title: Amplitude and frequency spectra 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 for determining 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 strongly stretching the RNA with a back-pulling voltage across the membrane, and stiffening the translocated part of the RNA by biochemical means.
authors.affiliation: Institute for Theoretical Physics, Universiteit Utrecht, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands.
authors.forename: Henk
authors.initials: H
authors.lastname: Vocks
authors.forename: Debabrata
authors.initials: D
authors.lastname: Panja
authors.forename: Gerard T
authors.initials: GT
authors.lastname: Barkema