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Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device.

Swarnadeep Seth1, Arthur Rand2, Walter Reisner3

  • 1Department of Physics, University of Central Florida, Orlando, FL, 32816-2385, USA.

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Brownian dynamics simulations identify key parameters for distinguishing protein tags on DNA translocating through nanopores. This research enhances dual-nanopore setup efficiency and accuracy for analyzing DNA constructs.

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Area of Science:

  • Computational Biophysics
  • Nanotechnology
  • Molecular Dynamics

Background:

  • Protein tags on DNA constructs are crucial for various biotechnological applications.
  • Experimental dual-nanopore setups offer a promising method for analyzing these constructs.
  • Understanding the physical parameters governing tag behavior in nanopores is essential for optimizing experimental outcomes.

Purpose of the Study:

  • To identify key parameters controlling experimentally measurable characteristics of protein tags on dsDNA.
  • To validate Brownian dynamics simulation schemes for analyzing DNA translocation through nanopores.
  • To enhance the efficiency and accuracy of experimental dual-nanopore setups.

Main Methods:

  • Brownian dynamics simulations were employed to model dsDNA translocation through a double nanopore setup.
  • In silico validation reproduced experimental dwell time distributions of oligonucleotide flap markers.
  • Analysis focused on the effects of electric fields and sub-nanometer dynamics, incorporating nonequilibrium tension propagation theory.

Main Results:

  • Simulation results explained the asymmetric dwell time distributions observed experimentally.
  • A power-law dependence of average dwell time on pore position revealed effective charges and masses of protein tags.
  • Calculated Péclet numbers showed close agreement with experimental data, validating the simulation model.

Conclusions:

  • Brownian dynamics simulations are a powerful tool for discriminating protein tags based on their physical characteristics.
  • The study provides insights into optimizing dual-nanopore setups for increased efficiency and accuracy.
  • Simulation strategies can differentiate various neutral and charged tags on dsDNA constructs.