Comparison of hybridization behavior between double and single strand of targets and the application of asymmetric PCR targets in cDNA microarray

Journal of Biochemistry and Molecular Biology

Volumn 37, Issue 4, 2004, Pages 439-444

  Wei, Qing ^a   Liu, Sanzhen ^b   Huang, Jianfeng ^b   Mao, Xueying ^b   Chu, Xiaohui ^b   Wang, Yu ^a   Qiu, MinYan ^b   Mao, Yumin ^a   Xie, Yi ^a   Li, Yao ^a  

^a FUDAN UNIVERSITY   (China)

^b Shanghai BioStar Genechip Institute   (China)

Author keywords

Asymmetric PCR; cDNA microarray; Hybridization; Sensitivity; Single stranded DNA

Indexed keywords

DOUBLE STRANDED DNA; SINGLE STRANDED DNA;

ARTICLE; DNA MICROARRAY; GENETIC CODE; HYBRIDIZATION; RELIABILITY; REPRODUCIBILITY; VALIDATION PROCESS;

EID: 4444358681     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: 10.5483/bmbrep.2004.37.4.439     Document Type: Article

References (24)

1. Aimee, M., Dudley, J. A., Steffen, M. A. and George M. (2002) Church. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99, 7554-7559.
2. DeRisi, J., Penland, L., Brown, P. O., Bittner, M. L., Meltzer, P. S., Ray, M., Chen, Y., Su, Y. A. and Trent, J. M. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457-460.
3. Epstein, C. B., Hale, W. and Butow, R. A. (2001) Numerical methods for handling uncertainty in microarray data: an example analyzing perturbed mitochondrial function in yeast. Methods Cell Biol. 65, 439-452.
4. Farbrother, P., Muller, S., Noegel, A. A. and Eithinger, L. (2002) Comparison of probe preparation methods for DNA microarrays. Biotechniques 33, 884-888.
5. Kinjo, M. (1998) Detection of asymmetric PCR products in homogeneous solution by fluorescence correlation spectroscopy. Biotechniques 25, 706-715.
6. Kooperberg, C., Fazzio, T. G., Delrow, J. J. and Tsukiyama, T. (2002) Improved background correction for spotted DNA microarrays. J. Comput. Biol. 9, 55-66.
7. Li, Y., Li, Y., Tang, R., Xu, H., Qiu, M., Chen, Q., Chen, J., Fu, Z., Ying, K., Xie, Y. and Mao, Y. (2002) Discovery and analysis of hepatocellular carcinoma genes using cDNA microarrays. J. Cancer Res. Clin. Oncol. 128, 369-379.
8. Mao, H. and Rosenthal, K. S. (1999) Synthesis of radioactive single-stranded DNA probes using asymmetrical PCR and oligonucleotide random priming. Biotechniques 27, 674-678.
9. Miki, R., Kadota, K., Bono, H., Mizuno, Y., Tomaru, Y., Carninci, P., Itoh, M., Shibata, K., Kawai, J., Konno, H., Watanabe, S., Sato, K., Tokusumi, Y., Kikuchi, N., Ishii, Y., Hamaguchi, Y., Nishizuka, I., Goto, H., Nitanda, H., Satomi, S., Yoshiki, A., Kusakabe, M., DeRisi, J. L., Eisen, M. B., Iyer, V. R., Brown, P. O., Muramatsu, M., Shimada, H., Okazaki, Y. and Hayashizaki, Y. (2001) Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc. Natl. Acad. Sci. USA 98, 2199-2204.
10. Nallur, G., Luo, C., Fang, L., Cooley, S., Dave, V., Lambert, J., Kukanskis, K., Kingsmore, S., Lasken, R. and Schweitzer, B. (2001) Signal amplification by rolling circle amplification on DNA microarrays. Nucleic Acids Res. 29, E118.
11. Peterson, A. W., Heaton, R. J. and Georgiadis, R. M. (2001) The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 29, 5163-5168.
12. Quackenbush, J. (2002) Microarray data normalization and transformation. Nat. Genet. 32, 496-501.
13. Salin, H., Vujasinovic, T., Mazurie, A., Maitrejean, S., Menini, C., Mallet, J. and Dumas, S. (2002) A novel sensitive microarray approach for differential screening using probes labelled with two different radioelements. Nucleic Acids Res. 30, 17.
14. Sambrook, J., Fritsch, E. F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, New York, USA.
15. Schena, M., Heller, R. A., Theriault, T. P., Konrad, K., Lachenmeier, E. and Davis, R. W. (1998) Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16, 301-306.
16. 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.
17. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O. and Davis, R. W. (1996) Parallel human genome analysis: Microarray based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93, 10614-10619.
18. Shchepinov, M. S., Case-Green, S. C. and Southern, E. M. (1997) Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays. Nucleic Acids Res. 25, 1155-1161.
19. Southern, E., Mir, K. and Shchepinov, M. (1999) Molecules interactions on microarrays. Nat. Genet. 21, 5-9.
20. Stears, R. L., Martinsky, T. and Schena, M. (2003) Trends in microarray analysis. Nat. Med. 9, 140-145.
21. Wang, E., Miller, L. D., Ohnmacht, G. A., Liu, E. T. and Marincola, F. M. (2000) High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol. 18, 457-459.
22. Wang, H. Y., Malek, R. L., Kwitek, A. E., Greene, A. S., Luu, T. V., Behbahani, B., Frank, B., Quackenbush, J. and Lee, N. H. (2003) Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. Genome Biol. 4, 5.
23. Winzeler, E. A., Schena, M. and Davis, R. W. (1999) Fluorescence-based expression monitoring using microarrays. Methods Enzymol. 306, 3-18.
24. Yue, H., Eastman, P. S., Wang, B. B., Minor, J., Doctolero, M. H., Nuttall, R. L., Stack, R., Becker, J. W., Montgomery, J. R., Vainer, M. and Johnston, R. (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nucleic Acids Res. 29, E41-1.