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Formylindole Modifier CE-Phosphoramidite

Formylindole Modifier CE-Phosphoramidite

Phosphoramidite for the incorporation of an aldehyde function internally or at the 5' end of an oligonucleotide.
  • Introduces reactive aldehyde functionality into oligo for conjugation.
  • Sugar unit of the pseudo nucleoside is unmodified allowing multiple incorporations of dR-formylindole.
  • Modification is stable to most cleavage and deprotection conditions.
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Product information

The aldehyde function is often used to conjugate biopolymers to other molecules by processes such as reductive amination or adduct formation with hydroxylamines, hydrazines and semicarbazides.

Aldehydes have also been used as a means of immobilising oligonucleotides onto solid surfaces. (1)

The use of this functionality has been hampered by the complexity of existing routes such as post synthetic periodate oxidation of a diol to produce the aldehyde, and the lack of conveniently available ready-made phosphoramidites or supports to incorporate an aldehyde functionality into an oligonucleotide.

This formylindole modifier (2) can be placed either in the centre of or at the 5'-end of an oligonucleotide, but an extended coupling time of 15min for this modifier is recommended to provide a coupling efficiency of >95%.

Since the sugar unit of the pseudo nucleoside is unmodified, multiple incorporations of dR- formylindole are possible. This not only provides multiple conjugation sites but formylindole is known to act as a universal base resulting in destabilisation of the duplex by 7-10 ºC per addition when compared with the natural duplex. This modification is stable to most cleavage and deprotection conditions.

Post-synthetic modification of oligonucleotides bearing this moiety, and still bound to the solid support, has also been achieved. In essence, the options for post-synthetic modification of the aldehyde functionalised oligonucleotide are limited only by the reactive nature of aldehydes and the conditions to which the conjugate is stable.

We have used the aldehyde function to conveniently attach molecules such as O-benzylhydroxylamine and diphenylhydrazine. The use of DMT ON oligonucleotides produced extremely hydrophobic material with these substituents, however, DMT OFF oligonucleotides reacted in a mixture of acetate buffer (pH 4.7) and DMSO (1:1) at 37 °C overnight to give conjugation yields in excess of 70% when modified in the centre and in excess of 80% when modified at the 5'-end of the oligonucleotide.


  1. 134 For a review of this area see: Use of carbonyl group addition-elimination reactions for synthesis of nucleic acid conjugates, T.S. Zatsepin, D.A. Stetsenko, M.J. Gait and T.S. Oretskaya, Bioconjugate Chemistry, 16, 471-489, 2005.
  2. A facile incorporation of the aldehyde function into DNA: 3-formylindole nucleoside as an aldehyde containing universal nucleoside, A. Okamoto, K.Tainaka and I. Saito, Tetrahedron Lett., 43, 4581-4583, 2002.

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