Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif‐Selective Binding by Fluorogenic Base Probes. Issue 2 (24th November 2021)

• Record Type: Journal Article
• Authors: Liang, Yufeng; Miao, Shiqin; Mao, Jie; Devari, Shekaraiah; Gonzalez, Maricarmen; Bong, Dennis
• Is Part Of: Chemistry. Volume 28:Issue 2(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2021-11-24
• Subjects: fluorescent probes -- noncanonical pairs -- nucleobases -- RNA recognition -- synthetic bases; Chemistry -- Periodicals; 540
• DOI: 10.1002/chem.202103616
• Languages: English
• ISSNs: 0947-6539

Abstract

Abstract: We hypothesize that programmable hybridization to noncanonical nucleic acid motifs may be achieved by macromolecular display of binders to individual noncanonical pairs (NCPs). As each recognition element may individually have weak binding to an NCP, we developed a semi‐rational approach to detect low affinity interactions between selected nitrogenous bases and noncanonical sites in duplex DNA and RNA. A set of fluorogenic probes was synthesized by coupling abiotic (triazines, pyrimidines) and native RNA bases to thiazole orange (TO) dye. This probe library was screened against duplex nucleic acid substrates bearing single abasic, single NCP, and tandem NCP sites. Probe engagement with NCP sites was reported by 100–1000× fluorescence enhancement over background. Binding is strongly context‐dependent, reflective of both molecular recognition and stability: less stable motifs are more likely to bind a synthetic probe. Further, DNA and RNA substrates exhibit entirely different abasic and single NCP binding profiles. While probe binding in the abasic and single NCP screens was monotonous, much richer binding profiles were observed with the screen of tandem NCP sites in RNA, in part due to increased steric accessibility. In addition to known binding interactions between the triazine melamine (M) and T/U sites, the NCP screens identified new targeting elements for pyrimidine‐rich motifs in single NCPs and 2×2 internal bulges. We anticipate that semi‐rational approaches of this type will lead to programmable noncanonical hybridization strategies at the macromolecular level. Abstract : A semi‐rational approach to detect low affinity binding to noncanonical pair (NCP) sites in duplex DNA and RNA has been developed. A set of fluorogenic thiazole orange probes bearing abiotic (triazines, pyrimidines) and native RNA bases was screened against dsDNAs and dsRNAs with single abasic, single NCP and tandem NCP sites. Fluorogenic probe engagement revealed novel and selective base interactions with NCPs, setting the stage for a new strategy of targeting noncanonical motifs in RNA.