Described herein are various methods of removing uracils due to the
deamination of unmethylated cytosines in an
assay using engineered
cytosine deaminases to deaminate methylated cytosines. The Chemoenzymatic
Uracil Replacement of Nucleobases (ChURN) method includes providing a sample comprising single stranded
DNA library fragments in which a
cytosine deaminase has deaminated methylated cytosines; contacting the sample with an
uracil DNA glycosylase (UDG) to deglycosylate
uracil residues to form abasic sites having a
hemiacetal formation within the single stranded
DNA library fragments; contacting the sample with a reactive
cytosine nucleobase analog to install a cytosine at abasic sites thru a noncanonical linkage; and subjecting the sample to
polymerase chain reaction (PCR) amplification resulting in
double stranded DNA corrected
library fragments. The
Uracil Enzymatic Removal and Substitution at Errors (U-ERASE) method includes providing a sample comprising single stranded DNA library fragments in which a
cytosine deaminase has deaminated methylated cytosines, synthesizing
double stranded DNA library fragments in which the second strand is tagged to facilitate its downstream degradation, treating the
double stranded DNA library fragments with an
uracil DNA glycosylase and an
endonuclease resulting in the removal of uracil bases and single
nucleotide gaps at those sites, and repairing the single
nucleotide gaps through treatment with a
polymerase, dCTP, and a ligase, resulting in replacement of false positive uracil bases with a mismatched base, such as cytosine. Subsequently, the second strand is selectively degraded, allowing for selective amplification of the original DNA strand via PCR.