Ulrich Gerland et al 2004 Phys. Biol. 1 19 doi:10.1088/1478-3967/1/1/002
Translocation of structured polynucleotides through nanopores
Ulrich Gerland1,3, Ralf Bundschuh2 and Terence Hwa1
Show affiliationsWe 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.
- PACS
- Subjects
- Dates
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Issue 1 (March 2004)
Received 26 November 2003, accepted for publication 13 January 2004
Published 12 February 2004
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Translocation of structured polynucleotides through nanopores
Ulrich Gerland et al 2004 Phys. Biol. 1 19
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