TY  - JOUR
A1  - Liaqat, Anam
A1  - Sednev, Maksim V.
A1  - Stiller, Carina
A1  - Höbartner, Claudia
T1  - RNA-Cleaving Deoxyribozymes Differentiate Methylated Cytidine Isomers in RNA
JF  - Angewandte Chemie International Edition
N2  - 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 (m\(^3\)C), N\(^4\)-methylcytidine (m\(^4\)C), and 5-methylcytidine (m\(^5\)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 m\(^3\)C-, m\(^4\)C- or m\(^5\)C-modified RNA. An additional deoxyribozyme is strongly inhibited by any of the three methylcytidines, but effectively cleaves unmodified RNA. The m\(^X\)C-detecting deoxyribozymes are programmable for the interrogation of natural RNAs of interest, as demonstrated for human mitochondrial tRNAs containing known m\(^3\)C and m\(^5\)C sites. The results underline the potential of synthetic functional DNA to shape highly selective active sites.
KW  - Deoxyribozymes
KW  - Epitranscriptomics
KW  - RNA Modification
KW  - Site-Specific RNA Cleavage
KW  - in vitro Selection
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-254544
VL  - 60
IS  - 35
ER  - 
TY  - JOUR
A1  - Liaqat, Anam
A1  - Stiller, Carina
A1  - Michel, Manuela
A1  - Sednev, Maksim V.
A1  - Höbartner, Claudia
T1  - N\(^6\)-Isopentenyladenosine in RNA Determines the Cleavage Site of Endonuclease Deoxyribozymes
JF  - Angewandte Chemie International Edition
N2  - RNA-cleaving deoxyribozymes can serve as selective sensors and catalysts to examine the modification state of RNA. However, site-specific endonuclease deoxyribozymes that selectively cleave posttranscriptionally modified RNA are extremely rare and their specificity over unmodified RNA is low. In this study, we report that the native tRNA modification N\(^6\)-isopentenyladenosine (i\(^6\)A) strongly enhances the specificity and has the power to reconfigure the active site of an RNA-cleaving deoxyribozyme. Using in vitro selection, we identified a DNA enzyme that cleaves i\(^6\)A-modified RNA at least 2500-fold faster than unmodified RNA. Another deoxyribozyme shows unique and unprecedented behaviour by shifting its cleavage site in the presence of the i\(^6\)A RNA modification. Together with deoxyribozymes that are strongly inhibited by i\(^6\)A, these results highlight intricate ways of modulating the catalytic activity of DNA by posttranscriptional RNA modifications.
KW  - Deoxyribozymes
KW  - Epitranscriptomics
KW  - in vitro selection
KW  - RNA modification
KW  - site-specific RNA cleavage
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-212121
ET  - Early View
ER  -