Interfacing solid-state nanopores with gel media to slow DNA translocations.
We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the regime of DNA movement exiting a nanopore interfaced with a gel medium, it is possible to address the issue of rapid biomolecule translocations through nanopores-presently one of the largest hurdles facing nanopore-based analysis-without affecting the signal quality or capture efficiency.
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
Matthew
M
Waugh
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
Autumn
A
Carlsen
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
David
D
Sean
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
Gary W
GW
Slater
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
Kyle
K
Briggs
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
Harold
H
Kwok
Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
Vincent
V
Tabard-Cossa
D000180:Acrylic Resins / Q000737:chemistry*; D004247:DNA / Q000302:isolation & purification*; D058608:Nanopores; D036103:Nanotechnology / Q000379:methods*; D012685:Sepharose / Q000737:chemistry*
D000180:Acrylic Resins; C016680:polyacrylamide gels; D004247:DNA; D012685:Sepharose
Agarose; Bionanotechnology; Next-generation sequencing; Polyacrylamide; Solid-state nanopore