Real-time DNA microarray analysis

Nucleic Acids Research

Volumn 37, Issue 20, 2009, Pages

  Hassibi, Arjang ^a,b   Vikalo, Haris ^b,c   Riechmann, José Luis ^d,e   Hassibi, Babak ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b California Institute of Technology   (United States)

^c The University of Texas at Austin   (United States)

^d CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^e UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOSENSOR; DNA MICROARRAY; DNA TRANSCRIPTION; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE EXPRESSION; HYBRIDIZATION; IN VITRO STUDY; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; GENE EXPRESSION PROFILING; KINETICS; METHODOLOGY; THEORETICAL MODEL; VALIDATION STUDY;

FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE EXPRESSION PROFILING; KINETICS; MODELS, THEORETICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 76149136364     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp675     Document Type: Article

References (53)

1. Hall, E.A.H. (1991) Biosensors. Prentice-Hall, Englewood Cliffs, NJ.
2. Schena, M. (2003) Microarray Analysis. Wiley, New York, NY.
3. SantaLucia, J. Jr., Allawi, H.T. and Seneviratne, P.A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry, 35, 3555-3562.
4. Pease, A.C., Solas, D., Sullivan, E.J., Cronin, M.T., Holmes, C.P. and Fodor, S.P. (1995) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl Acad. Sci. USA, 91, 5022-5026.
5. 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.
6. 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. (1996) Accessing genetic information with high-density DNA arrays. Science, 274, 610-614.
7. Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680.
8. Lockhart, D.J. and Winzeler, E.A. (2000) Genomics, gene expression and DNA arrays. Nature, 405, 827-836.
9. 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.
10. Hardenbol, P., Baner, J., Jain, M., Nilsson, M., Namsaraev, E.A., Karlin-Neumann, G.A., Fakhrai-Rad, H., Ronaghi, M., Willis, T.D., Landegren, U. et al. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol., 21, 673-678.
11. Kennedy, G.C., Matsuzaki, H., Dong, S., Liu, W.M., Huang, J., Liu, G., Su, X., Cao, M., Chen, W., Zhang, J. et al. (2003) Large-scale genotyping of complex DNA. Nat. Biotechnol., 21, 1233-1237.
12. Berg, H.C. (1993) Random Walks in Biology. Princeton University Press, New Jersey, NJ.
13. Levine, N. (1999) Quantum Chemistry. Prentice-Hall, New York, NY.
14. Van Kampen, N.G. (1981) Stochastic Processes in Physics and Chemistry. North-Holland, Amsterdam.
15. Steinfield, J.I., Fransisco, J.S. and Hase, W.L. (1998) Chemical Kinetics and Dynamics, 2nd edn. Prentice-Hall, New York, NY.
16. Hubble, J. (2000) Monte-Carlo simulation of biospecific interactions. Biotechnol. Lett., 22, 1483-1486.
17. Dai, H., Meyer, M., Stepaniants, S., Ziman, M. and Stoughton, R. (2002) Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res., 30, e86.
18. Heaton, R.J., Peterson, A.W. and Georgiadis, R.M. (2001) 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, 3701-3704.
19. Hassibi, A., Vikalo, H. and Hajimiri, A. (2007) On noise processes and limits of performance in biosensors. J. Appl. Phys., 102, 0149091-01490912.
20. Das, S., Vikalo, H. and Hassibi, A. (2009) On scaling laws of biosensors: a stochastic approach. J. Appl. Phys., 105, 102021-102027.
21. Tu, Y., Stolovitzky, G. and Klein, U. (2002) Quantitative noise analysis for gene expression microarray experiments. Proc. Natl Acad. Sci. USA, 99, 14031-14036.
22. Hassibi, A., Zahedi, S., Navid, R., Dutton, R.W. and Lee, T.H. (2005) Biological shot-noise and quantum-limited signal-to-noise ratio in affinity-based biosensors. J. Appl. Phys., 97, 1-10.
23. Linneti, K. and Kondratovich, M. (2004) Partly nonparametric approach for determining the limit of detection. Clin. Chem., 50, 732-740.
24. Shalon, D., Smith, S.J. and Brown, P.O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res., 6, 639-645.
25. Lacowicz, R. (1999) Principles of Fluorescence Spectroscopy, 2nd edn. Plenum, New York, NY.
26. Ota, N., Hirano, K., Warashina, M., Andrus, A., Mullah, B., Hatanaka, K. and Taira, K. (1998) Determination of interactions between structured nucleic acids by fluorescence resonance energy transfer (FRET): selection of target sites for functional nucleic acids. Nucleic Acids Res., 26, 735-743.
27. Okamura, Y., Kondo, S., Sase, I., Suga, T., Mise, K., Furusawa, I., Kawakami, S. and Watanabe, Y. (2000) Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucleic Acids Res., 28, e107.
28. Ghosh, S.S., Eis, P.S., Blumeyer, K., Fearon, K. and Millar, D.P. (1994) Real time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer. Nucleic Acids Res., 22, 3155-3159.
29. Rajendran, M. and Ellington, A.D. (2003) In vitro selection of molecular beacons. Nucleic Acids Res., 31, 5700-5713.
30. Marras, S.A.E., Tyagi, S. and Kramer, F.R. (2006) Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. Clin. Chim. Acta, 363, 48-60.
31. Watterson, J.H., Raha, S., Kotoris, C.C., Wust, C.C., Gharabaghi, F., Jantzi, S.C., Haynes, N.K., Gendron, N.H., Krull, U.J., Mackenzie, A.E. and Piunno, P.A.E. (2004) Rapid detection of single nucleotide polymorphisms associated with spinal muscular atrophy by use of a reusable fibre-optic biosensor. Nucleic Acids Res., 32, e18.
32. Zeng, J., Almadidy, A., Watterson, J. and Krull, U.J. (2003) Interfacial hybridization kinetics of oligonucleotides immobilized onto fused silica surfaces. Sensors Actuat. B, 90, 68-75.
33. Peterson, A.W., Heaton, R.J. and Georgiadis, R.M. (2001) The effect of surface probe density on DNA hybridization. Nucleic Acid Res., 29, 5163-5168.
34. Georgiadis, R., Peterlinz, K.P. and Peterson, A.W. (2000) Quantitative measurements and modeling of kinetics in nucleic acid monolayer films using SPR spectroscopy. J. Am. Chem. Soc., 122, 3166-3173.
35. Abdueva, D., Skvortsov, D. and Tavare, S. (2006) Non-linear analysis of GeneChip arrays. Nucleic Acids Res., 34, e105.
36. Skvortsov, D., Abdueva, D., Curtis, C., Schaub, B. and Tavare, S. (2007) Explaining differences in saturation levels for Affymetrix GeneChip® arrays. Nucleic Acids Res., 35, 4154-4163.
37. Vikalo, H., Hassibi, B. and Hassibi, A. (2008) Modeling and estimation for real-time microarrays. IEEE J. Select. Topics Signal Process. Special Issue Genomic Proteomic Signal Process., 2, 286-296.
38. Homola, J., Yee, S.S. and Gauglitz, G. (1999) Surface plasmon resonance sensors: review. Sensors Actuat. B: Chem., 54, 3-15.
39. Smith, E.A. and Corn, R.M. (2003) Surface plasmon resonance imaging as a tool to monitor biomolecular interactions in an array based format. Appl. Spectrosc., 57, 320A-332A.
40. Chen, S.-J., Su, Y.-D., Hsiu, F.-M., Tsou, C.-Y. and Chen, Y.-K. (2005) Surface plasmon resonance phase-shift interferometry: real-time DNA microarray hybridization analysis. J. Biomed. Optics, 10, 034005-1-034005-6.
41. Bassil, N., Maillart, E., Canva, M., Lévy, Y., Millot, M.-C., Pissard, S., Narwa, R. and Goossens, M. (2003) One hundred spots parallel monitoring of DNA interactions by SPR imaging of polymer-functionalized surfaces applied to the detection of cystic fibrosis mutations. Sensors Actuat. B: Chem., 94, 313-323.
42. Fritz, J., Cooper, E., Gaudet, S., Sorger, P.K. and Manalis, S.R. (2002) Electronic detection of DNA by its intrinsic molecular charge. Proc. Natl Acad. Sci. USA, 99, 14142-14146.
43. Schienle, M. et al. (2004) A fully electronic DNA sensor with 128 positions and in-pixel A/D conversion. J. Solid-State Circuits, 39, 2438-2445.
44. Hassibi, A. and Lee, T.H. (2006) A programmable 0.18-mm CMOS electrochemical sensor microarray for biomedical detection. IEEE Sensors J., 60, 1380-1388.
45. Yamaguchi, S., Shimomura, T., Tatsuma, T. and Oyama, N. (1993) Adsorption, immobilization, and hybridization of DNA studied by the use of quartz crystal oscillators. Anal. Chem., 65, 1925-1927.
46. Su, H., Chong, S. and Thompson, M. (1997) Kinetics of hybridization of interfacial RNA homopolymer studied by thickness-shear mode acoustic wave sensor. Biosens. Bioelectron., 12, 161-167.
47. Savran, C.A., Knudson, S.M., Ellington, A.D. and Manalis, S.R. (2004) Micromechanical detection of proteins using aptamer-based receptor molecules. Anal. Chem., 76, 3194-3198.
48. Towery, R.B., Fawcett, N.C., Zhang, P. and Evans, J.A. (2001) Genomic DNA hybridizes with the same rate constant on the QCM biosensor as in homogeneous solution. Biosens. Bioelectron., 16, 1-8.
49. Stimpson, D.I., Hoijer, J.V., Hsieh, W.T., Jou, C., Gordon, J., Theriault, T., Gamble, R. and Baldeschwieler, J.D. (1995) Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical waveguides. Proc. Natl Acad. Sci. USA, 92, 6379-6383.
50. Bishop, J., Chagovetz, A. and Blair, S. (2007) Competitive displacement of DNA during surface hybridization. Biophys. J., 92, L10-L12.
51. Belosludtsev, Y., Iverson, B., Lemeshko, S., Eggers, R., Wiese, R., Lee, S., Powdrill, T. and Hogan, M. (2001) DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Anal. Biochem., 292, 250-256.
52. Beissbarth, T., Fellenberg, K., Brors, B., Arribas-Prat, R., Boer, J.M., Hauser, N.C., Scheideler, M., Hoheisel, J.D., Schuetz, G., Poustka, A. et al. (2000) Processing and quality control of DNA array hybridization data. Bioinformatics, 16, 1014-1022.
53. Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A. and Vingron, M. (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics, 18, 96-104.