Photochemical RNA Editing of C to U by Using Ultrafast Reversible RNA Photo‐crosslinking in DNA/RNA Duplexes

Abstract

RNA editing, which is used to edit nucleobases in RNA strands; is more feasible for use in medical applications than DNA editing. We previously reported the photochemical conversion of cytosine to uracil, which required photo‐crosslinking, deamination, and photo‐splitting. Here, we evaluated the influence of the bases surrounding the target cytosine on the conversion of cytosine to uracil in the RNA strand. The photo‐crosslinker 3‐carboxyvinylcarbazole(OHVK), which is more hydrophilic than 3‐cyanovinylcarbazole(CNVK), 3‐carboxyamidevinylcarbazole(NH2VK), and 3‐methoxy carbonylvinylcarbazole(OMeVK), induced faster deamination of cytosine. Furthermore, inosine, which forms two hydrogen bonds with cytosine, was the most efficiently paired base for accelerating photochemical RNA editing. Upon evaluation of the conversion from cytosine to uracil in RNA, the use of oligodeoxynucleotides containing OHVK and inosine and the polarity of the bases surrounding the target cytosine were found to be crucial.

The emerging roles of N6-methyladenosine (m6A)-modified long non-coding RNAs in human cancers

“…The CLIP builds covalent bonds between proteins and RNAs with direct contact with ultraviolet (UV) light irradiation and is a state-of-the-art method that spread the practice to stabilize direct protein-RNA interactions. This technology, initially matured in Escherichia coli, is widely recognized as an essential procedure for researching dynamic protein interactions in multitudes of cellular processes in multifarious biological systems [ 67 , 68 ]. CLIP consists of photo-crosslinking-assisted m 6 A sequencing (PA-m 6 A-Seq) [ 69 ], m 6 A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) [ 70 ], and m 6 A-CLIP.…”

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

“…Other advantages are that they are generally more accessible and pan acting, thus enabling transcriptome-wide interrogations. Conversely, internal cross-linking reagents are installed in the RNA scaffold prior to the study either chemically or enzymatically and include coumarins, 52 carbazoles, 45 thionucleotides, 53 diazirines, 54 and platinum complexes 55 among others and have recently been reviewed. 56 Four classes of external cross-linking reagents (Figure 2) are predominantly used, and each offers unique advantages and reacts with distinct functional groups on the RNA scaffold to establish intra-or intermolecular cross-links.…”

Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids

“…Recently, the reaction rate 46 was further improved by changing the sugar structure and the wavelength of the forward and reverse reactions 47 was lengthened by changing the vinylcarba-zole base structure. This type of crosslinking has been used for many applications, such as the inhibition of translation, 48,49 RNA editing, 50,51 RNA fluorescence in situ hybridization, [52][53][54] functional gel material engineering, 55 and DNA origami. 56 In DNA nanotechnology, the photoreversible crosslinking property of CNV K is one of the advantages of creating smart materials.…”