Some DNA bases and labels are not compatible with ammonium hydroxide deprotection. Although deprotection with ammonium hydroxide at room temperature sometimes may allow oligos containing these bases and labels to be isolated, it is not optimal and a new deprotection strategy is needed. The use of a combination of Pac-dA, Ac-dc and iPr-Pac-dG allows complete deprotection with potassium carbonate in methanol at room temperature for four hours as long as capping is carried out using phenoxyacetic anhydride rather than acetic anhydride. (With ultramild reagents, ammonium hydroxide at room temperature for two hours is also effective.) If acetic anhydride is used, a small amount of transamidation occurrs at dG residues and overnight treatment with potassium carbonate or ammonium hydroxide is required to deprotect formed Ac-dG residues.
UltraMild DNA synthesis reagents are available for use when DNA bases and labels are not compatible with ammonium hydroxide deprotection.