Rapid, Binary-Mode Nucleic Acid Sequence Detection

<p>Technical abstract: Detection of specific nucleic acid (NA) sequences is crucial to infectious disease diagnostics, genetic screening for hereditary diseases, personalized medicine, criminology, paternity disputes, and animal and plant breeding, among many other applications. Although polymerase chain reaction (PCR) technology, coupled with oligonucleotide array chips, has enabled specific identification of multiple sequences present in a sample at very low copy number, this method requires added labels and reagents to detect the target NA. These labels and the hardware (e.g., optics) required to sense them significantly increase the analysis time, cost, and footprint of devices for detecting specific NA sequences. As an alternative to current approaches, this project will develop novel nanopores capable of detecting pathogenic nucleic acids with single molecule resolution. These nanopores will be fabricated in silicon and will be engineered to contain beads labeled with complementary NA sequences. Binding of target oligonucleotides to the beads will result in the change of electrophoretic properties and will lead to nanopores becoming occluded by the beads. This event will be detected electrochemically for binary yes/no readout of the target NA. Non-technical abstract: There is a need to develop simple and inexpensive methods for detecting pathogens for medical or food safety applications. This proposal will develop a new approach based on small pores containing beads. The beads will react to pathogen biomarkers, will clog the pores and will result in the change of electrical current. This method is envisioned to have improved sensitivity and be simpler than the current approaches.</p>