Se-Derivatization of Functional RNAs for Structure Study

Brooklyn College, New York NY

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Abstract

DESCRIPTION (provided by applicant): The goal of this research is to selectively replace oxygen atoms of nucleic acids, especially functional RNAs, with selenium atoms for X-ray crystal structure determination using Multiwavelengh Anomalous Dispersion (MAD) phasing technique. Analogous to the selenium isomorphous substitution of the sulfur in the methonine residue for protein MAD phasing, selenium may also be used to substitute nucleotide oxygen, as selenium (atomic radii, 1.2 Angstroms), sulfur (1.1 Angstroms), and oxygen (0.68 Angstroms) are in the same Family VIA in the Periodic Table. Since the space surrounding nucleotide oxygen atoms is usually available to accommodate a larger atom, such as selenium, the steric issue of selenium replacing oxygen atom should not be a problem. Therefore, it is hypothesized that selenium can be chemically and stably incorporated into nucleic acid by selectively substituting oxygen, and such selective substitution is structurally and chemically isomorphous to its oxygen-containing counterpart. Unlike the conventional derivatization with bromine, which is limited to the 5-positions of the pyrimidines, selenium can be selectively incorporated into all nucleotide building blocks (A, C, G, U, and T, in both ribose and deoxyribose series) at various positions, such as, 2'-, 3'-, 5'-ribose oxygen, phosphate non-bridging oxygen, and nucleobase oxygen. A greater choice in the substitution allows avoidance of structural and functional perturbation on functional RNAs. The Se-phosphoramidite and triphosphate building blocks will be designed and synthesized from the corresponding nucleoside derivatives containing selenium at various positions. The Se-phosphoramidites and Se-triphosphates will be applied in chemical and enzymatic derivatization of functional RNAs with selenium. This selenium-substitution strategy also has great potential in derivatization of RNA-protein and DNA-protein complexes by labeling nucleic acids instead of the protein counterparts. This selenium strategy will greatly facilitate 3-D crystal structure determination of nucleic acids and their complexes with drugs and proteins.