Some Rights Reserved.


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