The Organic and Macromolecular Chemistry Program in the Chemistry Division at the National Science Foundation supports Professor Kazunori Koide of the University of Pittsburgh who proposes to chemically synthesize small molecule-based cell-permeable RNA sensors that fluoresce when bound to specific RNA. Chemical synthesis is concise and amenable to tuning sensitivity and specificity. Previously, it was thought that a library of RNA chemosensor candidates must be synthesized and screened against specific RNA. However, it is exceedingly difficult to rationally design specific RNA ligands and strenuous to chemically synthesize a library of small molecules. The significance of this proposed research is that one does not need to create RNA ligands to develop RNA chemosensors; rather, the proposed research will take advantage of well-established in vitro RNA selection as a means to engineer specific RNA-small molecule interaction with some help from synthetic organic chemistry. This reversed paradigm for RNA sensor development is highly innovative and will have significant impact on how others will design experiments to develop other RNA sensors. The biology of RNA in live cells is poorly understood due to the lack of probes. This research focuses on developing chemosensors that fluoresce only when bound to specific RNA. The approach is based on the combination of rational design and library-based discovery. The outcome of this study will have broad impact on bioimaging and the biology of DNA transcription.
Research by Professor Koide could significantly impact chemistry, biology, the pharmaceutical industry, and the general public. This project will train students and postdoctoral fellows to become scientists who will be able to bridge the gap between chemistry and biology. Leaders in pharmaceutical and biotechnology companies require knowledge in both fields to invent drugs or diagnostic tools, for which this project will produce well-trained scientists. Students trained by this research project will understand synthetic, analytical, and spectroscopic chemistry as well as biology, and will be able to be engaged in multidisciplinary efforts that are at the forefront of science.
Analysis of trace metals routinely uses inductively coupled-plasma mass spectrometry (ICP-MS) or inductively coupled-plasma optical emission spectroscopy (ICP-OES). These methods are sensitive and robust, spanning several orders of magnitude in their dynamic range. Nonetheless, the everyday use of these techniques is hindered by expensive instrumentation, low throughput, and lack of availability at the sites in which samples are produced. Optical methods based on catalysis have been developed to quantify trace metals; however, none of these has been implemented in real-world settings because of the inherent time-dependence for catalysis and narrow linear dynamic ranges for absorption or emission signals. Palladium is one of the scarcest metals on earth but is the most frequently used transition metal in synthetic organic chemistry, the latter of which creates safety concerns in the pharmaceutical industry. We report the development of a rapid, colorimetric method for palladium quantification, employing the cleavage of an allylic ether from the chemodosimeter to release a deep-purple dye, shifting the color of the solution from yellow to purple. Uniquely, the method exhibited an autonomous, reversible stalling under the reaction conditions, allowing for the reaction to stop after a controlled amount of time. Fine-tuning reaction components allowed the reaction to continue for longer periods of time. This new method, through stop-and-go cycles, could quantify palladium concentrations ranging over 5 orders of magnitude, rivaling ICP-MS and ICP-OES. The deallylation of the chemodosimeter to form the purple dye was tested successfully in residual palladium quantification in pharmaceuticals, ores, and organic polymers.
