A biophysicist's guide to translocation of double-stranded nucleic acids through solid-state nanopores

Area of Science:

• Nanotechnology
• Biophysics
• Analytical Chemistry

Background:

• Biosensing with solid-state nanopores (SSNPs) offers a versatile method for analyzing double-stranded DNA, RNA, and hybrids.
• This complements biological nanopores used for single-stranded nucleic acids and proteins.

Purpose of the Study:

• To systematically review how operational parameters affect double-stranded nucleic acid translocation through SSNPs.
• To dissect the physical mechanisms governing these dependencies.
• To provide a practical guide for optimizing and interpreting SSNP experiments.

Main Methods:

• Systematic review of experimental findings on SSNP translocation.
• Analysis of key performance metrics: resolution (translocation time, signal-to-noise ratio) and throughput (event frequency, unfolded fraction).
• Dissection of physical mechanisms: electrophoretic driving, hydrodynamic friction, electro-osmotic flow, and entropic effects.

Main Results:

• Operational parameters like bias voltage, pore geometry, and buffer properties significantly impact double-stranded nucleic acid translocation.
• Understanding these parameters is crucial for optimizing resolution and throughput in SSNP sensing.
• Physical models integrated with experimental data explain translocation dependencies.

Conclusions:

• SSNP biosensing is a powerful technique for double-stranded nucleic acid analysis.
• Optimizing operational parameters and understanding underlying physics are key to maximizing SSNP performance.
• The discussed concepts are transferable to other SSNP targets and nanoscale transport applications.