Salt concentration effects on equilibrium melting curves from DNA microarrays

Biophysical Journal

Volumn 99, Issue 6, 2010, Pages 1886-1895

  Fuchs, J ^a   Fiche, J B ^a   Buhot, A ^a   Calemczuk, R ^a   Livache, T ^a  

^a Departement de Recherches Fondamentales sur la Matiere Condensee CEA Grenoble   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77957365304     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.07.002     Document Type: Article

References (38)

1. Lockhart, D. J., H. L. Dong, E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14: 1675-1680.
2. Levicky, R., and A. Horgan. 2005. Physicochemical perspectives on DNA microarray and biosensor technologies. Trends Biotechnol. 23: 143-149.
3. Li, F. G., and G. D. Stormo. 2001. Selection of optimal DNA oligos for gene expression arrays. Bioinformatics. 17: 1067-1076.
4. Livache, T., B. Fouque, G. Mathis. 1998. Polypyrrole DNA chip on a silicon device: example of hepatitis C virus genotyping. Anal. Biochem. 255: 188-194.
5. Halperin, A., A. Buhot, and E. B. Zhulina. 2006. Hybridization at a surface: the role of spacers in DNA microarrays. Langmuir. 22: 11290-11304.
6. Peterson, A. W., R. J. Heaton, and R. M. Georgiadis. 2001. The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 29: 5163-5168.
7. Halperin, A., A. Buhot, and E. B. Zhulina. 2006. On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions. J. Phys. Condens. Matter. 18: S463-S490.
8. Bhanot, G., Y. Louzoun., C. DeLisi. 2003. The importance of thermodynamic equilibrium for high throughput gene expression arrays. Biophys. J. 84: 124-135.
9. Chan, V., D. J. Graves, and S. E. McKenzie. 1995. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys. J. 69: 2243-2255.
10. Livshits, M. A., and A. D. Mirzabekov. 1996. Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleo-tides. Biophys. J. 71: 2795-2801.
11. Schuck, P. 1997. Use of surface plasmon resonance to probe the equilibrium and dynamic aspects of interactions between biological macro-molecules. Annu. Rev. Biophys. Biomol. Struct. 26: 541-566.
12. Vainrub, A., and B. M. Pettitt. 2002. Coulomb blockage of hybridization in two-dimensional DNA arrays. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 66: 041905.
13. Halperin, A., A. Buhot, and E. B. Zhulina. 2004. Sensitivity, specificity, and the hybridization isotherms of DNA chips. Biophys. J. 86: 718-730. (Pubitemid 38209520)
14. Halperin, A., A. Buhot, and E. B. Zhulina. 2004. Hybridization isotherms of DNA microarrays and the quantification of mutation studies. Clin. Chem. 50: 2254-2262.
15. Zhang, Y., D. A. Hammer, and D. J. Graves. 2005. Competitive hybridization kinetics reveals unexpected behavior patterns. Biophys. J. 89: 2950-2959.
16. Bishop, J., S. Blair, and A. M. Chagovetz. 2006. A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants. Biophys. J. 90: 831-840.
17. Binder, H. 2006. Thermodynamics of competitive surface adsorption on DNA microarrays. J. Phys. Condens. Matter. 18: S491-S523.
18. Bishop, J., C. Wilson, S. Blair. 2007. Competitive displacement of DNA during surface hybridization. Biophys. J. 92: L10-L12.
19. Bishop, J., A. M. Chagovetz, and S. Blair. 2008. Kinetics of multiplex hybridization: mechanisms and implications. Biophys. J. 94: 1726-1734.
20. Fish, D. J., M. T. Horne, A. S. Benight. 2007. Multiplex SNP discrimination. Biophys. J. 92: L89-L91.
21. Peterlinz, K. A., R. M. Georgiadis, M. J. Tarlov. 1997. Observation of hybridization and dehybridization of thiol-tethered DNA using two-color surface plasmon resonance spectroscopy. J. Am. Chem. Soc. 119: 3401-3402.
22. Meunier-Prest, R., S. Raveau, . , N. Latruffe. 2003. Direct measurement of the melting temperature of supported DNA by electrochemical method. Nucleic Acids Res. 31: e150.
23. Gong, P., and R. Levicky. 2008. DNA surface hybridization regimes. Proc. Natl. Acad. Sci. USA. 105: 5301-5306.
24. Irving, D., P. Gong, and R. Levicky. 2010. DNA surface hybridization: comparison of theory and experiment. J. Phys. Chem. B. 114: 7631-7640.
25. Halperin, A., A. Buhot, and E. B. Zhulina. 2005. Brush effects on DNA chips: thermodynamics, kinetics, and design guidelines. Biophys. J. 89: 796-811.
26. Foret, L., and A. Würger. 2004. Disjoining pressure and algebraic screening of discrete charges at interfaces. J. Phys. Chem. B. 108: 5791-5799.
27. SantaLucia, Jr., J., and D. Hicks. 2004. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33: 415-440.
28. Fiche, J. B., J. Fuchs, . , T. Livache. 2008. Point mutation detection by surface plasmon resonance imaging coupled with a temperature scan method in a model system. Anal. Chem. 80: 1049-1057.
29. Guedon, P., T. Livache., Y. Levy. 2000. Characterization and optimization of a real-time, parallel, label-free, polypyrrole-based DNA sensor by surface plasmon resonance imaging. Anal. Chem. 72: 6003-6009.
30. Malic, L., T. Veres, and M. Tabrizian. 2009. Biochip functionalization using electrowetting-on-dielectric digital micr of luidics for surface plasmon resonance imaging detection of DNA hybridization. Biosens. Bioelectron. 24: 2218-2224.
31. Fiche, J. B., A. Buhot, . , T. Livache. 2007. Temperature effects on DNA chip experiments from surface plasmon resonance imaging: isotherms and melting curves. Biophys. J. 92: 935-946.
32. Fuchs, J., D. Dell'Atti, T. Livache. 2010. Effects of formamide on the thermal stability of DNA duplexes on biochips. Anal. Biochem. 397: 132-134.
33. Fotin, A. V., A. L. Drobyshev, A. D. Mirzabekov. 1998. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res. 26: 1515-1521.
34. Urakawa, H., S. El Fantroussi, . , D. A. Stahl. 2003. Optimization of single-base-pair mismatch discrimination in oligonucleotide microar-rays. Appl. Environ. Microbiol. 69: 2848-2856.
35. Marcy, Y., P. Y. Cousin, . , J. C. Avarre. 2008. Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays. Biotechniques. 44: 913-920.
36. Watterson, J. H., P. A. E. Piunno, . , U. J. Krull. 2000. Effects of oligonucleotide immobilization density on selectivity of quantitative transduction of hybridization of immobilized DNA . Langmuir. 16: 4984-4992.
37. Moreira, B. G., Y. You, R. Owczarzy. 2005. Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem. Biophys. Res. Commun. 327: 473-484.
38. Biswal, S. L., D. Raorane, . , A. Majumdar. 2006. Nanomechanical detection of DNA melting on microcantilever surfaces. Anal. Chem. 78: 7104-7109.