Kinetic model studies on the chemical ligation of oligonucleotides via hydrazone formation

We report on the suitability of hydrazone formation for activator-free ligation of oligonucleo tides. 5'-Acyl hydrazides were synthesized using a previously described phosphoramidite modifier, whereas 3'-hydrazides resulted from a hydrazinolysis of an ester group serving as a linker to the solid support. Aromatic aldehydes could be directly introduced on the 5'-terminus via the respective phosphoramidates. Aliphatic aldehydes were generated by periodate cleavage of the corresponding 3'- and 5'-modified diol precursors. Ligation of a 3'-hydrazide-modified oligonucleoticle with oligonucleotides bearing an aromatic aldehyde in 5'position showed a fast reaction kinetics (k(1) about 10(-1)) and irreversible hydrazone formation. The ligation of a 5'-hydrazide-modified oligonucleotide and a 3'-ribobisaldehyde appeared to proceed reversibly at the beginning, but became irreversible with increasing reaction time. Hydrazide-modified oligonucleotides were found to be somewhat unstable in aqueous solutions. (C) 2005 Elsevier Ltd. All rights reserved.