Patent ID: 8551709

Claim:
A method comprising: (a) cleaving a base portion of at least one non-canonical nucleotide from a polynucleotide, wherein the polynucleotide comprises at least one non-canonical nucleotide, wherein the cleaving comprises use of uracil N-glycosylase (UNG), thereby generating an abasic site in the polynucleotide; (b) fragmenting a phosphodiester backbone of the polynucleotide at the abasic site using N,N′-dimethylethylenediamine (DMED), thereby forming a polynucleotide fragment with a blocked 3′ end; (c) unblocking the blocked 3′ end of the polynucleotide fragment with an enzyme comprising a nonprocessive 3′ to 5′ exonuclease activity, thereby generating a polynucleotide fragment with a 3′ hydroxyl; and (d) extending the polynucleotide fragment with the 3′ hydroxyl from the 3′ hydroxyl using terminal deoxynucleotidyl transferase (TdT).