A DNA‐based assay for toxic chemicals in wastewater

Abstract

Chemical toxicants, particularly metal ions, are a major contaminant in global waterways. Live-organism bioassays used to monitor chemical toxicants commonly involve measurements of activity or survival of a freshwater cladoceran (Ceriodaphnia dubia) or light emitted by the marine bacterium Vibrio fischeri, used in the commercial Microtox® bioassay. Here we describe a novel molecule-based assay system employing DNA as the chemical biosensor. Metals bind to DNA, causing structural changes that expel a bound (intercalated) fluorescent reporter dye. Analyses of test data using 48 wastewater samples potentially contaminated by metal ions show that the DNA-dye assay results correlate with those from C. dubia and Microtox bioassays. All three assays exhibit additive, antagonistic, and synergistic responses that cannot be predicted by knowing individual metal concentrations. Analyses of metals in these samples imply the presence of chemical toxicants other than metal ions. The DNA-dye assay is robust, has a 12-month shelf life, and is only slightly affected by sample pH in the range 4 to 9. The assay is completed in a matter of minutes, and its portability makes it well suited as a screening assay for use in the field. We conclude that the DNA-dye test is a surrogate bioassay suitable for screening chemical toxicity.

Sensitivity limits of biosensors used for the detection of metals in drinking water

“…It is crucial that testing technology move away from infrastructure-intensive sensors such as atomic absorption spectroscopy (Vil'pan et al 2005), cold vapour atomic fluorescence spectrometry (Yan et al 2002), inductively coupled plasma mass spectrometry (Moreton and Delves 1998), electrochemical methods (Liu et al 2009), gas chromatography (Fitzgerald and Gill 1979) and high-performance liquid chromatography (Balarama Krishna et al 2007). There is a need to develop new portable and rapid biosensors that can be used even by school children with minimal training (Foreman et al 2011). However, important considerations of biosensors designed for use in rural areas of developing countries are low cost, and a long shelve half-life of certain reagents (e.g., enzymes and oligonucleotides) (Fernandez-Lafuente 2009; Gibson et al 1992;Panjan et al 2017).…”

“…The widespread industrial and domestic uses of these bioassays are typically limited by high costs, long assay times, the requirement for specialised infrastructure, ethical considerations, significant data variability and low specificity towards specific metals. Recently, SYBR Green I-based sensors such as HazardScreen® (HS®) assay have been used to assess additive, synergistic or antagonistic toxicity effects of heavy metals in water (Foreman et al 2011). Strong correlations of results have been shown between the Microtox® sensor, the Ceriodaphnia dubia bioassays and the HazardScreen DNA-based sensor.…”

“…Strong correlations of results have been shown between the Microtox® sensor, the Ceriodaphnia dubia bioassays and the HazardScreen DNA-based sensor. Until recently, bioassays have been unable to identify the individual toxicants that contribute to the overall toxicity of complex aqueous solutions (Chang et al 1981;Foreman et al 2011). Recently developed sensors use a variety of methods of quantifying the toxicity of trace quantities of metals in drinking water.…”

A review of heavy metal cation binding to deoxyribonucleic acids for the creation of chemical sensors

“…Ni has been recently shown to intercalate between BPs in DNA (Wu et al 2012). Destabilisation of dsDNA by Ni may be used to dislodge reporter molecules (such as fluorescent dyes (Foreman et al 2011)) into solution from within the DNA molecule to provide a measurable change in quantum yield/signalling. The question to ask is whether DNA conformation changes are significantly varied between metals to facilitate differentiation between Ni(II), Mn(II) and Co(II) and other metals in solution.…”