Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule

TL;DR

This study combines theory and simulations to analyze thermal fluctuations during RNA translocation through a nanopore, highlighting limitations in structural resolution and proposing methods to improve it.

Contribution

It provides a detailed analysis of thermal fluctuation spectra in RNA translocation, revealing resolution limits and suggesting experimental improvements.

Findings

Thermal fluctuations limit single-nucleotide resolution.

Frequency spectrum analysis characterizes these fluctuations.

Proposed methods could enhance structural resolution.

Abstract

Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which the elements of the secondary structure can be determined is limited by thermal fluctuations. We present a detailed study of these thermal fluctuations, including the frequency spectrum, and show that these rule out single-nucleotide resolution under the experimental conditions which we simulated. Two possible ways to improve this resolution are strong stretching of the RNA with a back-pulling voltage across the membrane, and stiffening of the translocated part of the RNA by biochemical means.