title: DNA millichips as a low-cost platform for gene expression analysis.
abstract: Our goal was to create a DNA chip that is as easy, convenient, and inexpensive as an agarose gel. For a first-generation solution, we describe a low-cost, easy-to-use de novo synthesis oligonucleotide microarray technology that draws on the inherent flexibility of the maskless array synthesizer for in situ synthesis of thousands of photolithographically produced oligonucleotides covalently attached to a microscope slide. The method involves physically subdividing the slide into 1 × 1 mm millichips that are hybridized to fluorescent RNA or DNA of biological origin, in a microfuge tube at an ordinary laboratory benchtop, rather than in dedicated hybridization chambers. Fluorescence intensity is then measured with a standard microscope rather than sophisticated DNA chip scanners. For proof of principle, we measured changes in the transcriptome of Arabidopsis (Arabidopsis thaliana) plants induced by growth in the presence of three major environmental abiotic stresses (temperature, light, and water status), in all possible combinations. Validation by comparison with quantitative reverse transcription PCR showed a high correlation coefficient and analysis of variance indicated a high technical reproducibility. These experiments demonstrate that low-cost DNA millichips can be made and reliably used at the benchtop in a normal laboratory setting, without assistance of core facilities containing costly specialized instrumentation.
authors.affiliation: Department of Biochemistry, Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706, USA.
authors.forename: Kurt W
authors.initials: KW
authors.lastname: Heinrich
authors.forename: Jamison
authors.initials: J
authors.lastname: Wolfer
authors.forename: DongGee
authors.initials: D
authors.lastname: Hong
authors.forename: Melissa
authors.initials: M
authors.lastname: LeBlanc
authors.forename: Michael R
authors.initials: MR
authors.lastname: Sussman
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D000704:Analysis of Variance; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000528:radiation effects; D005453:Fluorescence; D020869:Gene Expression Profiling / Q000191:economics / Q000295:instrumentation* / Q000379:methods; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008027:Light; D008856:Microscopy, Fluorescence; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics* / Q000295:instrumentation / Q000592:standards; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013696:Temperature; D059467:Transcriptome; D014867:Water
chemical_list: D014867:Water; D000040:Abscisic Acid