Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using gibbs free energy in a nearest-neighbor model

Journal of Physical Chemistry B

Volumn 111, Issue 48, 2007, Pages 13583-13590

  Weckx, Stefan ^a,e   Carton, Enrico ^b,c,d   De Vuyst, Luc ^e   Van Hummelen, Paul ^a,d  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b CNRS   (France)

^c UNIV LILLE   (France)

^d UNIVERSITY OF LEUVEN   (Belgium)

^e VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GIBBS FREE ENERGY; LANGMUIR PROBES; MICROARRAYS; THERMODYNAMICS; THREE DIMENSIONAL;

CROSS-HYBRIDIZATION; HYBRIDIZATION INTENSITY; LANGMUIR MODEL; MICROARRAY HYBRIDIZATIONS;

OLIGONUCLEOTIDES;

EID: 37249055563     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp075197x     Document Type: Article

References (29)

1. Kane, M. D.; Jatkoe, T. A.; Stumpf, C. R.; Lu, J., Thomas, J. D.; Madore, S. J. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 2000, 28, 4552-4557.
2. Hughes, T. R.; Mao, M.; Jones, A. R.; Burchard, J., Marton, M. J.; Shannon, K. W.; Lefkowitz, S. M.; Ziman, M.; Schelter, J. M.; Meyer, M. R. et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 2001, 19, 342-347.
3. Relogio, A.; Schwager, C.; Richter, A.; Ansorge, W.; Valcarcel, J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res. 2002, 30, e51.
4. Tiquia, S. M.; Wu, L.; Chong, S. C.; Passovets, S.; Xu, D.; Xu, Y.; Zhou, J. Evaluation of 50mer oligonucleotide arrays for detecting microbial populations in environmental samples. BioTechniques 2004, 36, 664-675.
5. Chou, C. C.; Chen, C. H.; Lee, T. T.; Peck, K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res. 2004, 32, e99.
6. Fotin, A. V.; Drobyshev, A. L.; Proudnikov, D. Y.; Perov, A. N.; Mirzabekov, A. D. Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res. 1998, 26, 1515-1521.
7. Dai, H.; Meyer, M.; Stepaniants, S.; Ziman, M.; Stoughton, R. Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res. 2002, 30, e86.
8. Dorris, D. R.; Nguyen, A.; Gieser, L.; Lockner, R.; Lublinsky, A., Patterson, M., Touma, E., Sendera, T. J.; Elghanian, R.; Mazumder, A. Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios. BMC Biotechnol. 2003, 5, e6.
9. Nielsen, H. B,; Wernersson, R.; Knudsen, S. Design of oligonucle-otides for microarrays and perspectives for design of multi-transcriptome arrays. Nucleic Acids Res. 2003, 31, 3491-3496.
10. Zhang, L.; Miles, M. F.; Aldape, K. D. A model of molecular interactions on short oligonucleotides microarrays. Nat. Biotechnol. 2003, 21, 818-821.
11. Luebke, K. J.; Balog, R. P.; Garner, H. R. Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. Nucleic Acids Res. 2003, 31, 750-758.
12. Hekstra, D.; Taussig, A. R.; Magnasco, M.; Naef, F.. Absolute mRNA concentrations from sequence-specific calibration of oligonucleotides arrays. Nucleic Acids Res. 2003, 31, 1962-1968.
13. Held, G. A., Grinstein, G.; Tu, Y. Modeling of DNA microarray data by using physical properties of hybridization. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7575-7580.
14. Matveeva, O. V.; Shabalina, S. A.; Nemtsov, V. A.; Tsodikov, A. D.; Gesteland, R. F.; Atkins J. F. Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res. 2003, 31, 4211-4217.
15. He, Z.; Wu, L.; Li, X.; Fields, M. W.; Zhou, J. Empirical establishment of oligonucleotide probe design criteria. Appl. Environ. Microbiol. 2005, 71, 3753-3760.
16. Wick, L. M.; Rouillard, J. M.; Whittam, T. S.; Gulari, E.; Tiedje, J. M.; Hashsham, S. A. On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res. 2006, 34, e26.
17. Liebich, J.; Schadt, C. W.; Chong, S. C.; He, Z.; Rhee, S. K.; Zhou, J. Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl. Environ. Microbiol. 2006, 72, 1688-1691.
18. Pozhitkov, A.; Noble, P. A.; Domazet-Lošo, T., Noite, A. W.; Sonnenberg, R.; Staehler, P.; Beier, M.; Tautz, D. Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res. 2006, 34, e66.
19. Zhang, L.; Wu, C.; Carta, R.; Zhao, H. Free energy of DNA duplex formation on short oligonucleotide microarrays. Nucleic Acids Res. 2007, 35, e18.
20. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I. Nucleic acids: Structures, Properties, and Functions; University Science Books: Sausalito, CA, 2000.
21. SantaLucia, J., Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 1460-1465.
22. Peyret, N.; Seneviratne, P. A.; Allawi, H. T.; SantaLucia, J., Jr. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. Biochemistry 1999, 38, 3468-3477.
23. SantaLucia, J.; Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 2004, 33, 415-440.
24. Hall, T. S.; Pancoska, P.; Riccelli, P. V.; Mandell, K.; Benight, A. S. Sequence contect and thermodynamic stability of a single base pair mismatch in short deoxyoligonucleotide duplexes. J. Am. Chem. Soc. 2001, 123, 11811-11812.
25. Halperin, A.; Buhot, A.; Zhulina, E. B. On the hybridization isotherms of DNA microarrays: Langmuir model and its extensions. J. Phys.: Condens. Matter 2006, 18, 463-490.
26. Carlon, E.; Heim, T. Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays. Physica A (Amsterdam, The Netherlands) 2006, 362, 433-449.
27. Guo, Z.; Guilfoyle, R. A.; Thiel, A. J.; Wang, R.; Smith, L. M. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res. 1994, 22, 5456-5465.
28. Shchepinov, M. S.; Case-Green, S. C.; Southern, E. M. Steric factors influencing hybridization of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 1997, 25, 1155-1161.
29. van Bakel, H.; Holstege, F. G P. In control: Systematic assessement of microarray performance. EMBO Rep. 2004, 5, 964-969.