Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing

Analytical Biochemistry

Volumn 380, Issue 1, 2008, Pages 84-90

  Mocanu, Daniel ^a   Kolesnychenko, Aleksey ^a   Aarts, Sonja ^a   Dejong, Amanda T ^a   Pierik, Anke ^a   Coene, Wim ^a   Vossenaar, Erik ^a   Stapert, Henk ^a  

^a PHILIPS RESEARCH LABORATORIES   (Netherlands)

Author keywords

DNA hybridization; Flowthrough microarray; Kinetic analysis; Melting curves

Indexed keywords

ASSOCIATION REACTIONS; BACTERIA; BIOASSAY; DISSOCIATION; DNA; DNA SEQUENCES; KINETICS; MELTING; POLYMERASE CHAIN REACTION; PROBES; STAPHYLOCOCCUS AUREUS; THERMOANALYSIS;

ASSOCIATION RATE CONSTANTS; DISSOCIATION RATE CONSTANT; DNA HYBRIDIZATION; FLOWTHROUGH; KINETIC ANALYSIS; MELTING CURVES; QUANTITATIVE INFORMATION; STAPHYLOCOCCUS EPIDERMIDIS;

RATE CONSTANTS;

DOUBLE STRANDED DNA;

ARTICLE; DNA HYBRIDIZATION; DNA MICROARRAY; INCUBATION TIME; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS; THERMODYNAMICS;

STAPHYLOCOCCUS AUREUS; STAPHYLOCOCCUS EPIDERMIDIS;

EID: 46749122211     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.05.034     Document Type: Article

References (25)

1. Veer L.G., Dal H., Vijver M.J., He Y.D., Hart A.A., Mao M., Peterse H.L., Kooy K., Marton M.J., Witteveen A.T., Schreiber G.J., Kerkhoven R.M., Roberts C., and Linsely P.S. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415 (2002) 530-535
2. Tang Y., Procop G.W., and Persing D.H. Molecular diagnostics of infectious diseases. Clin. Chem. 43 (1997) 2021-2038
3. Gingeras T.R., Higuchi R., Kricka L.J., Lo Y.M., and Witter C.T. Fifty years of molecular (DNA/RNA) diagnostics. Clin. Chem. 51 (2005) 661-671
4. Benoit V., Steel A., Torres M., Yu Y., Yang H., and Cooper J. Evaluation of three-dimensional microchannel glass biochips for multiplexed nucleic acid fluorescence hybridization assays. Anal. Chem. 73 (2001) 2412-2420
5. Cheek B.J., Steel A.B., Torres M.P., Yu Y.Y., and Yang H. Chemiluminescence detection for hybridization assays on the flow-thru chip, a three-dimensional microchannel biochip. Anal. Chem. 73 (2001) 5777-5783
6. Wu Y., Kievit P., Vahlkamp L., Pijnenburg D., Smit M., Dankers M., Melcers D., Stax M., Boender P.J., and Ingham C. Quantitative assessement of a novel flow-through porous microarray for the rapid analysis of gene expression profiles. Nucleic Acids Res. 32 (2004) e123
7. Beuningen R., 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
8. Shchepinov M.S., Case-Green S.C., and Southern E.M. Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25 (1997) 1155-1161
9. Vainrub A., and Pettitt B.M. Coulomb blockage of hybridization in two-dimensional DNA arrays. Phys. Rev. E 66 (2002) 041905
10. Halperin A., Buhot A., and Zhulina E.B. Sensitivity, specificity, and the hybridization isotherms of DNA chips. Biophys. J. 86 (2004) 718-730
11. Peterson A.W., Heaton R.J., and Georgiadis R.M. The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 29 (2001) 5163-5168
12. Saiki R.K., Walsh S., Levenson H.C., and Erlich H.A. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc. Natl. Acad. Sci. 86 (1989) 6230-6234
13. Savitzky A., and Golay M.J.E. Smoothing and differentiation of data by simplified least squares procedures. Anal. Chem. 36 (1964) 1627-1639
14. SantaLucia J., Alawi H.T., and Seneviratne A.P. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35 (1996) 3555-3562
15. SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Biochemistry 95 (1998) 1460-1465
16. Steel A.B., Herne T.M., and Tarlov M.J. Electrochemical quantitation of DNA immobilized on gold. Anal. Chem. 70 (1998) 4670-4677
17. Sinha R.P., and Hader D.P. UV-induced damage and repair: a review. Photochem. Photobiol. Sci. 1 (2002) 225-236
18. Heaton R.J., Peterson A.W., and Georgiadis R.M. Electrostatic surface plasmon resonance: direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free discrimination of base mismatches. Proc. Natl. Acad. Sci. USA 98 (2001) 3701-3704
19. Henry M.R., Stevens P.W., Sun J., and Kelso D.M. Real-time measurements of DNA hybridization on microparticles with fluorescence resonance transfer. Anal. Biochem. 276 (1999) 204-214
20. Parkhurst K.M., and Parkhurst L.J. Kinetic studies by fluorescence resonance energy transfer employing a double-labeled oligonucleotide: hybridization to the oligonucleotide complement and to single-stranded DNA. Biochemistry 34 (1995) 285-292
21. Tawa K., and Knoll W. Mismatching base-pair dependence of the kinetics of DNA-DNA hybridization studied by surface plasmon fluorescence spectroscopy. Nucleic Acids Res. 32 (2004) 2372-2377
22. Halperin A., Buhot A., and Zhulina E.B. On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions. J. Phys.: Condens. Matter. 18 (2006) S463-S490
23. Smith S.B., Cui Y.J., and Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271 (1996) 795-799
24. Vainrub A., and Pettitt B.M. Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. Biopolymers 68 (2003) 265-270
25. Halperin A., Buhot A., Zhulina E.B., and thermodynamics B.e.o.D.c.:. kinetics and design guidelines. Biophys. J. 89 (2005) 796-811