Toxic compounds are all around us. From household cleaners, to lawn/pest chemicals, to plastic containers and chemically-treated fabrics, we are consistently exposed to varying levels of hazardous chemicals. In a study published in 2011, researchers at UCSF presented data from more than 400 pregnant and non-pregnant women. 100% tested positive for several classes of chemicals, including PCBs. A larger group of more than 1,500 women tested 100% positive for lead. (11) Accurately measuring the levels of a wide range of toxic compounds in our environment and understanding the effects of exposure for developing fetuses, growing children, and adults is vitally important.

Bacterial Toxins

The Anthrax lethal toxin, Botulinum toxin, and Pertussis toxin, which causes whoping cough, are just three of the bacterial toxins in the National Biomonitoring Program run by the Centers for Disease Control (CDC). The CDC’s Division of Laboratory Sciences is working to improve testing methods for priority toxins, including ricin (produced from castor beans), shiga toxin (a bacterial toxin producd by some strains of e. coli), and brevetoxins (produced by Karenia algae). In addition to natural outbreaks, a wide variety of toxins from bacteria, fungi, algae, and plants can be exploited for bioterrorism, increasing the need for rapid tests to quickly characterize toxins in a large number of samples and quantify toxin levels for development and monitoring of treatments. (6) While the toxicity and small size of these molecules can hinder antibody production, aptamers are easily selected against small and toxic molecules, making them ideal affinity reagents for development of laboratory and field-based tests for the detection and quantification of toxins. Researchers at the Tongji University in Shanghai developed a simple, sensitive aptamer-based sensor for the detection of microcystin-LR (MC-LR), a toxin released by cyanobacteria found in eutrophic bodies of water. The aptamer-based sensor demonstrated the selectivity, sensitivity, reproducibility, and stability required for routine testing of real water samples at a reasonable cost. (3)

Heavy Metals

Heavy metals are very dense, naturally-occurring elements found in the earth’s crust.  Arsenic, cadmium, chromium, lead, and mercury are toxic at low levels and pose the greatest health risk. While some heavy metals are released through weathering and volcanic eruptions, most human exposure derives from mining, industrial production, and the domestic and agricultural use of metals. (8) Current methods for detection of heavy metal ions involve complex sample preparation and specialized instrumentation. There is a real need for environmental heavy metal tests that are faster, simpler, and more cost-effective. Researchers at Shanghai University developed a fluorescence-based sensor for the detection of Cadmium, Cd(II) using a DNA aptamer and fluorescence-quenching strand. A structure-switching aptamer which displayed reduced quenching, and increased fluorescence intensity, upon Cd(II) binding was selected. The sensor showed a concentration-dependent increase in fluorescence with a limit of detection of 40nM and was highly selective for Cd(II) in the presence of other heavy metal ions. (10)

Manufacturing Chemicals

Under the Toxic Substances Control Act (TSCA), the EPA maintains a list of all chemical substances manufactured or processed in the US. The list is currently at about 85,000 chemicals. (9) As more studies are conducted, we are learning that long-term exposure to many of these chemicals and / or exposure in utero can be linked to cancer, neurological disorders, and other health issues. While researchers are investigating many classes of chemicals, one example is discussed here. Polychlorinated biphenyls (PCBs) are a class of man-made organic chlorinated hydrocarbons manufactured between 1929 and their ban in 1979. Because they are non-flammable, chemically stable, and have good insulation properties, PCBs were widely used in building materials, heating equipment, and many other industrial applications. PCBs don’t readily break down and are easily transferred between air, soil, and water. They can accumulate in plants and animals. PCBs are carcinogenic and have also been shown to affect neurological development and thyroid function. (7) Because aptamers can be selected to differentiate between very similar small molecules, aptamers have been selected for the detection of multiple PCBs. Researchers in China recently developed an electrochemical sensor for the detection of PCB77 based on an aptamer-modified gold electrode. Differential pulse voltammetry (DPV) was used to detect binding of PCB77 to the aptamer. Change in current was proportional to the increase in PCB77 concentration. When tested with similar co-planar PCBs, the sensor was selective for PCB77. (12)


Researchers are continuing to study suspected links between pesticide exposure and neurological disorders including Parkinson’s disease, Alzheimers, and even ADHD. In a study including over 1,000 children, researchers at Harvard University observed elevated levels of organophosphate byproducts in the urine of children with ADHD. (2) Active principles (AP) in pesticides are carefully tested to determine acceptable daily intake (ADI) levels. Evidence has shown, however, that final formulations containing adjuvants to improve solubility, stability, and penetration can result in toxicities up to 1,000 times greater than the active principle tested alone. (5) As researchers continue to study the effects of pesticides and activists lobby for tighter restrictions, the need for highly selective, sensitive field-based tests is increasing. Due to the poor immunogenicity and toxicity of small molecule pesticides, it is difficult to raise antibodies for assay development. Researchers in China used gold nanoparticles (AuNP) and DNA aptamers for colorimetric detection of six different organophosphorous pesticides in river water in a single assay. They are continuing to work to improve aptamer affinity and assay sensitivity. (1) Researchers in Iran developed a fluorescent biosensor for the detection of the fungicide edifephos (EDI) using graphine oxide sheets and aptamer-conjugated quantum dots. The sensor was highly selective for EDI when tested with other pesticides with similar structures. (4)   While many different types of toxins are present in the environment, they all present a similar challenge: the rapid, sensitive, selective detection of small molecules in the presence of molecules with very similar structures. As shown in the examples above, aptamers are uniquely suited for the selective detection of toxic small molecules. Aptamer-based sensors offer the speed, simplicity, and stability required for field-based detection of a wide range of environmental toxins.

Base Pair has developed several aptamers to environmental toxins and is currently working on aptamers to several additional toxins through an SBIR grant and ongoing collaboration. Contact Base Pair to learn more.


1.  Bai, W. et al. (2015). Gold nanoparticle-based colorimetric aptasensor for rapid detection of six organophosphorous pesticides. Environmental Toxicology and Chemistry. 34(10):2244-49.

2. Bouchard, M. F., et al. (2010). Attention-deficit/hyperactivity disorder and urinary metabolites of organophosphate pesticides. Pediatrics. 125(6):1270-77. Doi:10.1542/peds.2009-3058.

3. Li, X. et al. (2016). A simple highly sensitive and selective aptamer-based colorimetric sensor for environmental toxins microcystin-LR in water samples. Journal of Hazardous Materials. 304:474-80.

4. Majid Arvand and An-zam A. Mirroshandel. (2017). Highly-sensitive aptasensor based on fluorescent resonance energy transfer between L-cysteine capped ZnS quantum dots and graphene oxide sheets for the determination of edifenphos fungicide. Biosensors and Bioelectronics. 96:324-31.

5. Mesnage, R. et al. (2014). Major pesticides are more toxic to human cells than their declared active principles. Biomed Research International. Vol 2014, Article ID 179691.

6. National Biomonitoring Program. CDC.  Accessed June 28, 2017.

7. Polychlorinated Biphenyls (PCBs). Accessed June 29, 2017.

8. Tchounwou, P. B. et al. (2012). Heavy metals toxicity and the environment. Molecular, Clinical, and Environmental Toxicology. V101:133-164.

9. TSCA Chemica Substance Inventory. Accessed June 29, 2017.

10. Wang, H. et al. (2016). Selection and characterization of DNA aptamers for the development of light-up biosensor to detect Cd(11). Talanta. 154:498-503.

11.  Woodruff, T. J. et al. (2011). Environmental chemicals in pregnant women in the United States: NHANES 2003 – 2004. Environmental Health Perspectives. 119(6):878-885.

12. Wu, L. et al. (2016) A novel electrochemical PCB77-binding DNA aptamer biosensor for selective detection of PCB77. Journal of Electroanalytical Chemistry. 771:45-49.