Factors influencing hairpin oligonucleotide cyclization by the uncatalyzed alkyne-azide cycloaddition (AAC) reaction

Cyclization of short hairpin oligonucleotides (ODNs) containing unactivated alkynes and alkyl azides produces triazole-linked products slowly in the absence of CuI catalysis. The factors affecting the rate of this cycloaddition reaction have been investigated on a variety of hairpin sequences. The reaction proceeds best at intermediate concentrations of sodium chloride, but is inhibited by phosphate and Tris buffers. It is accelerated by increasing the temperature provided that Watson–Crick base pairing can occur. The rationale for these observations is discussed.