Abstract: Provided are methylcytosine-selective deaminases, compositions, kits, and methods employing them, including a sequencing method involving (a) contacting a DNA substrate comprising cytosine (C) and at least one methylcytosine nucleobase selected from 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) or comprising C and both 5mC and 5hmC, with a methylcytosine-selective deaminase to produce a deamination product, wherein the methylcytosine-selective deaminase (i) is capable of deaminating 5mC to thymidine (T) and/or 5hmC to hydroxymethyluridine (hmU) and (ii) preferentially deaminates the at least one methylcytosine nucleobase relative to cytosine (C); and (b) sequencing the deamination product, or amplifying the deamination product to produce an amplification product, and sequencing the amplification product, in each case, to produce sequence reads, wherein positions of Cs and position of the at least one methylcytosine nucleobase in the DNA substrate is determined based on the sequence reads.

Abstract: The present disclosure relates, according to some embodiments, to enzymes, systems, compositions, methods, apparatus, and workflows for selectively cutting, cleaving, digesting and/or hydrolyzing duplex DNA strands or the DNA strand of a DNA/RNA hybrid.

Abstract: Provided herein, among other things, is a method for deaminating a double-stranded nucleic acid. In some embodiments, the method may comprise contacting a double-stranded DNA substrate that comprises cytosines and a double-stranded DNA deaminase having an amino acid sequence that is at least 80% identical to any of SEQ ID NOS: 21, 40, 47, 49, 50, 55, 58, 59, 62, 63, 65, 67, 70, 71, 76, 106, 107, 110, 112, 114, 117, 163 and/or 164 to produce a deamination product that comprises deaminated cytosines. Enzymes and kits for performing the method are also provided.

Abstract: Provided herein, among other things, is a method for deaminating a double-stranded nucleic acid. In some embodiments, the method may comprise contacting a double-stranded DNA substrate that comprises cytosines and a double-stranded DNA deaminase having an amino acid sequence that is at least 80% identical to any of SEQ ID NOS: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 19, 24, 26, 27, 28, 33, 40, 49, 50, 63, 95, 96, 97, and/or 99 to produce a deamination product that comprises deaminated cytosines. Enzymes and kits for performing the method are also provided.