Next Generation Plasmon Coupling Nanosensors

Trustees Of Boston University, Boston

Investigators

Abstract

Ribonucleic acid (RNA) molecules have diverse functions in controlling gene expression and controlling cellular behavior. RNA is also used by some viruses to store genetic information. These diverse and important functions motivate the development of sensors that allow for a sensitive detection and identification of RNA molecules. This project will develop RNA sensors for two specific classes of RNA molecules: i.) microRNA (miRNA), a regulatory class of RNA that has potential as biomarkers for diseases such as cancer, and ii.) viral RNA to enable a rapid detection of RNA viruses, such as the corona virus (Covid-19). The proposed sensor platform contains a DNA strand connected at its ends to two metal nanoparticles whose optical signal depend on their separation. The DNA sensor strand is designed to change its structure when it binds to a specific RNA target. This structural modification changes the separation between the nanoparticle probes and alters their signal, which is sensitively detected even for small nanoparticles via interference of the scattered signal with a reference light beam. The sensor will be designed to detect miRNA directly, but for viral RNA the coupled nanoparticle sensor will be combined with an enzymatic signal amplification step to obtain a sensitive and rapidly reconfigurable detection platform. The research will be integrated into education and outreach activities that include development of course work to support the research, organization of a summer workshop on the fundamentals of plasmonics and nanoscience for inner city high school students in the Boston area and their teachers that is designed to excite them about a career in science and technology, and development of an Instagram channel that will provide an excellent platform for educating a lay audience about plasmonic nanosensors. The project will combine molecular beacon like DNA structures whose ends are functionalized with noble metal nanoparticle (NP) probes with two-color interferometric scattering microscopy (iSCAT) detection to generate a plasmon coupling based sensor for two important classes of RNA: i.) regulatory miRNA and ii.) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Target RNA binding to the sensor induces a conformational change from a “closed” to an “open” conformation and alters the plasmon coupling between the NP labels bound to the DNA strand. Two-color iSCAT microscopy will be applied to enhance the sensitivity for detecting changes in the interferometric scattering signal associated with the opening of the sensor upon binding to its target. The DNA recognition element of the sensor will be designed to bind to miRNA directly, while for the viral RNA the plasmonic transducer will be combined with CRISPR-CAS13 detection and subsequent sample amplification to obtain a sensitive and reconfigurable viral RNA detection platform. Instead of directly binding to viral RNA, the molecular beacon will recognize RNA fragments generated through CAS13 trans-cleavage of a substrate. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.