Electrochemically directed synthesis of oligonucleotides for DNA microarray fabrication

Nucleic Acids Research

Volumn 33, Issue 14, 2005, Pages 1-7

  Egeland, Ryan D ^a,b   Southern, Edwin M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACID; OLIGONUCLEOTIDE;

ARTICLE; BASE MISPAIRING; CHEMICAL PROCEDURES; CHEMICAL REACTION; CONTROLLED STUDY; DNA MICROARRAY; DNA SYNTHESIS; ELECTROCHEMICAL ANALYSIS; MICROELECTRODE; OXIDATION; PRIORITY JOURNAL; CHEMISTRY; ELECTROCHEMISTRY; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBE; OXIDATION REDUCTION REACTION; SYNTHESIS; TECHNIQUE;

ACIDS; ELECTROCHEMISTRY; METHODS; MICROELECTRODES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; OXIDATION-REDUCTION;

EID: 24044497609     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gni117     Document Type: Article

References (35)

1. Lockhart,D.J., Dong,H.L., Byrne,M.C., Follettie,M.T., Gallo,M.V., Chee,M.S., Mittmann,M., Wang,C.W., Kobayashi,M., Horton,H. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
2. Schena,M., Shalon,D., Heller,R., Chai,A., Brown,P.O. and Davis,R.W. (1996) Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA, 93, 10614-10619.
3. Schena,M., Shalon,D., Davis,R.W. and Brown,P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
4. Chee,M., Yang,R., Hubbell,E., Berno,A., Huang,X.C., Stern,D., Winkler,J., Lockhart,D.J., Morris,M.S. and Fodor,S.P.A. (1996) Accessing genetic information with high-density DNA arrays. Science, 274 610-614.
5. Cargill,M., Altshuler,D., Ireland,J., Sklar,P., Ardlie,K., Patil,N., Shaw,N., Lane,C.R., Lim,E.P., Kalyanaraman,N. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nature Genet., 22, 231-238.
6. Halushka,M.K., Fan,J.B., Bentley,K., Hsie,L., Shen,N., Weder,A., Cooper,R., Lipshutz,R. and Chakravarti,A. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nature Genet., 22, 239-247.
7. Mir,K.U. and Southern,E.M. (2000) Sequence variation in genes and genomic DNA: Methods for large-scale analysis. Ann. Rev. Genom. Hum. Genet., 1, 329-360.
8. Wang,D.G., Fan,J.B., Siao,C.J., Berno,A., Young,P., Sapolsky,R., Ghandour,G., Perkins,N., Winchester,E., Spencer,J. et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280, 1077-1082.
9. Southern,E.M., Milner,N. and Mir,K.U. (1997) Discovering antisense reagents by hybridization of RNA to oligonucleotide arrays. Ciba Foundation Symposium, 209, 38-44.
10. Southern,E., Mir,K. and Shchepinov,M. (1999) Molecular interactions on microarrays. Nature Genet., 21, 5-9.
11. Southern,E.M., Case-Green,S.C., Elder,J.K., Johnson,M., Mir,K.U., Wang,L. and Williams,J.C. (1994) Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res., 22, 1368-1373.
12. Bulyk,M.L., Gentalen,E., Lockhart,D.J. and Church,G.M. (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol., 17, 573-577.
13. Brenner,S., Johnson,M., Bridgham,J., Golda,G., Lloyd,D.H., Johnson,D., Luo,S.J., McCurdy,S., Foy,M., Ewan,M. et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol., 18, 630-634.
14. Singh-Gasson,S., Green,R.D., Yue,Y.J., Nelson,C., Blattner,F., Sussman,M.R. and Cerrina,F. (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol., 17, 974-978.
15. Fodor,S.P.A. (1997) DNA sequencing - Massively parallel genomics. Science, 277, 393.
16. Gao,X.L., Yu,P.L., LeProust,E., Sonigo,L., Pellois,J.P. and Zhang,H. (1998) Oligonucleotide synthesis using solution photogenerated acids. J. Am. Chem. Soc., 120, 12698-12699.
17. Hughes,T.R., Linsley,P., Marton,M., Roberts,C., Jones,A., Stoughton,R., Shoemaker,D., Blanchard,A., Phillips,J., Ziman,M. et al. (2000) Large-scale discovery of gene functions using an ink-jet oligonucleotide synthesizer and a compendium of DNA microarray expression profiles. Am. J. Hum. Genet., 67, 212.
18. Ferguson,J., Steemers,F., Schauer,C., Michael,K., Taylor,L. and Walt,D.R. (2000) Randomly ordered, high-density, fiber-optic, microsensor-array sensors. Abstr. Pap. Am. Chem. Soc., 219, 235.
19. Giegrich,H., Eisele-Buhler,S., Hermann,C., Kvasyuk,E., Charubala,R. and Pfleiderer,W. (1998) New photolabile protecting groups in nucleoside and nucleotide chemistry - synthesis, cleavage mechanisms and applications. Nucleosides Nucleotides, 17, 1987-1996.
20. McGall,G.H., Barone,A.D., Diggelmann,M., Fodor,S.P.A., Gentalen,E. and Ngo,N. (1997) The efficiency of light-directed synthesis of DNA arrays on glass substrates. J. Am. Chem. Soc., 119, 5081-5090.
21. Gait,M.J. (1984)Oligonucleotide Synthesis: A Practical Approach. IRL Press, Oxford.
22. Southern,E.M., Maskos,U. and Elder,J.K. (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics, 13, 1008-1017.
23. Case-Green,S.C., Mir,K.U., Pritchard,C.E. and Southern,E.M. (1998) Analysing genetic information with DNA arrays. Curr. Opin. Biotechnol., 2, 404-410.
24. Stimpson,D.I., Cooley,P.W., Knepper,S.M. and Wallace,D.B. (1998) Parallel production of oligonucleotide arrays using membranes and reagent jet printing. BioTechniques, 25, 886-890.
25. Okamoto,T., Suzuki,T. and Yamamoto,N. (2000) Microarray fabrication with covalent attachment of DNA using bubble jet technology. Nat. Biotechnol., 18, 438-441.
26. Hughes,T.R., Mao,M., Jones,A.R., Burchard,J., Marton,M., Shannon,K.W., Lefkowitz,S.M., Ziman,M. and Schelter,J. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol., 19, 342-347.
27. Gray,D.E., Case-Green,S.C., Fell,T.S., Dobson,P.J. and Southern,E.M. (1997) Ellipsometric and interferometric characterization of DNA probes immobilized on a combinatorial array. Langmuir, 13, 2833-2842.
28. Polushin,N.N., Morocho,A.M., Chen,B.C. and Cohen,J.S. (1994) On the rapid deprotection of synthetic oligonucleotides and analogs. Nucleic Acids Res., 22, 639-645.
29. Livache,T., Bazin,H., Caillat,P. and Roget,A. (1998) Electroconducting polymers for the construction of DNA or peptide arrays on silicon chips. Biosens. Bioelectron., 13, 629-634.
30. Montgomery,D. (1998) United States patent no. PCT/US97/11463.
31. Egeland,R.D., Marken,F. and Southern,E.M. (2002) An electrochemical redox couple activitated by microelectrodes for confined chemical patterning of surfaces. Anal. Chem., 74, 1590-1596.
32. Hecker,K.H., Green,S.M. and Kobayashi,K. (2000) Analysis and purification of nucleic acids by ion-pair reversed-phase high-performance liquid chromatography. J. Biochem. Biophys. Methods 46, 83-93.
33. Beaucage,S.L. and Iyer,R.P. (1992) Advances in the synthesis of oligonucleotides by the phosphoramidite approach. Tetrahedron, 48, 2223-2311.
34. Septak,M. (1996) Kinetic studies on depurination and detritylation of CPG-bound intermediates during oligonucleotide synthesis. Nucleic Acids Res., 24, 3053-3058.
35. 2, and glucose distributions by an array of 400 individually addressable microelectrodes. Anal. Chem., 67, 1164-1170.