Fluorescence Quenching Causes Systematic Dye Bias in Microarray Experiments Using Cyanine Dye

  • Jeon, Ho-Sang (Department of Molecular Science and Technology, Ajou University) ;
  • Choi, Sang-Dun (Department of Molecular Science and Technology, Ajou University)
  • Published : 2007.09.30

Abstract

The development of microarray technology has facilitated the understanding of gene expression profiles. Despite its convenience, the cause of dye-bias that confounds data interpretation in dual-color DNA microarray experiments is not well known. In order to economize time and money, it is necessary to identify the cause of dye bias, since designing dye-swaps to reduce the dye-specific bias tends to be very expensive. Hence, we sought to determine the reliable cause of systematic dye bias after treating murine macrophage RAW 264.7 cells with 2-keto-3-deoxyoctonate (KDO), interferon-beta $(IFN-{\beta})$, and 8-bromoadenosine (8-BR). To find the cause of systematic dye bias from the point of view of fluorescence quenching, we examined the correlation between systematic dye bias and the proportion of each nucleotide in mRNA and oligonucleotide probe sequence. Cy3-dye bias was highly correlated with the proportion of adenines. Our results support the fact that systematic dye bias is affected by fluorescence quenching of each feature. In addition, we also found that the strength of fluorescence quenching is based on not only dye-dye interactions but also dye-nucleotide interactions as well.

References

  1. Atherton, S.J. and Harriman, A (1993). Photochemistry of intercalated methylene blue: Photoinduced hydrogen atom abstraction from guanine and adenine. J. Am. Chem. Soc. 115, 1816-1822 https://doi.org/10.1021/ja00058a028
  2. Cooper, J.P. and Hagerman, P.J. (1990). Analysis of fluorescence energy transfer in duplex and branched DNAmolecules. Biochem. 29, 9261-9268 https://doi.org/10.1021/bi00491a022
  3. Cox, W.G., Beaudet, M.P., Agnew, J.Y., and Ruth, J.L. (2004). Possible sources of dye-related signal correlation bias in two-color DNA microarray assays. Anal. Biochem. 331, 243-254 https://doi.org/10.1016/j.ab.2004.05.010
  4. Dobbin, K.K., Kawasaki, E.S., Petersen, D.W., and Simon, R.M. (2005). Characterizing dye bias in microarray experiments. Bioinformatics 21,2430-2437 https://doi.org/10.1093/bioinformatics/bti378
  5. Dombkowski, A.A, Thibodeau, B.J., Starcevic, S.L., and Novak, R.F. (2004). Gene-specific dye bias in microarray reference designs. Federation ofEuropean Biochemical Societies Letters 560, 120-124 https://doi.org/10.1016/S0014-5793(04)00083-3
  6. Fukui, K. et al. (1999). Distance dependence of electron transfer in acridine-intercalated DNA. J. Photochem. Photobiol. B: BioI. 50, 18-27 https://doi.org/10.1016/S1011-1344(99)00063-9
  7. Han, J., Lee, H., Nguyen, N.Y., Beaucage, S.L., and Puri, R.K. (2005). Novel multiple 5'-amino-modified primer for DNA microarrays. Genomics 86, 252-258 https://doi.org/10.1016/j.ygeno.2005.04.009
  8. Heinlein, T. et al. (2003). Photoinduced electron transfer between fluorescent dyes and guanosine residues in DNA-hairpins. J. Phys. Chem. 107,7957-7964 https://doi.org/10.1021/jp0348068
  9. Herz, A.H. (1974). Dye-dye interactions ofcyanines in solution and at AgBr surfaces. Photogr. Sci. Eng. 18, 323-335
  10. Marras, S.A.E. et al. (2002). Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30, e122 https://doi.org/10.1093/nar/gnf121
  11. Martin-Magniette, M.L. et al. (2005). Evaluation ofthe genespecific dye bias in cDNA microarray experiments. Bioinformatics 21, 1995-2000 https://doi.org/10.1093/bioinformatics/bti302
  12. Randolph, J.B. and Waggoner, A.S. (1997). Stability, specificity and fluorescence brightness of mUltiply-labeled fluorescent DNA probes. Nucleic Acids Research. 25, 2923-2929 https://doi.org/10.1093/nar/25.14.2923
  13. Rosenzweig, B.A. et al. (2004). Dye-bias correction in duallabeled cDNA microarray gene expression measurements. Environmental Health Perspectives 112, 480-487 https://doi.org/10.1289/ehp.6694
  14. Seidel, C.A.M. et al. (1996). Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies., J. Phys. Chem. 100, 5541-5553 https://doi.org/10.1021/jp951507c
  15. Spiess, A.N. et al. (2003). Amplified RNA degradation in T7-amplification methods results in biased microarray hybridizations. BMC Genomics 4, 44 https://doi.org/10.1186/1471-2164-4-44
  16. Steenken, S. and Jovanovic, S.V. (1997). How easily oxidizable is DNA? One-electron reduction potentials of adenosine and guanosine radicals in aqueous solutions. J. Am. Chem. Soc. 119, 617-618 https://doi.org/10.1021/ja962255b
  17. Tseng, G.C. et al. (2001). Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations, and assessment of gene effects. Nucleic Acids Res. 29, 2549-2557 https://doi.org/10.1093/nar/29.12.2549
  18. Uchida, S. et al. (2005). Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatiallydependent, and print-order biases. DNA Res. 12, 1-7 https://doi.org/10.1093/dnares/12.1.1
  19. Walter, N.G. and Burke, J.M. (1997). Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates. RNA 3, 392-404
  20. Yang, Y.H. et al. (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res. 30, e15 https://doi.org/10.1093/nar/30.4.e15