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Forces affecting double-stranded DNA translocation through synthetic nanopores.

Lei Chen¹, A T Conlisk

¹Department of Mechanical Engineering, The Ohio State University, 201 W. 19th Avenue, Columbus, OH 43210, USA. chen.990@osu.edu

Biomedical Microdevices

|February 1, 2011

Summary

This study analyzes forces opposing DNA translocation through nanopores. Viscous drag inside the nanopore is found to be significant, comparable to the electrical driving force, impacting DNA sequencing applications.

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Area of Science:

Nanotechnology
Biophysics
Molecular Biology

Background:

Nanopores are emerging as detectors for biomolecules, with nanopore-based sequencing offering rapid DNA analysis.
Understanding forces during DNA translocation is crucial for optimizing nanopore sequencing technology.

Purpose of the Study:

To analyze and quantify forces opposing electrical driving forces during DNA translocation through nanopores.
To determine the relative contributions of different forces, including entropic and viscous forces, to DNA translocation dynamics.

Main Methods:

Calculated magnitudes of entropic forces (DNA uncoiling/recoiling) and viscous drag forces (external and internal to the nanopore).
Employed a hydrodynamic model based on lubrication approximation to evaluate viscous drag on linear DNA within the nanopore.
Validated the hydrodynamic model against experimental data for DNA tethering forces.

Main Results:

Entropic forces and external viscous drag are generally minor compared to the electrical driving force.
Internal viscous drag on linear DNA within the nanopore is a significant opposing force, on the same order as the electrical driving force.
The hydrodynamic model accurately predicts viscous drag, validated by experimental tethering force data.

Conclusions:

Internal viscous drag is a critical factor influencing DNA translocation speed and accuracy in nanopore sequencing.
Accurate modeling of hydrodynamic forces is essential for advancing nanopore-based DNA analysis and sequencing technologies.
Further research can leverage these findings to improve nanopore device design and DNA translocation control.