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

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

2008-01-25

arxiv.org/abs/0801.3947v2

J. Phys.: Condens. Matter 21, 375105 (2009)

Physics

Condensed Matter

Statistical Mechanics

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

Scientific paper

10.1088/0953-8984/21/37/375105

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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