Using a microfluidic device for 1 μl DNA microarray hybridization in 500 s

Nucleic Acids Research

Volumn 33, Issue 8, 2005, Pages 1-11

  Wei, Cheng Wei ^a,b   Cheng, Ji Yen ^a,c   Huang, Chih Ting ^a   Yen, Meng Hua ^a,b   Young, Tai Horng ^b  

^a RESEARCH CENTER FOR APPLIED SCIENCES   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c NONE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

GLASS; BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; DNA BINDING PROTEIN; ONCOPROTEIN; TAL1 PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

ACUTE LYMPHOCYTIC LEUKEMIA; ARTICLE; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; DNA MICROARRAY; GENE TARGETING; GROWTH RATE; MICROFLUIDICS; MISMATCH REPAIR; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; T CELL LEUKEMIA; EVALUATION; GENETICS; INSTRUMENTATION; METHODOLOGY; MICROFLUIDIC ANALYSIS; TIME;

BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTORS; DNA-BINDING PROTEINS; MICROFLUIDIC ANALYTICAL TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; PROTO-ONCOGENE PROTEINS; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 27244444889     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni078     Document Type: Article

References (31)

1. Wang, H.Y., Malek, R.L., Kwitek, A.E., Greene, A.S., Luu, T.V., Behbahani, B., Frank, B., Quackenbush, J. and Lee, N.H. (2003) Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol., 4, R5.
2. Stillman, B.A. and Tonkinson, J.L. (2001) Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal. Biochem., 295, 149-157.
3. Sterrenburg, E., Turk, R., Boer, J.M., van Ommen, G.B. and den Dunnen, J.T. (2002) A common reference for cDNA microarray hybridizations. Nucleic Acids Res., 30, e116.
4. Bhanot, G., Louzoun, Y., Zhu, J.H. and DeLisi, C. (2003) The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys. J., 84, 124-135.
5. Sartor, M., Schwanekamp, J., Halbleib, D., Mohamed, I., Karyala, S., Medvedovic, M. and Tomlinson, C.R. (2004) Microarray results improve significantly as hybridization approaches equilibrium. Biotechniques, 36, 790-796.
6. Lukacs, G.L., Haggie, P., Seksek, O., Lechardeur, D., Freedman, N. and Verkman, A.S. (2000) Size-dependent DNA mobility in cytoplasm and nucleus. J. Biol. Chem., 275, 1625-1629.
7. Bard, A.J. and Larry, R.F. (1980) Electrochemical Methods - Fundamental and Applications. John Wiley & Sons Inc., New York.
8. Whitney, A.R., Diehn, M., Popper, S.J., Alizadeh, A.A., Boldrick, J.C., Relman, D.A. and Brown, P.O. (2003) Individuality and variation in gene expression patterns in human blood. Proc. Natl Acad. Sci. USA, 100, 1896-1901.
9. Wang, J., Robinson, J.F., Khan, H.M., Carter, D.E., McKinney, J., Miskie, B.A. and Hegele, R.A. (2004) Optimizing RNA extraction yield from whole blood for microarray gene expression analysis. Clin. Biochem., 37, 741-744.
10. Cheek, B.J., Steel, A.B., Torres, M.P., Yu, Y.Y. and Yang, H. (2001) Chemiluminescence detection for hybridization assays on the flow-thru chip a three-dimensional microchannel biochip. Anal. Chem., 73, 5777-5783.
11. Adey, N.B., Lei, M., Howard, M.T., Jensen, J.D., Mayo, D.A., Butel, D.L., Coffin, S.C., Moyer, T.C., Slade, D.E., Spute, M.K. et al. (2002) Gains in sensitivity with a device that mixes microarray hybridization solution in a 25-mu m-thick chamber. Anal. Chem., 74, 6413-6417.
12. Liu, Y.J. and Rauch, C.B. (2003) DNA probe attachment on plastic surfaces and microfluidic hybridization array channel devices with sample oscillation. Anal. Biochem., 317, 76-84.
13. Wang, Y., Vaidya, B., Farquar, H.D., Stryjewski, W., Hammer, R.P., McCarley, R.L., Soper, S.A., Cheng, Y.W. and Barany, F. (2003) Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations. Anal. Chem., 75, 1130-1140.
14. Cheng, J.-Y., Wei, C.-W., Hsu, K.-H. and Young, T.-H. (2002) In Baba, Y., Shoji, S. and Berg, A.v.d. (eds), Micro Total Analysis Systems 2002. Kluwer, Nara, Japan, Vol. 1, pp. 458-460.
15. Erickson, D., Li, D.Q. and Krull, U.J. (2003) Modeling of DNA hybridization kinetics for spatially resolved biochips. Anal. Biochem., 317, 186-200.
16. Yaralioglu, G.G., Wygant, I.O., Marentis, T.C. and Khuri-Yakub, B.T. (2004) Ultrasonic mixing in microfluidic channels using integrated transducers. Anal. Chem., 76, 3694-3698.
17. Stroock, A.D., Dertinger, S.K., Ajdari, A., Mezic, I., Stone, H.A. and Whitesides, G.M. (2002) Chaotic mixer for microchannels. Science, 295, 647-651.
18. Tice, J.D., Lyon, A.D. and Ismagilov, R.F. (2004) Effects of viscosity on droplet formation and mixing in microfluidic channels. Anal. Chim. Acta, 507, 73-77.
19. Ottino, J.M. (1989) The Kinematics of Mixing: Stretching, Chaos, and Transport. Cambridge University, Cambridge.
20. Tice, J.D., Song, H., Lyon, A.D. and Ismagilov, R.F. (2003) Formation of droplets and mixing in multiphase microfluidics at low values of the Reynolds and the capillary numbers. Langmuir, 19, 9127-9133.
21. Song, H., Bringer, M.R., Tice, J.D., Gerdts, C.J. and Ismagilov, R.F. (2003) Experimental test of scaling of mixing by chaotic advection in droplets moving through microfluidic channels. Appl. Phys. Lett., 83, 4664-4666.
22. Song, H., Tice, J.D. and Ismagilov, R.F. (2003) A microfluidic system for controlling reaction networks in time. Angew. Chem.-Int. Edit., 42, 768-772.
23. Cheng, J.-Y., Wei, C.-W., Hsu, K.-H. and Young, T.-H. (2004) Direct-write laser micromachining and universal surface modification of PMMA for device development. Sens. Actuator B-Chem., 99, 186-196.
24. Zammatteo, N., Jeanmart, L., Hamels, S., Courtois, S., Louette, P., Hevesi, L. and Remacle, J. (2000) Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal. Biochem., 280, 143-150.
25. Peterson, A.W., Heaton, R.J. and Georgiadis, R.M. (2001) The effect of surface probe density on DNA hybridization Nucleic Acids Res., 29, 5163-5168.
26. Fixe, F., Dufva, M., Telleman, P. and Christensen, C.B.V. (2004) Functionalization of poly(methyl methacrylate) (PMMA) as a substrate for DNA microarrays. Nucleic Acids Res., 32, e9.
27. Franssen-van Hal, N.L., Vorst, O., Kramer, E., Hall, R.D. and Keijer, J. (2002) Factors influencing cDNA microarray hybridization on silylated glass slides. Anal Biochem., 308, 5-17.
28. Aboul-ela, F., Koh, D., Tinoco, I., Jr and Martin, F.H. (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res., 13, 4811-4824.
29. Ikuta, S., Takagi, K., Wallace, R.B. and Itakura, K. (1987) Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing different single mismatched base-pairs. Nucleic Acids Res., 15, 797-811.
30. 't Hoen, P.A., de Kort, F., van Ommen, G.J.B. and den Dunnen, J.T. (2003) Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Res., 31, e20.
31. Tsai, C.C., Chung, Y.D., Lee, H.J., Chang, W.H., Suzuku, Y., Sugano, S. and Lin, J.Y. (2003) Large-scale sequencing analysis of the full-length cDNA library of human hepatocellular carcinoma. J. Biomed. Sci., 10, 636-643.