5’-(4,4’-dimethoxytrityl)-5-[N-(6-trifluoroacetylaminohexyl)- 3-acrylamido]-2’-deoxyuridine-3’-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite

- Formula:

C50H62F3N6O10P

- Molecular Weight:

995.03

- Appearance:

white solid

- Extinction Coefficient at 260 nm:

8400

Prior to dilution ensure that all product is at the bottom of the vial. Dilute to the recommended concentration and mix thoroughly in the sealed vial to ensure that all contents are dissolved.

Dilution:

100mg/mL

Deprotection conditions:

To avoid a secondary alkylation acryonitrile reacton, which occurs during normal cleavage and deprotection of amine modified oligos, flush column for 15 minutes with 1 mL of 10% Diethylamine (Aldrich #471216) in MeCN and rinse column with MeCN before cleavage and deprotection of the amine labeled oligo with NH4OH. If using standard amidites [i.e., A(Bz), G(iBu)] deprotect in concentrated NH4OH for 5 hours at 60 °C. If using fast deprotecting amidites [i.e., C(Ac), G(DMF), G(PAC)] deprotect in concentratied NH4OH for 1 hour at 60 °C. Note: under these condtions the TFA group will be removed.

Amine Labeling: Amino Modifier C6 T reacts in a manner identical to a normal phosphoramidite monomer. If labeling the 5' terminus, the DMT group may be left on after the synthesis for reverse-phase cartridge purification. Oligo should be cleaved, deprotected, and purified before labeling. For reporter groups, protein labels, NHS, and enzymes see manufacturer's labeling protocol.

Image of cleaved and deprotected structure:

The mass this product adds after conjugation and work-up (the additional mass seen by mass spectrometry) is:

458.4