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.
An alternative protecting scheme for the normal CE phosphoramidites should allow UltraMILD deprotection and should not react with a wider variety of tags and labels.
Beta L-DNA is the mirror image version of naturally occurring D-DNA. L-DNA and D-DNA share identical structures that differ only in terms of stereochemistry and generally have identical physical and chemical properties.
An alternative protecting scheme for the normal CE phosphoramidites should allow UltraMILD deprotection and should not react with a wider variety of tags and labels. Glen Research offers supports to support UltraMild DNA synthesis.