Poster abstracts
Poster number 45 submitted by Xue Tang
Development of bifacial Peptide Nucleic Acids for Probing Structural Motifs Containing Non-canonical Pairs in RNA and DNA
Xue Tang (Department of Chemistry and Biochemistry), Debmalya Bhunia (Department of Chemistry and Biochemistry)
Abstract:
RNA is an important target for chemical probes and therapeutics; however, RNA non-canonical pair (NCP) targets are underexploited due to lack of understanding and identifying of the noncovalent interactions between NCP motifs and small molecules. Our group has previously reported bPNA(+) triplex hybridization for targeting and fluorescence labeling UxU and TxT NCPs in structured RNA and DNA. To extend the binding repertoire of bPNAs beyond oligo-U/T bulges, we designed and synthesized bPNA variants that recognize other NCPs in addition to UxU and TxT. We then carried out binding screens for these bPNA variants using DNA and RNA duplexes with internal bulge sequences that have NCPs. We have observed clear band shifts on native gels for bPNA that have good binding behavior with certain NCPs. Thus, new binding strategies for structural motifs containing NCPs have been identified. With the broadened recognition of bPNA, we generally provided a solution for specifically labeling various native RNA sequences that contain NCP motifs, which can be further exploited to develop fluorescent probes that function in vitro and in vivo.
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