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bioRxiv · 10.1101/2021.06.21.449299

Stochastic Resonance Behavior of DNA Translocation with an Oscillatory Electric Field

Muthukumar, M.·Jou, I. A.·Duff, R. A.
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Abstract

Stochastic resonance (SR) describes the synchronization between noise of a system and an applied oscillating field to achieve an optimized response signal. In this work, we use simulations to investigate the phenomenon of SR of a single stranded DNA driven through a nanopore when an oscillating electric field is added. The system is comprised of a MspA protein nanopore embedded in a membrane and different lengths of DNA is driven from one end of the pore to the other via a constant potential difference. We superimposed an oscillating electric field on top of the existing electric field. The source of noise is due to thermal fluctuations, since the system is immersed in solution at room temperature. Here, the signal optimization we seek is the increase in translocation time of DNA through the protein nanopore. Normally, translocation time scales linearly with DNA length and inversely with driving force in a drift dominated regime. We found a non-monotonic dependence of the mean translocation time with the frequency of the oscillating field. This non-monotonic behavior of the translocation time is observed for all lengths of DNA, but SR occurs only for longer DNA. Furthermore, we also see evidence of DNA extension being influenced by the oscillating field while moving through the nanopore.

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Muthukumar, M., Jou, I. A., Duff, R. A.. 2021-06-22. Stochastic Resonance Behavior of DNA Translocation with an Oscillatory Electric Field. https://doi.org/10.1101/2021.06.21.449299

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