A dimensionless number analysis of the hybridization process in diffusion- and convection-driven DNA microarray systems

Journal of Biotechnology

Volumn 123, Issue 4, 2006, Pages 381-396

  Pappaert, Kris ^a   Desmet, Gert ^a  

^a VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

Convective hybridization; Hybridization; Microarray; Modeling

Indexed keywords

CONCENTRATION (PROCESS); DIFFUSION; MATHEMATICAL MODELS; PARAMETER ESTIMATION;

DAMKOHLER NUMBER DA; HYBRIDIZATION RATES; MEASURABLE PARAMETERS; MICROARRAYMIC SYSTEMS;

DNA;

ARTICLE; DIFFUSION; DNA DETERMINATION; DNA HYBRIDIZATION; DNA MICROARRAY; EXPERIMENTAL DESIGN; GEOMETRY; MATHEMATICAL MODEL; PARAMETER; PRIORITY JOURNAL; STATISTICAL ANALYSIS; THEORETICAL STUDY; THERMODYNAMICS; BIOLOGICAL MODEL; KINETICS; MATHEMATICAL COMPUTING; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION;

DIFFUSION; KINETICS; MODELS, GENETIC; NUCLEIC ACID HYBRIDIZATION; NUMERICAL ANALYSIS, COMPUTER-ASSISTED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33747044446     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2005.12.025     Document Type: Article

References (28)

1. Abramowicz, and Stegun I. Handbook of Mathematical Functions (1965), Dover Publications, Inc., New York
2. Bier F.F., and Kleinjung F. Feature-size limitations of microarray technology-a critical review. Fresenius J. Anal. Chem. 371 2 (2001) 151-156
3. Brown P.O., and Botstein D. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21 1 Suppl. (1999) 33-37
4. Chan V., Graves D.J., and McKenzie S.E. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys. J. 69 6 (1995) 2243-2255
5. Erickson D., Li D., and Krull U.J. Modeling of DNA hybridization kinetics for spatially resolved biochips. Anal. Biochem. 317 (2003) 186-200
6. Gadgil C., Yeckel A., Derby J.J., and Hu W.S. A diffusion-reaction model for DNA microarray assays. J. Biotechnol. 114 1/2 (2004) 31-45
7. Hacia J.G. Resequencing and mutational analysis using oligonucleotide microarrays. Nat. Genet. 21 1 Suppl. (1999) 42-47
8. Hagan M.F., and Chakraborty A.K. Hybridization dynamics of surface immobilized DNA. J. Chem. Phys. 120 10 (2004) 4958-4968
9. Henry M.R., Stevens P.W., Sun J., and Kelso D. Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer. Anal. Biochem. 276 (1999) 204-224
10. Kassegne S.K., Reese H., Hoko D., Heller M.J., and Madou M.J. Numerical modeling of transport and accumulation of DNA on electronically active biochips. Sens. Actuators B 94 (2003) 81-98
11. Levicky R., and Horgan A. Physicochemical perspectives on DNA microarray and biosensor technologies. Trends Biotechnol. 23 (2005) 143-149
12. Myszka D.G., He X., Dembo M., Morton T.A., and Goldstein B. Extending the range of rate constants available from BIACORE: interpreting mass transport-influenced binding data. Biophys. J. 75 (1998) 583-594
13. Pappaert K., Vanderhoeven J., Dutta B., Van Hummelen P., Clicq D., Baron G.V., and Desmet G. Enhancement of DNA micro-array analysis using a shear-driven micro-channel flow system. J. Chromatogr. A 1014 (2003) 1-9
14. Pappaert K., Van Hummelen P., Vanderhoeven J., Baron G.V., and Desmet G. Diffusion-reaction modelling of DNA hybridization kinetics on biochips. Chem. Eng. Sci. 58 (2003) 4921-4930
15. Pappaert K., Biesemans J., Clicq D., Vankrunkelsven S., and Desmet G. Measurements of diffusion coefficients in 1D micro-and nanochannels using shear-driven flows. Lab on a Chip 5 (2005) 1104-1110
16. Sadana A., and Vo-Dinh A. Single- and dual-fractal analysis of hybridization binding kinetics: biosensor applications. Biotechnol. Progr. 14 5 (1998) 782-790
17. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative Mmonitoring of the gene-expression patterns with a complementary-DNA microarray. Science 270 5235 (1995) 467-470
18. Schena M., Shalon D., Heller R., Chai A., Brown P.O., and Davis R.W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. U.S.A. 93 20 (1996) 10614-10619
19. Shalon D., Smith S.J., and Brown P.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6 7 (1996) 639-645
20. Stenberg M., Stiblert L., and Nygren H. External diffusion in solid-phase immunoassays. J. Theor. Biol. 120 (1986) 129-140
21. Stillman B.A., and Tonkinson J.L. Expression microarray hybridization kinetics depend on length of the immobilized DNA but are independent of immobilization substrate. Anal. Biochem. 295 (2001) 149-157
22. Toegl A., Kirchner R., Gauer C., and Wixforth A. Enhancing results of microarray hybridizations through micro-agitation. J. Biomol. Tech. 14 (2003) 197-204
23. Van Beuningen R., Van Damme H., Boender P., Bastiaensen N., Chan A., and Kievits T. Fast and specific hybridization using flow-through microarrays on porous metal oxide. Clin. Chem. 47 (2001) 1931-1933
24. Vanderhoeven J., Pappaert K., Dutta B., Van Hummelen P., and Desmet G. DNA microarray enhancement using a continuously and discontinuously rotating micro-chamber. Anal. Chem. 77 14 (2005) 4474-4480
25. Vijayendran R.A., Ligler F.S., and Leckband D.E. A computational reaction-diffusion model for the analysis of transport-limited kinetics. Anal. Chem. 71 (1999) 5405-5412
26. Vontel S., Ramakrishnan A., and Sadana A. An evaluation of hybridization kinetics in biosensors using a single-fractal analysis. Biotechnol. Appl. Biochem. 31 Pt. 2 (2000) 161-170
27. Walas S.M. Modeling with Differential Equations in Chemical Engineering (1991), Butterworth-Heinemann, London
28. Wylie C.R., and Barret L.C. Advanced Engineering Mathematics. 6th ed. (1995), McGraw-Hill, Inc., New York