Superfund Research Program

The Development of DNA Biomarkers for Ecological Risk Assessment

Release Date: 12/01/1999

Damage to DNA is considered a key beginning step in the sequence of events that lead to cancer. Among the causes of DNA injury are reactive oxygen species such as the hydroxyl radical, which bind readily to the carriers of genetic information, nucleotide bases, to form DNA adducts. Sometimes these slight DNA modifications are overlooked by cellular defense mechanisms, especially when large amounts of reactive oxygen species overwhelm the cell's antioxidant defenses. When this happens, genetic mutations can occur that are transferred to future generations of cells, and subsequent events can lead to the development of cancer. In addition to the creation of base injury, reactive oxygen species can alter the phosphodiester and sugar portion of the molecule, thus potentially creating more extensive structural changes.

Exposure to environmental contaminants appears to be a significant source of reactive oxygen species and free radical-induced DNA damage. For example, wild fish living in chemically contaminated bodies of water have elevated levels of hydroxy-DNA adducts in comparison to those from relatively clean bodies of water. Because damage to DNA is a reliable indicator of exposure to toxic chemicals, quantification of this damage in fish can provide a means for assessing the risk of genotoxic injury in chemically-contaminated bodies of water.

Researchers at the Pacific Northwest Research Institute - a partner in the University of Washington Superfund Basic Research Program - have been developing DNA biomarkers and related predictive models for cancer risk assessment. One method, which can measure radical-induced and other structural alterations in DNA of fish, was included in a patent recently granted by the U.S. Patent Office. The technique is based on Fourier Transform Infrared (FT-IR) spectroscopy and advanced statistical techniques, such as principal components analysis (PCA).

The combination of PCA with FT-IR spectroscopy has proven to be a powerful tool for characterizing differences in the chemical makeup of DNA samples from normal and exposed fish. Because the magnitude of response between fish from contaminated and clean areas is high, the potential exists for using DNA structural changes in fish as a biomarker to monitor the presence and biological effects of genotoxic chemicals in the environment.

How this method works is that FT-IR spectroscopy records the interaction of infrared radiation with DNA, measuring both the frequencies at which a DNA sample absorbs radiation and the intensities of the absorption. The resulting IR spectrum provides specific information about the DNA samples, which is then analyzed by PCA, a statistical technique that is applied to the spectral data to discover the variation among spectra and the relation of this variation to subgroups, such as cancerous versus non-cancerous forms of DNA.

Recent activities have been focused on reducing the amount of DNA required for the FT-IR analysis so that non-destructive tissue biopsies can be performed on fish, allowing them to be returned to the environment.

This technology is proving to be a sensitive means for identifying changes in DNA relating to environmental contaminant exposures and for discriminating between environments that have varying degrees and types of contamination. The researchers believe this technique and the data acquired through it will form a solid basis for formulating cancer prediction models and undertaking remedial actions at Superfund sites.

For More Information Contact:

Donald C. Malins
Pacific NW Research Institute
Biochemical Oncology Program
Seattle, Washington 98122
Phone: 206-726-1240

To learn more about this research, please refer to the following sources:

  • Malins DC, Polissar NL, Gunselman SJ. 1997. Infrared spectral models demonstrate that exposure to environmental chemicals leads to new forms of DNA. Proc Natl Acad Sci U S A 94(8):3611-3615. PMID:9108025
  • Malins DC, Polissar NL, Su Y, Gardner HS, Gunselman SJ. 1997. A new structural analysis of DNA using statistical models of infrared spectra. Nat Med 3(8):927-930. PMID:9256288
  • Malins DC, Polissar NL, Garner MM, Gunselman SJ. 1996. Mutagenic DNA base modifications are correlated with lesions in nonneoplastic hepatic tissue of the English sole carcinogenesis model. Cancer Res 56(24):5563-5565. PMID:8971153

To receive monthly mailings of the Research Briefs, send your email address to