Modification of DNA on magnetic beads

A method for treating DNA to quantify DNA methylation in fragmented, small DNA, the method comprising:

• a) to a sample solution comprising small DNA, adding NaOH to produce a solution comprising strands of single-stranded small DNA;
• b) to said solution comprising strands of single-stranded small DNA, adding a sulfonation reagent comprising ammonium hydrogen sulfite to produce a mixture of small DNA in a solution comprising ammonium hydrogen sulfite, and incubating the mixture at a temperature of 65° C. to 68° C. for 2 hours or less to produce sulfonated small DNA;
• c) combining the sulfonated small DNA in the mixture of step b) with an alcohol-free binding buffer comprising guanidine hydrochloride and silica-coated magnetic beads, and incubating to produce bead-bound sulfonated small DNA;
• d) collecting bead-bound small DNA from the binding buffer and contacting the collected bead-bound sulfonated small DNA with a desulfonation reagent comprising NaOH and isopropanol to produce bead-bound converted small DNA;
• e) eluting converted small DNA to provide an analytical sample comprising converted small DNA;
• and
• f) quantifying DNA methylation by identifying or enumerating methylated cytosines, if present, in the converted small DNA in the analytical sample;
• wherein said small DNA is 200 or fewer bases in length and wherein the amount of small DNA in the analytical sample is at least 90% of the amount of small DNA contacted with the sulfonation reagent.