During alkali treatment, double stranded DNA (dsDNA) is treated with sodium hydroxide, a strong base, to denature the dsDNA and cleave DNA at embedded ribonucleotide sites. This generates single-stranded DNA (ssDNA) fragments with exposed two ends: one 2′,3′-cyclic phosphate end and an opposite 5′-hydroxyl end. The alkaline solution is then neutralized, and the ssDNA is purified.
