The DADE linker is a pre-activated carboxyl linker for the 5’ terminus of an oligonucleotide. It was designed for the solid phase conjugation of amine bearing compounds directly to an oligonucleotide, although it has other applications. If it is left in its activated form when the oligonucleotide is deprotected, it will react with the prevalent nucleophile in the solution (ammonia in ammonium hydroxide forming the amide, the hydroxyl in sodium hydroxide forming carboxylic acid, etc.). Its major advantage is that it can be used for solid phase conjugation to amine bearing compounds, negating the need for costly succinimidyl esters. This allows high throughput screening, and the reuse of compound that did not conjugate in the first reaction. It also allows for the use of large excesses that will enhance conjugation efficiencies, and reduce cost. It has many other applications.
The main difference 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. MMT is the best choice when you want a pure amino labeled oligonucleotide. Since the MMT group is more nonpolar, it 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.
What is the longest oligonucleotide TriLink can synthesize?
TriLink has successfully synthesized 220mer unmodified DNA and 110mer unmodified RNA. However, TriLink is willing to try longer sequences.
Post a comment below to discuss your needs.
I need a DNA oligo with a fluorescent dye attached for an fluorescence polarization assay. The linker between DNA and dye should be as rigid as possible and the dye most likely a BODIPYdye, dansyl or fluorescein dye. Attachment either internal or at the 5′ of the oligo. What solution do you have for that? – Chris Gloeckner, Illumina
A shorter linker will provide the most rigidity between an oligo and a dye. Our shortest linker is the dT-C2 amino linker. The linker arm is attached to the Thymidine base and the dye would be conjugated onto the amino group post-synthetically. Another option would be to use our C7 internal amino linker. Read More…
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