title: Translocation of structured polynucleotides through nanopores.
abstract: We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e. the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FECs) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that, with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.
authors.affiliation: Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA. Ulrich.Gerland@physik.uni-muenchen.de
authors.forename: Ulrich
authors.initials: U
authors.lastname: Gerland
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
authors.forename: Terence
authors.initials: T
authors.lastname: Hwa
mesh_terms: D000818:Animals; D001483:Base Sequence; D001693:Biological Transport, Active; D055592:Biophysical Phenomena; D001703:Biophysics; D007700:Kinetics; D008954:Models, Biological; D008969:Molecular Sequence Data; D049329:Nanostructures; D009690:Nucleic Acid Conformation; D011119:Polynucleotides / Q000737:chemistry / Q000378:metabolism*; D016053:RNA, Protozoan / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016808:Tetrahymena thermophila / Q000235:genetics; D013816:Thermodynamics
chemical_list: D011119:Polynucleotides; D016053:RNA, Protozoan