PCR amplification on microarrays of gel immobilized oligonucleotides

This invention relates to polymerase chain reaction (PCR) amplification using microarrays of gel immobilized oligonucleotide primers in gel pads on a microchip (also known as a biochip). The invention also relates to a method of separating the individual gel pads on a microchip by immersing pads in a hydrophobic liquid, such as oil, as well as to novel structures for the gel pads which improves the efficacy of the PCR reactions in the immersed microchip. The primers can be selectively activated, inactivated, or detached from the gel matrix, and can be selected to perform combinatorial or multiplex PCR amplification. The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.