Preparation of alpha-Oxo semicarbazone oligonucleotide microarrays

This unit describes the preparation of alpha-oxo aldehyde functionalized oligodeoxynucleotides, the preparation and characterization of semicarbazide glass slides, and the fabrication of alpha-oxo semicarbazone microarrays by site-specific ligation of alpha-oxo-aldehyde oligodeoxynucleotides to the semicarbazide glass slides. The alpha-oxo aldehyde group COCHO is extensively used in ligation chemistry for the preparation of large molecular constructs. It is stable toward air oxidation and mainly present in aqueous solution in the hydrated form COC(OH)(2). It reacts efficiently with hydrazine derivatives, in particular, with the semicarbazide group. The reaction occurs spontaneously in water at pH 5.5. Site-specific immobilization of glyoxylyl oligodeoxynucleotides on semicarbazide glass slides allows the preparation of high-quality microarrays that can be used directly in hybridization experiments.