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

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.

Significantly expanded compared to previous version, 13 pages, 4 figures, to appear in J. Phys.: Condens. Matter

References in corpus (6)

• Anomalous Dynamics of Unbiased Polymer Translocation through a Narrow Pore
• Pore-blockade Times for Field-Driven Polymer Translocation
• Effective charge and free energy of DNA inside an ion channel
• Passage Times for Polymer Translocation Pulled through a Narrow Pore
• Polymer Translocation out of Planar Confinements
• Effect of Inhomogeneity in Translocation of Polymers through Nanopores

Cited by in corpus (2)

• Rouse Modes of Self-avoiding Flexible Polymers
• Probabilistic Phase Space Trajectory Description for Anomalous Polymer Dynamics