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arXiv · 0801.3947

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

Henk Vocks·Debabrata Panja·Gerard T. Barkema
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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.

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Henk Vocks, Debabrata Panja, Gerard T. Barkema. 2009-08-03. Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule. https://doi.org/10.1088/0953-8984%2F21%2F37%2F375105

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