What is the difference between the TFA C6-Amino Linker and the MMT C6-Amino Linker?
A – The main difference between the two is the protecting group. The MMT linker is protected with a monomethoxytrityl group and the TFA linker is protected with a trifluoroacetate group. The MMT linker is acid labile, whereas the TFA group is base labile. The MMT is the best choice when you want a pure amino labeled oligonucleotide. Since the MMT group is more nonpolar, you can leave the MMT group acts as a purification handle on reverse phase HPLC just like the DMT group. The TFA protected linker is better for crude conjugations where the oligonucleotide is used after deprotection. As a word of caution, remember to exchange the ammonia for another salt prior to conjugation since excess ammonia will severely reduce the efficiency of many conjugations.
