Programmable Multi-Target Detection Using an Aptamer-Integrated Nanopore

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DESCRIPTION (provided by applicant): This proposal addresses an interdisciplinary strategy that integrates the use of highly sensitive, highly specific aptamers with nanopore-based single molecule technology. The long term goal is to develop aptamer-integrated nanopore probes for biomedical detections. Aptamers are engineered DNA/RNA that can specifically recognize broad species of proteins with high affinities. Upon binding, these powerful molecules can inhibit pathogen protein, catalyze chemical reactions, control gene expression, and regulate cellular functions. Therefore aptamers can potentially be applied as tools for exploring biological systems. Motivated by such small, but sophisticated molecules, we would like to integrate aptamer technology with our nanopore probe to construct a new generation of single molecule detector that would aid greatly in diverse disease-related detections. Nanopore technology can "visually" capture the dynamic binding of a single molecule to a ligand in a nanometer-scaled pore through the discrete changes in conductance upon binding. We propose the combined use of nanopore with laboratory nanofabrication, bio-friendly surface engineering, and molecular engineering to accomplish the following specific aims: 1. Understand and manipulate various properties of nanopores for improvement of single molecule detection; 2. Establish a fundamental model for single molecule detection with aptamer-equipped nanopores. Broad target species with varied aptamer types (DNA/RNA) will be tested, including Immunoglobulin E, HIV-1 reverse transcriptase, and large influenza A viral particle; 3. Establishing an advanced model that employs engineered Transfer Aptamer (t-Aptamer) to mediate detection. The t-Aptamer, which composes an aptamer and a universal carrier, acts as a "translator" to encode target information into the frequency of hybridization between the carrier and the immobilized receptor in the nanopore. Such a t-Aptamer-mediated detection is robust, programmable, and will ultimately lead to a universal nanopore that can discriminate different targets and perform simultaneous multi-target detection. The success of this research will greatly expand the capability of nanopores as the new generation of detection technology for biomedical analysis and high-throughput screening. Fashioning such tools is significant in nanomedicine for the quantitative characterization and precise control of molecular scale components (or nanomachinery) of living cells.