RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA.
Deoxyribozymes are emerging as modification-specific endonucleases for the analysis of epigenetic RNA modifications. Here, we report RNA-cleaving deoxyribozymes that differentially respond to the presence of natural methylated cytidines, 3-methylcytidine (m3 C), N4 -methylcytidine (m4 C), and 5-methylcytidine (m5 C), respectively. Using in vitro selection, we found several DNA catalysts, which are selectively activated by only one of the three cytidine isomers, and display 10- to 30-fold accelerated cleavage of their target m3 C-, m4 C- or m5 C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The mX C-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m3 C and m5 C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.
['Liaqat|Anam|A|', 'Sednev|Maksim V|MV|0000-0001-6746-1598', 'Stiller|Carina|C|', 'Höbartner|Claudia|C|0000-0002-4548-2299']
D020029:Base Pairing D003562:Cytidine D021881:DNA, Catalytic D009690:Nucleic Acid Conformation D012313:RNA D059367:RNA Cleavage D013379:Substrate Specificity
deoxyribozymes RNA modification in vitro selection epitranscriptomics site-specific RNA cleavage