The detection and quantification of short nucleic acid sequences has many potential applications in studying biological processes, monitoring disease initiation and progression, and evaluating environmental systems.

Nucleic acids consist of chains or sequences of bases stretching from just a few to millions of elements long. The exact order in which these bases are found, even over short distances, is strongly tied to their functions, and therefore can be used as direct indicators of what is going on inside cells and tissue.

Biomedical engineers at the Wake Forest University School of Medicine (Winston-Salem, NC, USA) and their colleagues used nanotechnology to determine whether a specific target nucleic acid sequence exists within a mixture, and to quantify it if it does through a simple electronic signature. The team first demonstrated that the technology could effectively identify a specific sequence among a background of competing nucleic acids, and then applied their technique to one particular microRNA (mi-R155) known to indicate lung cancer in humans. They showed that the approach could resolve the minute amount of microRNAs that can be found in patient.

Complementary oligonucleotides were hybridized by incubating the samples at a 1:1 molar ratio in pure deionized water at 95 °C for 10 minutes and gradually cooling to room temperature to generate duplex material (dsBio34 or 23 bp heteroduplex) at a final concentration of 8 μM, as confirmed by spectrophotometry. Hybridization was confirmed by gel electrophoresis and Gel images were captured using a Gel Doc system (Bio-Rad Laboratories; Hercules, CA. USA). Silicon chips (4.4 mm) containing 25 nm thick, free-standing silicon nitride membranes were obtained commercially (Norcada, Inc.; Edmonton, AB, Canada) . In each membrane, an individual nanopore (diameter 7.5−9.0 nm) was fabricated using an Orion Plus scanning helium ion microscope (Carl Zeiss; Jena, Germany).

The scientist’s assay based on the solid-state nanopore platform identified specific sequences in solution. They demonstrated that hybridization of a target nucleic acid with a synthetic probe molecule enables discrimination between duplex and single-stranded molecules with high efficacy. The approach required limited preparation of samples and yielded an unambiguous translocation event rate enhancement that can be used to determine the presence and abundance of a single sequence within a background of nontarget oligonucleotides.

Adam R. Hall, PhD, assistant professor of biomedical engineering lead author of the study, said, “We envision this as a potential first-line, noninvasive diagnostic to detect anything from cancer to the Ebola virus. Although we are certainly at the early stages of the technology, eventually we could perform the test using a few drops of blood from a simple finger prick. If the sequence you are looking for is there, it forms a double helix with a probe we provide and you see a clear signal. If the sequence isn't there, then there isn't any signal. By simply counting the number of signals, you can determine how much of the target is around.” The study was published on January 29, 2016, in the journal Nano Letters.

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