DNA Detection with Nanopores

Measurement of trapped single molecules of DNA


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An application of artificial lipid bilayers that has received major recent interest is nanopore DNA sequencing, where single stranded DNA is threaded through a nm-scale pore protein while the current through the protein is measured. Fluctuations of this current resulting from the identity of the bases on the DNA strand contained within the pore, potentially allow the sequence identification. One pore protein explored for this technology has been a-hemolysin. To study a-hemolysin's potential DNA sequencing resolution, we immobilized DNA molecules of known sequence within the pore and systematically changed single bases at different locations along the strand, finding that the measured current was sensitive to the base identity at a number of positions along the DNA strand.



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In our system, micron-size beads acquire negative charge only when the NA sequence of interest is present. These negatively charged beads are electrophoretically driven to the capillary pore and obstruct it, which is easily measurable electrically.


Detection of specific DNA or RNA sequences is highly desired in a range of diverse applications such as genetic disease screening, food safety pathogen identification, and more. For many of these applications, only a 'yes or no' answer regarding the presence of a particular DNA/RNA sequence is needed. The majority of conventional sequence-specific DNA or RNA detection platforms rely on chemical processing or expensive instrumentation to detect nucleic acid hybridization. Detection of individual DNA molecules traveling through a nanopore involves precise electronic measurement of picoampere-level currents at a high bandwidth. We have developed a sequence specific nucleic acid detection system based on a microscale bead obstructing a pore in borosilicate glass . The chemistry of the system was designed such that when the target nucleic acid is present, the bead will block the pore, creating a large, easily measured change in electrical signal. This novel approach is potentially cost effective, requires no chemical labeling, and outputs a simple binary result that is valuable in numerous applications.


References
  1. “Sequence-specific Nucleic Acid Detection from Binary Pore Conductance Measurement.” Esfandiari, L., Monbouquette, H.G., Schmidt, J.J. Journal of the American Chemical Society, 134 (38) DOI: 10.1021/ja3059205. (2012)
  2. "Discrimination of Single Base Substitutions in a DNA Strand Immobilized in a Biological Nanopore." Purnell, R.F., Schmidt, J. ACS Nano, 3 (9), 2533-2538. (2009)
  3. "Nucleotide identification and orientation discrimination of DNA homopolymers immobilized in a protein nanopores." Purnell, R.F., Mehta, K.K., Schmidt, J.J. Nano Letters, 8 (9), 3029-3034. (2008)