A photochemical/chemical direct method of synthesizing high-performance deoxyribonucleic acid chips for rapid and parallel gene analysis

We propose a new method of synthesizing perfect sets of probe deoxyribonucleic acid (DNA) on a chip to produce high-performance DNA chips. Two different methods of direct synthesis are combined to generate single strands of probe DNA on the chip's surface. The first is an area-specific photosensitive synthesis of DNA that exploits photolithographic techniques. The other is a non-photosensitive synthesis of DNA. This is a much more reliable method of synthesis and is used for the remaining sequences of probe DNA, i.e. those outside the photosynthesis region. In the synthesis procedure, photosensitive reagents are only used to make certain variations to the probe DNA and areas with several kinds of probe DNA (4 to 16 nucleotides in length) were synthesized on each 50 μm² of the probe. We examined the application of our DNA chip to single-nucleotide polymorphism (SNP) analysis, which is used to check for the mutant promoters of liver cancer. We found that no non-specific signals from a hybridization reaction of the sample DNA variants appeared and that this DNA chip successfully discriminated slight differences in genomic (DNA) information at the single base-pair level.