Fabrication of DNA microarrays using unmodified oligonucleotide probes

Microarrays printed on glass slides are often constructed by covalently lin king oligonucleotide probes to a derivatized surface. These procedures typi cally require relatively expensive amine- or thiol-modified oligonucleotide probes that add considerable expense to larger arrays. We describe a syste m by which unmodified oligonucleotide probes are bound to either non-deriva tized or epoxy-silane-derivatized glass slides. Biotinylated PCR products a re heat denatured, hybridized to the arrays, and detected using an enzymati c amplification system. Unmodified probes appear to detach from the slide s urface at high pH (>10.0), suggesting that hydrogen bonding plays a signifi cant role in probe attachment. Regardless of surface preparation, high temp erature (up to 65 degreesC) and low ionic strength (deionized water) do not disturb probe attachment; hence, the fabrication method described here is suitable for a wide range of hybridization stringencies and conditions. We illustrate kinetics of room temperature hybridizations for probes attached to nonderivatized slides, and we demonstrate that unmodified probes produce hybridization signals equal to amine-modified, covalently bound probes. Ou r method provides a cost-effective alternative to conventional attachment s trategies that is particularly suitable for genotyping PCR products with nu cleic acid microarrays.