Sequences with high GC content may contain mismatches and still hybridize because of the high stability of the G-C base pair. The N4-ethyl analogue of dC (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair is reduced to about the level of an AT base pair.
Coupling N6-Me-dA (10-1003) and N4-Et-dC (10-1068) with 1H-tetrazole leads to a trace of branching at the secondary amine positions, while DCI leads to around 15% branching. In collaboration with Berry and Associates, the acetyl protected monomers were prepared. Acetyl protection was chosen since it would block branching reactions. Oligonucleotides synthesized using these monomers proved to be compatible with all popular deprotection strategies from UltraMild to UltraFast. When the acetyl protected monomers were compared with the unprotected monomers using DCI as activator, branching was reduced from 15% to zero.
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.