Mirror Image Aptamers: Next Generation RNA-Binding Reagents for Basic Research and Therapeutic Applications
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Project Summary/The increasing appreciation of RNA''s structure-function relationship has led to a demand for newtechnologies that enable targeting of specific RNA structures. Such technologies are essential for thedevelopment of probes to study RNA function and therapeutics to treat RNA-mediated diseases. However,outside of antibiotics binding the ribosome, structure-specific RNA-binding reagents are very rare. Thus,developing of new technologies that enable structure-specific targeting of RNA remains an important challengein many fields. The central vision of my research program is to address the deficit of structure-specific RNA-bindingreagents using a radically different type of nucleic acid affinity reagent: L-aptamers. L-Aptamers are uniquebecause they are comprised of L-(deoxy)ribose-based nucleic acids (L-DNA and L-RNA), which are mirrorimages (enantiomers) of natural D-nucleotides. Because oligonucleotides of opposite stereochemistry (Dversus L) are incapable of forming contiguous Watson-Crick base pairs with each other, we are able to evolveL-aptamers that adaptively bind structured D-RNA targets through tertiary interactions (shape) rather thanprimary sequence. In other words, L-aptamers escape the tyranny of Watson-Crick base pairing, enabling amore nuanced mode of molecular recognition to be discovered. As a result, L-aptamers bind structured RNAswith greater affinity and specificity compared to conventional affinity reagent. Binding RNAs based on theirshape rather than Watson-Crick base pairing represents a significant departure from traditionaloligonucleotide-based approaches and represents a major advance in aptamer technology. During the next five year, my research group aims to further develop L-aptamer technology in order torealize its promise as a practical research and therapeutic tool. In particular, we will focus on incorporation ofmodified nucleotides that bestow protein-like functionality on L-aptamers, thus generating a novel class ofRNA-targeted antibody mimetics. Because these technological developments will be carried out in the contextof disease associated RNAs, such as oncogenic microRNAs and viral RNAs, this work will have an immediateimpact by generating lead reagents to probe the etiology of disease and develop new therapeutic strategies. Inline with my vision, we aim to determine the structure of an L-aptamerâ€“D-RNA complex, which will provideinsight into this novel mode of recognition and inform future L-aptamer design.