Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule
arXiv:0801.3947 · doi:10.1088/0953-8984/21/37/375105
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.
arXiv commentSignificantly expanded compared to previous version, 13 pages, 4 figures, to appear in J. Phys.: Condens. Matter
References in corpus (11)
- Fast DNA translocation through a solid-state nanopore
- Unzipping Kinetics of Double-Stranded DNA in a Nanopore
- 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
- Translocation of structured polynucleotides through nanopores
- Passage Times for Polymer Translocation Pulled through a Narrow Pore
- Polymer Translocation out of Planar Confinements
- Coupled dynamics of RNA folding and nanopore translocation
- Reaching large lengths and long times in polymer dynamics simulations
- Effect of Inhomogeneity in Translocation of Polymers through Nanopores