Translocation of structured polynucleotides through nanopores

TL;DR

This paper presents a theoretical study on how nanopores can be used to determine the basepairing patterns of structured polynucleotides by analyzing translocation dynamics and unzipping events, enabling insights into nucleic acid folding.

Contribution

It introduces a method to infer full basepairing patterns, including pseudoknots, from translocation dynamics with high spatial resolution, advancing nanopore-based nucleic acid analysis.

Findings

Translocation dynamics reveal basepairing patterns.

High spatial resolution enables detection of pseudoknots.

Nanopores can be used to study nucleic acid folding.

Abstract

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e., the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FEC's) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.