Interfacing solid-state nanopores with gel media to slow DNA translocations

Area of Science:

• Biophysics
• Materials Science
• Nanotechnology

Background:

• Nanopore sequencing faces challenges with rapid biomolecule translocation.
• Existing methods to slow translocation often compromise signal quality or capture efficiency.

Purpose of the Study:

• To investigate slowing DNA translocation through solid-state nanopores using gel media.
• To explore two distinct DNA reptation regimes within gel pores.
• To overcome limitations of previous methods for controlling translocation speed.

Main Methods:

• Interfacing the trans side of solid-state nanopores with gel media (agarose and polyacrylamide).
• Analyzing DNA translocation dynamics for different DNA fragment lengths (5 kbp and 100 bp dsDNA).
• Characterizing translocation time distributions under varying gel pore conditions and intermolecular crowding.

Main Results:

• Agarose gels showed a wide distribution of translocation times for 5 kbp dsDNA.
• Polyacrylamide gels, under specific conditions, narrowed translocation time distributions for 100 bp dsDNA.
• Controlled DNA movement regimes significantly slowed translocation without degrading signal-to-noise ratio or capture rate.

Conclusions:

• Controlling DNA reptation regimes within gel media is a viable strategy to manage rapid nanopore translocation.
• This approach offers a solution to a major hurdle in nanopore-based analysis.
• The method preserves signal quality and capture efficiency, enhancing nanopore applications.