Oligo Synthesis : CEPs

Stability in Solution: 1-2 days

Conjugation using Click Chemistry

The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction betweenazides and alkynes to form 1,2,3-triazoles, as reported¹ bySharpless, was found to be so exquisitely regioselective and efficient at eventhe most mild conditions that Sharpless coined the term ‘Click Chemistry’ todescribe it. The use of this method for DNA modification has been somewhatdelayed by the fact that copper ions damage DNA, typically yielding strandbreaks.² As these problems have now been overcome by the use ofcopper(I)-stabilizing ligands (e.g., tris(benzyltriazolylmethyl)amine,TBTA³), Carell et al. and Seela et al. discovered that the CuAACreaction can be used to functionalize alkyne-modified DNA nucleobases withextremely high efficiency.⁴

Oligonucleotides bearing a single nucleosidic alkyne group can be preparedusing a C8-Alkyne-dC or dT-CE Phosphoramidite. Purified oligonucleotides areusually modified with 2-5 equivalents of the corresponding marker-azide (e.g.,fluorescent-dye azides). After the addition of precomplexed Cu(I), completeconversion to the labelled oligo is observed in a time span between 30 min and 4hours. After a simple precipitation step, labelled oligonucleotides can berecovered in near quantitative yields. Using a combination of C8-Alkyne,C8-TIPS-Alkyne and C8-TMS-Alkyne, it is possible to label oligonucleotides in upto three separate click reactions. The alkyne groups on the last two monomersare protected, respectively, with triisopropylsilyl (TIPS) and trimethylsilyl(TMS) protecting groups.5,6 The first click reaction on solid phase on aC8-Alkyne yields the singly modified oligonucleotide with full retention of theTIPS and/or TMS protecting group. For double click, a C8-TIPS-Alkyne is used asthe second nucleoside and the TIPS protecting group is cleaved withtetrabutylammonium fluoride (TBAF) without causing any damage to the DNA. Thesecond click reaction in solution yields the doubly modified oligonucleotide inexcellent yield. For the introduction of three different labels, all threenucleosides are introduced into oligonucleotides. The first click reaction isperformed directly on the resin. The singly modified oligonucleotide issubsequently cleaved from the support with concomitant cleavage of the TMS groupand retention of the TIPS protecting group. The second click reaction isperformed in solution. Precipitation of the doubly modified oligonucleotide,cleavage of the TIPS group with TBAF, and a subsequent third click reaction insolution furnishes the desired triply modified oligonucleotide in excellentoverall yield.