Novel PT(II) Reagents for RNA Biochemistry

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With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. Victoria DeRose from the University of Oregon to develop new metal-based compounds for predicting the structure of ribonucleic acid (RNA) biopolymers. A major realization in the post-genomic era is the extent to which cellular RNA governs gene expression through different mechanisms, many of which are still being discovered. The prediction and determination of the structure of large RNAs are significant challenges in the pursuit of the elucidation of these mechanisms. Small chemical probes can be powerful tools for the identifying structural elements of RNA. The platinum-based compounds and methods developed in this project are designed to provide such new tools for high-throughput RNA structure prediction. As this project requires use of a combination of synthesis, molecular biology, and analytical and computational methods, it fosters interdisciplinary interactions between different branches of chemistry, and it provides a workforce training environment for undergraduate and graduate students, including women, who prepare for careers in STEM fields. The specific goals of this program are to develop square-planar, exchange-inert Pt(II) complexes as RNA crosslinking reagents and use them as tools for RNA structure characterization. Pt(II) compounds crosslink purine-rich but noncanonical regions of RNA, such as internal loops and junctions. Pt(II)-crosslinked species are robust through RNA isolation methods but reversible in mild conditions. To enable crosslink analysis, azide- or alkyne-modified Pt(II)-"Click" reagents with installed handles for selective post-treatment modification of Pt(II)-RNA species will be synthesized. Structure analysis protocols will be developed based on the unique chemistry of the Pt(II) complexes, including high-throughput sequencing methods and high-resolution mass spectrometry. Phosphorothioate "bait" ligands will be incorporated in RNA to create new crosslinking sites for the metal complexes. Efforts to enhance the properties of Pt(II) reagents for RNA structure analysis will include modification of clickable mononuclear compounds with longer linkers and testing of multinuclear Pt(II) compounds. The Pt(II)-based crosslinking methods described here have the potential to become tools for RNA structure prediction and in-cell probes of RNA accessibility to small molecules.