Precise control of the size and noise of solid-state nanopores using high electric fields

Department of Physics, University of Ottawa, Ottawa, ON, Canada.
Nanotechnology (Impact Factor: 3.82). 09/2012; 23(40):405301. DOI: 10.1088/0957-4484/23/40/405301
Source: PubMed


We present a methodology for preparing silicon nitride nanopores that provides in situ control of size with sub-nanometer precision while simultaneously reducing electrical noise by up to three orders of magnitude through the cyclic application of high electric fields in an aqueous environment. Over 90% of nanopores treated with this technique display desirable noise characteristics and readily exhibit translocation of double-stranded DNA molecules. Furthermore, previously used nanopores with degraded electrical properties can be rejuvenated and used for further single-molecule experiments.

Download full-text


Available from: Vincent Tabard-Cossa, Oct 08, 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Nanopore method is an emerging technique, which extends gel-electrophoresis to the single-molecule level and allows the analysis of DNAs, RNAs and DNA-protein complexes. The strength of the technique stems from two fundamental facts: First, nanopores due to their nanoscale size can be used to uncoil biopolymers, such as DNA or RNA and slide them in a single file manner that allows scanning their properties. Consequently, the method can be used to probe short as well as extremely long biopolymers, such as genomic DNA with high efficiency. Second, electrostatic focusing of charged biopolymers into the nanopore overcomes thermally driven diffusion, thus facilitating an extremely efficient end-threading (or capture) of DNA. Thus, nanopores can be used to detect minute DNA copy numbers, circumventing costly molecular amplification such as Polymerase Chain Reaction. A critical factor, which determines the ability of nanopore to distinguish fine properties within biopolymers, such as the location of bound small-molecules, proteins, or even the nucleic acid's sequence, is the speed at which molecules are translocated through the pore. When the translocation speed is too high the electrical noise masks the desired signal, thus limiting the utility of the method. Here I will discuss new experimental results showing that modulating the surface charge inside the pore can effectively reduce the translocation speed through solid-state nanopores fabricated in thin silicon nitride membranes. I will present a simple physical model to account for these results.
    Full-text · Article · Mar 2013
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Solid-state nanopores have emerged as a versatile tool for the characterization of single biomolecules such as nucleic acids and proteins(1). However, the creation of a nanopore in a thin insulating membrane remains challenging. Fabrication methods involving specialized focused electron beam systems can produce well-defined nanopores, but yield of reliable and low-noise nanopores in commercially available membranes remains low(2,3) and size control is nontrivial(4,5). Here, the application of high electric fields to fine-tune the size of the nanopore while ensuring optimal low-noise performance is demonstrated. These short pulses of high electric field are used to produce a pristine electrical signal and allow for enlarging of nanopores with subnanometer precision upon prolonged exposure. This method is performed in situ in an aqueous environment using standard laboratory equipment, improving the yield and reproducibility of solid-state nanopore fabrication.
    Full-text · Article · Oct 2013 · Journal of Visualized Experiments
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Nanopores can be used to detect and analyse biomolecules. However, controlling the translocation speed of molecules through a pore is difficult, which limits the wider application of these sensors. Here, we show that low-power visible light can be used to control surface charge in solid-state nanopores and can influence the translocation dynamics of DNA and proteins. We find that laser light precisely focused at a nanopore can induce reversible negative surface charge densities as high as 1 C m(-2), and that the effect is tunable on submillisecond timescales by adjusting the photon density. By modulating the surface charge, we can control the amount of electroosmotic flow through the nanopore, which affects the speed of translocating biomolecules. In particular, a few milliwatts of green light can reduce the translocation speed of double-stranded DNA by more than an order of magnitude and the translocation speed of small globular proteins such as ubiquitin by more than two orders of magnitude. The laser light can also be used to unclog blocked pores. Finally, we discuss a mechanism to account for the observed optoelectronic phenomenon.
    Full-text · Article · Nov 2013 · Nature Nanotechnology
Show more