Biochemical assays of immobilized oligonucleotides with mass spectrometry

This paper reports the use of mass spectrometry to characterize oligonucleotides immobilized to the surfaces of biochips. Biotinylated oligonucleotides were immobilized to self-assembled monolayers that present a streptavidin layer and then treated with a complementary strand to present short duplexes. Treatment of the surface with 5-methoxysalicylic acid and ammonium citrate matrix allows the individual oligonucleotides to be observed by matrix-assisted laser desorption/iozation and time-of-flight mass spectrometry (MALDI-TOF MS). Examples are shown wherein this method is applied to assays of hybridization, of cleavage by a deoxyribozyme, of a dephosphorylation reaction, and of the adducts formed on treatment of DNA with cis-platin. This work provides an early example of the application of mass spectrometry to DNA biochips and may substantially expand the applications of the now common oligonucleotide arrays.