Methods for treating nucleic acid including: (a) providing an alkali environment to a nucleic acid sample; (b) reacting the nucleic acid sample with a bisulphite reagent and incubating the reaction so as to form a treated nucleic acid sample where methylated nucleotides in the nucleic acid sample remain unchanged while unmethylated nucleotides are converted to another form; (c) removing unwanted reagents or diluents from the treated nucleic acid sample; and (d) carrying out de-sulphonation of the precipitated treated nucleic acid at a temperature from 70° C. to 95° C. by adjusting the precipitated treated nucleic acid to a pH of between 10 and less than 12.5 to remove sulphonate groups present on the treated nucleic acid and obtain a nucleic acid sample substantially free of sulphonate groups.