Selective Characterization of mRNA 5′ End-Capping by DNA Probe-Directed Enrichment with Site-Specific Endoribonucleases

The N7-methyl guanosine cap structure is an essential 5 ' end modification of eukaryotic mRNA. It plays a critical role in many aspects of the life cycle of mRNA, including nuclear export, stability, and translation. Equipping synthetic transcripts with a 5 ' cap is paramount to the development of effective mRNA vaccines and therapeutics. Here, we report a simple and flexible workflow to selectively isolate and analyze structural features of the 5 ' end of an mRNA by means of DNA probe-directed enrichment with site-specific single-strand endoribonucleases. Specifically, we showed that the RNA cleavage by site-specific RNases can be effectively steered by a complementary DNA probe to recognition sites downstream of the probe-hybridized region, utilizing a flexible range of DNA probe designs. We applied this approach using human RNase 4 to isolate well-defined cleavage products from the 5 ' end of diverse uridylated and N1-methylpseudouridylated mRNA 5 ' end transcript sequences. hRNase 4 increases the precision of the RNA cleavage, reducing product heterogeneity while providing comparable estimates of capped products and their intermediaries relative to the widely used RNase H. Collectively, we demonstrated that this workflow ensures well-defined and predictable 5 ' end cleavage products suitable for analysis and relative quantitation of synthetic mRNA 5 ' cap structures by UHPLC-MS/MS.