Methods for identifying nucleic acid modifications

A method for enhancing identification of a modification of interest, the method comprising:

• a) providing a DNA template comprising the modification of interest, the modification of interest being characterized by a first kinetic signature during processing by a polymerase, wherein the modification of interest is a methylated base or a hydroxymethylated base;
• b) converting the modification of interest into a further modification, by subjecting the DNA template to a treatment to introduce the further modification, wherein the treatment comprises exposure to a modifying agent selected from the group consisting of a glycosylase, bisulfite, a hydroxylase, a glucosyltransferase, NMIA, and CDI, wherein the further modification is characterized by a second kinetic signature during processing by the polymerase, and further wherein the second kinetic signature is distinct from the first kinetic signature;
• c) providing the polymerase, which is capable of processing the DNA template;
• d) contacting the DNA template comprising the further modification with the polymerase;
• e) monitoring processing of the DNA template comprising the further modification by the polymerase;
• and
• f) detecting a change in the kinetics of the polymerase during the processing, wherein the change is indicative of the second kinetic signature, thereby detecting the further modification, and enhancing identification of the modification of interest that was present in the DNA template prior to the converting.