Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids

Abstract

Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.

Fig. 1. The Systematic Evolution of Ligands by EXponential Enrichment (SELEX).

Fig. 2. Types of functional nucleic acids. (a) Aptamers bind the small molecule. (b) Molecular beacon structure-switching biosensor. (c) Split aptamer structure-switching biosensor. (d) Structure-switching biosensor. Reprinted (adapted) with permission from B. A. Manuel, S. A. Sterling, A. A. Sanford and J. M. Heemstra, Anal. Chem., 2022, 94(17) 6436–6440, https://doi.org/10.1021/acs.analchem.2c00422. Copyright 2022 American Chemical Society. (e) DNA catalysed reaction.

Fig. 3. Functional DNA-based detection strategies for small molecule environmental contaminants. (a) Covalent interfaces for aptasensors. (b) Non-covalent interfaces for aptasensors. (c) Colorimetric readouts for aptasensors. (d) Fluorescent readouts for aptasensors. (e) Electrochemical readouts for aptasensors.

Fig. 4. DNAzyme based strategies for detection of heavy metal environmental contaminants. (a) Covalent interfaces for DNAzyme sensors. (b) Non-covalent interfaces for DNAzyme sensors. (c) Electrochemical readouts for DNAzyme sensors. (d) Colorimetric readouts for DNAzyme sensors. Reproduced from ref. , https://doi.org/10.3389/fmicb.2018.00179, under the terms of the CC BY 4.0 license https://creativecommons.org/licenses/by/4.0/. (e) Fluorescent readouts for DNAzyme sensors.

Fig. 5. Aptamer-based methods for sequestration of environmental contaminants. (a) Nanoparticle-based aptamer support. (b) Liposome-based aptamer support. (c) Aptamer column filtration.Reproduced from ref. , https://doi.org/10.1155/2017/3712070, under the terms of CC BY 4.0 license.(d) Aptamer membrane filtration.