Fluorescent Nucleosides and Oligonucleotides

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DESCRIPTION (provided by applicant): The goal of the proposed program is to design, synthesize and implement new fluorescent nucleoside analogs as probes for nucleic acids structure, dynamics and recognition. The main criteria directing the proposed work are to maintain the highest possible structural similarity to the natural nucleobases, to shift the emission to longer wavelengths, and to retain adequate emission quantum efficiency. The specific aims of this project are: (1) To design "ideal" fluorescent nucleoside analog that will possess the following characteristics: (i) A high structural similarity to the native nucleobases to faithfully mimic their size and shape, as well as hybridization and recognition properties, (ii) A red shifted absorption spectrum to minimize overlap with the absorption of the natural bases, (iii) A respectable emission quantum efficiency and a long emission wavelength (preferably in the visible range); (2) To devise concise synthetic approaches to the desired nucleobase analogs; (3) To examine the photophysical characteristics of the new nucleosides; (4) To synthesize and characterize modified DNA and RNA oligonucleotides; (5) To biophysically and photophysically characterize the modified oligonucleotides; and (6) To implement the promising emissive analogs in biophysical and discovery assays. The increased appreciation for nucleic acids modifications and their impact on diseases, as well as the rapid emergence of resistant pathogens, necessitate the development of new tools for the effective study of nucleic acids, including their recognition properties and alteration by exogenous agents. The emissive nucleoside analogs will be implemented into novel fluorescence-based assays. These assays will facilitate: (i) the detection of DNA lesions (e.g., 8-oxoG), that play important roles in carcinogenesis, (ii) the discovery of new antibiotics targeting the bacterial ribosome, assisted by fluorescent A-site analogs, (iii) the discovery of novel anti-HIV agents, assisted by fluorescent DIS constructs, and (iv) the detection of protein toxins, such as ricin, via emissive probes that detect their depurinated RNA products. These investigations will advance the fundamental understanding of key biological processes related to disease development and will have long-term impact on improving human health by facilitating drug discovery. PUBLIC HEALTH RELEVANCE: Nucleic acids (DNA and RNA) play central roles in biology and, as such, have immense impact on the development of diseases and, as such, on human health. Advancing effective fluorescence-based tools for exploring the modification of DNA and RNA or their interactions with potential therapeutic agents will advance new diagnostic approaches and will facilitate drug discovery.