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. Author manuscript; available in PMC: 2024 Nov 29.
Published in final edited form as: Annu Rev Anal Chem (Palo Alto Calif). 2024 Jul 2;17(1):47–68. doi: 10.1146/annurev-anchem-061622-125954

Table 1.

Cleavage specificity and limitation of enzymes available for RNA modification mapping.

Enzyme Cleavage specificity Limitations Ref
RNase T1 all unmodified guanosine residues and 3’-end of the modified nucleoside N2 -methyl guanosine (m2G) RNase T1 does not generate high sequence coverage especially when there are G-rich sequence redundancies available (56)
RNase A canonical pyrimidines and the modified nucleoside Ψ (pseudouridine) RNase A generates shorter degradation products that are not useful for modification placement (57)
RNase U2 canonical purines with a slight selectivity towards adenosine RNase U2 does not increase the sequence coverage of mapped modifications (58)
Human RNase 4 uridine residues prior to purines (slight preference for UA relative to UG) RNase 4 best for mRNA and other long RNA substrates/requires addition of T4 polynucleotide kinase to avoid generation of 2’,3’ cyclic phosphates (59)
MC1 uridine and pseudouridine at the 5’ end MC1 is commercially unavailable (53)
Cusativin cytidine and 5-methylcytidine (m5C) at the 3’ end Cusativin is commercially unavailable (60)