Dissociation analysis in polymerase chain reaction and 1X SSC buffer as a prerequisite for selection of 13mer microarray probe sets with uniform hybridization behavior

Molecular Biotechnology

Volumn 29, Issue 1, 2005, Pages 1-9

  Pfunder, Monika ^a   Frey, Juerg E ^a  

^a Swiss Federal Research Station for Fruit Growing Viticulture and Horticulture   (Switzerland)

Author keywords

Chip; Cross hybridization; Diagnostics; Dissociation curve; False positives; Melting temperature; Microarray; Probe design; Tm

Indexed keywords

ALGORITHMS; DIAGNOSIS; MELTING;

CHIP; CROSS-HYBRIDIZATION; DISSOCIATION CURVE; MELTING TEMPERATURE; MICROARRAY;

BIOTECHNOLOGY;

BUFFER;

ALGORITHM; ARTICLE; DISSOCIATION; DNA HYBRIDIZATION; DNA MICROARRAY; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PREDICTION;

EID: 26444546906     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1385/mb:29:1:01     Document Type: Article

References (25)

1. Shchepinov, M. S., Case-Green, S. C., and Southern, E. M. (1997) Steric factors influencing hybridization of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25, 1155-1161.
2. Bodrossy, L., Stralis-Pavese, N., Murrell, J. C., Radajewski, S., Weilharter, A., and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5, 566-582.
3. Southern, E., Mir, K., and Shchepinov, M. (1999) Molecular interactions on microarrays. Nature Genet. 21 Suppl., 5-9.
4. Zhang, L., Miles, M. F., and Aldape, K. D. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol. 21, 818-821.
5. 4 endloops: evaluation of the nearest-neighbor stacking interactions in DNA. Biopolymers 32, 849-864.
6. Wahl, G. M., Berger, S. L., and Kimmel, A. R. (1987) Molecular hybridization of immobilized nucleic acids: theoretical concepts and practical considerations. Methods Enzymol. 152, 399-407.
7. 2+, deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin. Chem. 47, 1956-1961.
8. Fotin, A. V., Drobyshev, A. L., Proudnikov, D. Y., Perov, A. N., and Mirzabekov, A. D. (1998) Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res. 26, 1515-1521.
9. Matveeva, O. V., Shabalina, S. A., Nemtsov, V. A., Tsodikov, A. D., Gesteland, R. F., and Atkins, J. F. (2003) Thermodynamic calculations and statistical correlations for oligo-probes design. Nucleic Acids Res. 31, 4211-4217.
10. Breslauer, K. J., Frank, R., Blöcker, H., and Marky, L. A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83, 3746-3750.
11. Sugimoto, N., Nakano, S., Yoneyama, M., and Honda, K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res. 24, 4501-4505.
12. SantaLucia J Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460-1465.
13. Gotoh, O. and Tagashira, Y. (1981) Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 20, 1033-1042.
14. Stralis-Pavese, N., Sessitsch, A., Weilharter, A., et al. (2004) Optimisation of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6, 347-363.
15. Reyes-López, M. Á., Méndez-Tenorio, A., Maldonado-Rodríguez, R., Doktycz, M. J., Fleming, J. T., and Beattie, K. L. (2003) Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribo-nucleotide microarrays and virtual hybridization. Nucleic Acids Res. 31, 779-789.
16. Doktycz, M. J., Morris, M. D., Dormady, S. J., Beattie, K. L., and Jacobson, K. B. (1995) Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability. J. Biol. Chem. 270, 8439-8445.
17. Peyret, N., Seneviratne, P. A., Allawi, H. T., and SantaLucia J Jr. (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A*A, C*C, G*G, and T*T mismatches. Biochemistry 38, 3468-3477.
18. Loy, A., Lehner, A., Lee, N., et al. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68, 5064-5081.
19. Pfunder, M., Holzgang, O., and Frey, J. E. (2004) Development of microarray-based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase I vs. cytochrome b as genetic markers. Mol. Ecol. 13, 1277-1286.
20. Lipsky, R. H., Mazzanti, C. M., Rudolph, J. G., et al. (2001) DNA melting analysis for detection of single nucleotide polymorphisms. Clin. Chem. 47, 635-644.
21. Vasiliskov, V. A., Prokopenko, D. V., and Mirzabekov, A. D. (2001) Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29, 2303-2313.
22. Owczarzy, R., Dunietz, I., Behlke, M. A., Klotz, I. M., and Walder, J. A. (2003) Thermodynamic treatment of oligonucleotide duplex-simplex equilibria. Proc. Natl. Acad. Sci. USA 100, 14840-14845.
23. Owczarzy, R., Vallone, P. M., Gallo, F. J., Paner , T. M., Lane, M. J., and Benight, A. S. (1997) Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 217-239.
24. Bommarito, S., Peyret, N., and SantaLucia J Jr. (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28, 1929-1934.
25. Drobyshev, A. L., Machka, C., Horsch, M., et al. (2003) Specificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies. Nucleic Acids Res. 31, e1-1.