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

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.