Skip to main content
Log in

Overview of DNA chip technology

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

DNA chip technology utilizes microscopic arrays (microarrays) of molecules immobilized on solid surfaces for biochemical analysis. Microarrays can be used for expression analysis, polymorphism detection, DNA resequencing, and genotyping on a genomic scale. Advanced arraying technologies such as photolithograpy, micro-spotting and ink jetting, coupled with sophisticated fluorescence detection systems and bioinformatics, permit molecular data gathering at an unprecedented rate. Microarray-based characterization of plant genomes has the potential to revolutionize plant breeding and agricultural biotechnology. This review provides an overview of DNA chip technology, focusing on manufacturing approaches and biological applications.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Ananiev, EV, Riera-Lizarazu O, Rines HW, Phillips RL: Oatmaize chromosome addition lines: a new system for mappingthe maize genome. Proc Natl Acad Sci USA 94: 3524–3529 (1997).

    Google Scholar 

  2. Augenlicht L: United States Patent 4, 981, 783 (1991).

    Google Scholar 

  3. Azpiroz-Leehan R, Feldman KA: T-DNA insertion mutagenesis in Arabidopsis: going back and forth. Trends Genet 13:152–156 (1997).

    Google Scholar 

  4. Bains W, Smith GC: A novel method for nucleic acid sequence determination. J Theor Biol 135: 303–307 (1988).

    Google Scholar 

  5. Bartel PL, Roecklein JA, SenGupta D, Fields S: A protein linkage map of Escherichia coli bacteriophage T7. Nat Genet 12: 72–77 (1996).

    Google Scholar 

  6. Blanchard A: Synthetic DNA arrays. in Genetic Engineering, Principles and Methods, Plenum Press, in press (1998).

  7. Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SPA: Accessing genetic information with high-density DNA arrays. Science 274: 610–614 (1996).

    Google Scholar 

  8. Cronin MT, Fucini RV, Kim SM, Masino RS, Wespi RM, Miyada CG: Cystic Fibrosis Mutation Detection by Hybridization to Light-Generated DNA Probe Arrays. Human Mutation 7: 244–255 (1996).

    Google Scholar 

  9. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM: Use of a cDNA microarray to analyze gene expression patterns in human cancer. Nat Genet 14: 457–460 (1996).

    Google Scholar 

  10. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680–686.

    Google Scholar 

  11. de Saizieu A, Certa U, Warrington J, Gray C, Keck W, Mous J: Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays. Nature Biotech 16: 45–48 (1988).

    Google Scholar 

  12. Donson J, Kearney CM, Hilf ME, Dawson WO: Systemic expression of a bacterial gene by a tobacco mosaic virus-based vector. Proc Natl Acad Sci USA 88: 7204–7208 (1991).

    Google Scholar 

  13. Drmanac R, Crkvenjakov R: Method of sequencing of genomes by hybridization with oligonucleotide probes. Yugoslav patent application 570/87 (1987).

  14. Drmanac RT, Crkvenjakov RB (1993) Method of sequencing of genomes by hybridization of oligonucleotide probes. United States Patent 5,202,231.

  15. Drmanac S, Kita D, Labat I, Hauser B, Schmidt C, Burczak JD, Drmanac R: Accurate sequencing by hybridization for DNA diagnostics and individual genomics. Nature Biotech. 16: 54–58 (1998).

    Google Scholar 

  16. Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature 340: 245–246 (1989).

    Google Scholar 

  17. Fodor SPA, Read JL, Pirrung MC, Stryer L, Tsai Lu A, Solas D: Light-directed, spatially addressable parallel chemical synthesis. Science 251: 767–773 (1991).

    Google Scholar 

  18. Guo Z, Guilfoyle RA, Thiel AJ, Wang R, Smith LM: Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucl Acids Res 22: 5456–5465 (1994).

    Google Scholar 

  19. Hacia JG, Brody LC, Chee MS, Fodor SPA, Collins FS: Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis.Nature Genet 14: 441–447 (1996).

    Google Scholar 

  20. Hardenbol, P, Wang JC, Van Dyke MW: Identification of preferred hTBP DNA binding sites by the combinatorial method REPSA. Nucl Acids Res 25: 3339–3344 (1997).

    Google Scholar 

  21. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW: Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA. 94: 2150–2155 (1997).

    Google Scholar 

  22. Kallioniemi A. Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258: 818–821 (1992).

    Google Scholar 

  23. Khrapko KR, Lysov Yu P, Khorlyn AA, Shick VV, Florentiev VL, Mirzabekov AD: An oligonucleotide hybridization approach to DNA sequencing. Febs Letters: 256: 118–122 (1989).

    Google Scholar 

  24. Khrapko KR, Khorlin AA, Ivanov IB, Chernov BK, Lysov Yu P, Vasilenko SK, Florent'ev VL, Mirzabekov AD: Hybridization of DNA with oligonucleotides immobilized in gel: a convenient method for detecting single base substitutions. Mol Biol 25: 581–591 (1991).

    Google Scholar 

  25. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, Gingeras TR: Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Med. 2: 793–799 (1996).

    Google Scholar 

  26. Lamture JB, Beattie KL, Burke BE, Eggers MD, Ehrlich, DJ, Fowler R, Hollis MA, Kosicki BB, Reich RK, Smith SR, Varma RS, Hogan ME: Direct detection of nucleic acid hybrdication on the surface of a charge coupled device. Nucl Acids Res 22: 2121–2125 (1994).

    Google Scholar 

  27. Lashkari DA, DeRisi JL, McCusker, JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW: Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94: 13057–13062 (1997).

    Google Scholar 

  28. Liu Y G, Mitsukawa N, Oosumi T, Whittier RF: Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J 8: 457–463 (1995).

    Google Scholar 

  29. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression Monitoring by Hybridization to High-Density Oligonucleotide Arrays. Nature Biotechnol 14: 1675–1680 (1996).

    Google Scholar 

  30. Maier E, Meier-Ewert S, Ahmadi AR, Curtis J, Lehrach H: Application of robotic technology to automated sequence fingerprint analysis by oligonucleotide hybridisation. J Biotechnol 35: 191–203 (1994).

    Google Scholar 

  31. Maskos U, Southern EM: Oligonucleotide hybridizations on glass supports: a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesised in situ. Nucl Acids Res 20: 1679–1684 (1992).

    Google Scholar 

  32. McCusker JH, Clemons KV, Stevens DA, Davis RW: Genetic characterization of pathogenic Saccharomyces cerevisiae isolates. Genetics 136: 1261–1269 (1994).

    Google Scholar 

  33. Monfort A, Vicient CM, Raz R, Puigdomenech P, Martinez-Izquierdo JA: Molecular analysis of a putative transposable retroelement from the Zea genus with internal clusters of tandem repeats. DNA Res 2: 255–261 (1995).

    Google Scholar 

  34. Nelson SF, McCusker JH, Sander MA, Kee Y, Modrich P, Brown PO: Genomic mismatch scanning: a new approach to genetic linkage mapping. Nature Genet 4: 11–18 (1993).

    Google Scholar 

  35. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SPA: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 91: 5022–5026 (1994).

    Google Scholar 

  36. Raz R, Puigdomenech P, Martinez-Izquierdo JA: A new family of repetitive nucleotide sequences is restricted to the genus Zea. Gene 105: 151–158 (1991).

    Google Scholar 

  37. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, Bennetzen JL: Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765–768 (1996).

    Google Scholar 

  38. Sapolsky RJ, Lipshutz RJ: Mapping Genomic Library Clones Using Oligonucleotide Arrays. Genomics 33: 445–456 (1996).

    Google Scholar 

  39. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470 (1995).

    Google Scholar 

  40. Schena M: Genome Analysis with Gene Expression Microarrays. BioEssays 18: 427–431 (1996).

    Google Scholar 

  41. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW: Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 93: 10614–10619 (1996).

    Google Scholar 

  42. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW: Microarrays: Biotech's discovery platform for functional genomics. Trends Biotech 16: 301–306 (1998).

    Google Scholar 

  43. Schena M, Davis RW: Parallel Analysis with Biological Chips. in PCR Methods Manual, Academic Press, San Diego, in press (1998).

    Google Scholar 

  44. Shalon D, Smith SJ, Brown PO: A DNA micro-array system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6: 639–645 (1996).

    Google Scholar 

  45. Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW: Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genet 14: 450–456 (1996).

    Google Scholar 

  46. Southern E: Method and apparatus for analysing polynucleotide sequences. European Patent Specification PCT/GB89/00460 (1989).

  47. Southern EM: DNA chips: analysing sequence by hybridization to oligonucleotides on a large scale. Trends Genet 12: 110–115 (1996).

    Google Scholar 

  48. Winter G, Milstein C: Man-made antibodies. Nature 349: 293–299 (1991).

    Google Scholar 

  49. Wodicka L, Dong H, Mittmann M, Ho M-H, Lockhart DJ: Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotech. 15: 1359–1367 (1997).

    Google Scholar 

  50. Yershov G, Barsky V, Belgovsky A, Kirillov E, Kreindlin E, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S, Mirzabekov A: DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci USA 93: 4913–4918 (1996).

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lemieux, B., Aharoni, A. & Schena, M. Overview of DNA chip technology. Molecular Breeding 4, 277–289 (1998). https://doi.org/10.1023/A:1009654300686

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1009654300686

Navigation