It has been shown that the 5-position of pyrimidine and the 7-position of 7-deazapurine nucleosides are the ideal positions to introduce functionalities, as these sites lie in the major groove of the DNA providing steric freedom. In order to enable efficient click-chemistry labeling of alkyne modified oligonucleotides, our nucleosides provide a 5-(octa-1,7-diynyl) sidechain. Phosphoramidites of nucleosides 1-4 were shown to be incorporated into DNA oligomers by solid-phase synthesis with excellent coupling efficiency (e.g. 1: > 99 %). Another feature of the octadiynyl-sidechain is their stabilizing effect on DNA duplexes (e.g. 1: Tm increase of 1-2 °C).
Purified oligonucleotides bearing a single alkyne moiety are usually modified with 2-5 equivalents of the corresponding marker-azide (e.g. fluorescent-dye azides). After the addition of precomplexed Cu(I), complete conversion to the labeled oligo is observed in a time span between 30 min and 4 hours. After a simple precipitation step, labeled oligonucleotides can be recovered in near quantitative yields. Below some examples of MALDI-mass spectra measured directly after the click reaction and the precipitation step, without further purification.
Example: 16mer, internal alkyne reacted with 2 equivalents Fluorescein-Azide (FAM-Azide), 3 h at 37 °C. Ethanol precipitation with 99% recovery of the labeled oligo. MALDI-mass analysis of the crude product -> 100% oligo-dye conjugate.