This project is funded by the Chemical Measurement & Imaging program of the Chemistry Division of the National Science Foundation. Professor Thomas Hermann of the University of California, San Diego, develops nano-sized, self-assembling sensors for biologically-active molecules (analytes) including toxins in the environment and metabolites in organisms. The sensors are made from biocompatible building blocks which self-assemble upon analyte detection by exploiting recognition principles encoded in natural nucleic acids. The design approach allows the construction of sensors that detect a variety of different analytes simultaneously. A signal is generated only if a threshold concentration is reached for all analytes at the same time. The sensors constitute a novel application of biological materials in nanotechnology which is a rapidly emerging field of research for medical devices and environmental monitoring. The broader impact of the work is related to the development of novel RNA-based nanosensors whose function relies on the self-assembly from short oligonucleotides, triggered by analyte recognition. Students involved in the research gain broad and interdisciplinary training in areas of materials and device development for biological and medical applications.
This research develops sensors for biologically-active analytes based on modular RNA nanostructures that contain several copies of an aptamer which self-assemble to a signaling configuration in a cooperative response to ligand binding. By coupling sensor RNA assembly with multivalent cooperative ligand binding, sensing devices are created with nonlinear dose response over a wide dynamic range. The design concept for the sensors is based on previously developed self-assembling RNA nanostructures, including double-stranded RNAs in the shape of a square or triangle. The RNA nanosensors capitalize on two unique properties of RNA nanostructures: their modular design, which facilitates the rapid iterative optimization of sensor constructs for a variety of ligands, and their self-assembly from short oligonucleotides in an all-or-nothing process. The nanostructures design provides the basis for nonlinear cooperativity of ligand binding at multiple recognition sites. Modular design facilitates the design of a wide variety of RNA nanosensors with up to 4 ligand recognition sites within a single construct, allowing the design of AND-gated as well as OR-gated sensors. The sensor signaling is dependent on either the simultaneous or exclusive presence of two different ligands. Self-assembly of the complete signaling-competent RNA nanosensor depends on ligand binding to all aptamer units and gives rise to cooperative recognition behavior of multiple binding sites. The novel RNA nanosensors are capable of nonlinear dose response over a wide dynamic range. The research is performed by graduate and undergraduate students who are trained in a diverse array of technical skills including nucleic acid biochemistry, fluorescence assays, cloning, and biochemical in vitro assay development. The graduate students involved in the research gain a broad and interdisciplinary training, which renders the project ideally suited for the Chemical Biology graduate track at UCSD. Professor Hermann continue outreach efforts by recruiting members of groups underrepresented in science through self-initiated and campus-supported programs and by outreach to local high schools.
