Boron trifluoride-methanol complex as a non-depurinating detritylating agent in DNA synthesis.

We have found that boron trifluoride-methanol complex (BTMC) is an effective non-depurinating detritylating agent in automated DNA synthesis. Dichloroacetic acid (DCA) is at present widely used for the deprotection of the 5'-hydroxyl group prior to coupling the next nucleotide (1); however, the protected purine bases, 6'-isobutyryl-2'-deoxyguanosine and 4'-benzoyl-2'-deoxyadenosine, are unstable to acid and can undergo base modification during the deprotection step, leading to depurination and chain cleavage during the final amide deprotection step with ammonium hydroxide. Oligomers which have a high purine content or which have purines clustered near the 3'-end undergo considerable depurination with DCA. Unlike DCA, BTMC (2) does not act as a protonic acid but rather as a Lewis acid by complexing with an electron pair of the ether oxygen. Methanol then supplies the proton necessary to complete the ether cleavage. We compared BTMC as a detritylating agent with DCA in three ways: (i) yield of product, (ii) freedom from base modification, and (iii) template activity.