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Liu J, Li N, Ye L, Zhou L, Chen G, Tang J, Zhang H, Yang H. Triple modal aptasensor arrays driven by CHA-mediated DNAzyme for signal-amplified atrazine pesticide accumulation monitoring in agricultural crops. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135172. [PMID: 38996685 DOI: 10.1016/j.jhazmat.2024.135172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Developing sensors with high selectivity and sensitivity is of great significance for pesticide analysis in environmental assessment. Herein, a versatile three-way sensor array was designed for the detection of the pesticide atrazine, based on the integration of catalytic hairpin assembly (CHA) amplification and three-mode signal transducers. With atrazine, CHA was triggered to generate abundant G-quadruplex. The produced G-quadruplex hybrid could assemble with thioflavin T (TFT) or hemin to mimic enzyme and induce the fluorescence enhancement by TFT, or the colorimetric increase by the oxidized chromogenic substrate and the naked-eye color change by inhibiting the L-cysteine-mediated aggregation of gold nanoparticles. A distinctive three-mode array was successfully constructed with convenience, on-site accessibility and high sensitivity for enzyme-free practical analysis of atrazine. It is also effective and reliable for analyzing real samples including paddy water, paddy soil and polished rice. The detection limits for atrazine were as low as 7.4 pg/mL by colorimetric observation and 0.25 pg/mL by fluorescent detection. Furthermore, the array was exploited to monitor the residue, distribution and bioaccumulation of atrazine in maize and rice for food security and environmental assessment. Hence, this work presented a versatile example for sensitive and on-site all-in-one pesticide analysis arrays with multiple signal report modes.
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Affiliation(s)
- Jintong Liu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Li
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Linyao Ye
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lin Zhou
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanghao Chen
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Tang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Heng Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Yang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing 210095, China.
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Wang H, Li M, Zhang H, Yang L. A Tunable Threshold Colorimetric DNA Logic Gate for Intuitive Assessment of Chemical Contaminant Exceedance. Anal Chem 2024; 96:11862-11868. [PMID: 38989925 DOI: 10.1021/acs.analchem.4c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Current molecular logic gates are predominantly focused on the qualitative assessment of target presence, which has certain limitations in scenarios requiring quantitative assessment, such as chemical contaminant monitoring. To bridge this gap, we have developed a novel DNA logic gate featuring a tunable threshold, specifically tailored to the limits of contaminants. At the core of this logic gate is a DNA-gold nanoparticle (AuNP) hybrid film that incorporates aptamer sequences to selectively bind to acetamiprid (ACE) and atrazine (ATR). Upon interaction with these contaminants, the film degrades, releasing AuNPs that, in the presence of Hg2+, catalyze the oxidation of TMB, resulting in a visible blue coloration on test paper. This aptamer-enabled process effectively establishes an OR logic gate, with ACE and ATR as inputs and the appearance of blue color as the output. A key innovation of our system is its tunable input threshold. By adjusting the concentration of Hg2+, we can fine-tune the color mutation points to match the input threshold to predefined limits, such as Maximum Residue Limits (MRLs). This alignment allows semiquantitative assessment of contaminant levels, providing intuitive visual feedback of contaminant exceedance. Validation experiments with spiked samples confirm its accuracy and reliability by closely matching HPLC results. Therefore, our colorimetric DNA logic gate is emerging as a promising tool for easy and semiquantitative monitoring of chemical contaminants across diverse applications.
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Affiliation(s)
- Hao Wang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Mingming Li
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Hanyang Zhang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Limin Yang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
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Santiago-Maldonado X, Rodríguez-Martínez JA, López L, Cunci L, Bayro M, Nicolau E. Selection, characterization, and biosensing applications of DNA aptamers targeting cyanotoxin BMAA. RSC Adv 2024; 14:13787-13800. [PMID: 38681844 PMCID: PMC11046380 DOI: 10.1039/d4ra02384f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024] Open
Abstract
Scientists have established a connection between environmental exposure to toxins like β-N-methylamino-l-alanine (BMAA) and a heightened risk of neurodegenerative disorders. BMAA is a byproduct from certain strains of cyanobacteria that are present in ecosystems worldwide and is renowned for its bioaccumulation and biomagnification in seafood. The sensitivity, selectivity, and reproducibility of the current analytical techniques are insufficient to support efforts regarding food safety and environment monitoring adequately. This work outlines the in vitro selection of BMAA-specific DNA aptamers via the systematic evolution of ligands through exponential enrichment (SELEX). Screening and characterization of the full-length aptamers was achieved using the SYBR Green (SG) fluorescence displacement assay. Aptamers BMAA_159 and BMAA_165 showed the highest binding affinities, with dissociation constants (Kd) of 2.2 ± 0.1 μM and 0.32 ± 0.02 μM, respectively. After truncation, the binding affinity was confirmed using a BMAA-conjugated fluorescence assay. The Kd values for BMAA_159_min and BMAA_165_min were 6 ± 1 μM and 0.63 ± 0.02 μM, respectively. Alterations in the amino proton region studied using solution nuclear magnetic resonance (NMR) provided further evidence of aptamer-target binding. Additionally, circular dichroism (CD) spectroscopy revealed that BMAA_165_min forms hybrid G-quadruplex (G4) structures. Finally, BMAA_165_min was used in the development of an electrochemical aptamer-based (EAB) sensor that accomplished sensitive and selective detection of BMAA with a limit of detection (LOD) of 1.13 ± 0.02 pM.
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Affiliation(s)
- Xaimara Santiago-Maldonado
- Department of Chemistry, University of Puerto Rico San Juan PR 00925-2437 USA +1-787-522-2150 +1-787-292-9820
| | | | - Luis López
- Department of Chemistry, University of Puerto Rico San Juan PR 00925-2437 USA +1-787-522-2150 +1-787-292-9820
| | - Lisandro Cunci
- Department of Chemistry, University of Puerto Rico San Juan PR 00925-2437 USA +1-787-522-2150 +1-787-292-9820
| | - Marvin Bayro
- Department of Chemistry, University of Puerto Rico San Juan PR 00925-2437 USA +1-787-522-2150 +1-787-292-9820
- Molecular Science Research Center, University of Puerto Rico San Juan 00931-3346 USA
| | - Eduardo Nicolau
- Department of Chemistry, University of Puerto Rico San Juan PR 00925-2437 USA +1-787-522-2150 +1-787-292-9820
- Molecular Science Research Center, University of Puerto Rico San Juan 00931-3346 USA
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Berkal MA, Palas Q, Ricard E, Lartigau-Dagron C, Ronga L, Toulmé JJ, Parat C, Nardin C. Glyphosate-Exonuclease Interactions: Reduced Enzymatic Activity as a Route to Glyphosate Biosensing. Macromol Biosci 2023; 23:e2200508. [PMID: 36808212 DOI: 10.1002/mabi.202200508] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/13/2023] [Indexed: 02/23/2023]
Abstract
N-phosphonomethyle-glycine (glyphosate) is the most widely used pesticide worldwide due to its effectiveness in killing weeds at a moderate cost, bringing significant economic benefits. However, owing to its massive use, glyphosate and its residues contaminate surface waters. On site, fast monitoring of contamination is therefore urgently needed to alert local authorities and raise population awareness. Here the hindrance of the activity of two enzymes, the exonuclease I (Exo I) and the T5 exonuclease (T5 Exo) by glyphosate, is reported. These two enzymes digest oligonucleotides into shorter sequences, down to single nucleotides. The presence of glyphosate in the reaction medium hampers the activity of both enzymes, slowing down enzymatic digestion. It is shown by fluorescence spectroscopy that the inhibition of ExoI enzymatic activity is specific to glyphosate, paving the way for the development of a biosensor to detect this pollutant in drinking water at suitable detection limits, i.e., 0.6 nm.
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Affiliation(s)
| | - Quentin Palas
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - Estelle Ricard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | | | - Luisa Ronga
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - Jean-Jacques Toulmé
- ARNA Laboratory, Inserm U1212, CNRS UMR5320, University of Bordeaux, Bordeaux, 33076, France
- Novaptech, 146 rue Léo Saignat, Bordeaux, 33076, France
| | - Corinne Parat
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - Corinne Nardin
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
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Sanford AA, Manuel BA, Romero-Reyes MA, Heemstra JM. Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids. Chem Sci 2022; 13:7670-7684. [PMID: 35865900 PMCID: PMC9258336 DOI: 10.1039/d2sc00117a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
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.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Brea A Manuel
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Misael A Romero-Reyes
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Chemistry, Hanover College Hanover Indiana 47243 USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
- Department of Biomedical Engineering, Georgia Institute of Technology, Emory University Atlanta GA 30332 USA
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Roueinfar M, Templeton HN, Sheng JA, Hong KL. An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031114. [PMID: 35164379 PMCID: PMC8839139 DOI: 10.3390/molecules27031114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is best known for its role in genomic editing. It has also demonstrated great potential in nucleic acid biosensing. However, the specificity limitation in CRISPR/Cas has created a hurdle for its advancement. More recently, nucleic acid aptamers known for their high affinity and specificity properties for their targets have been integrated into CRISPR/Cas systems. This review article gives a brief overview of the aptamer and CRISPR/Cas technology and provides an updated summary and discussion on how the two distinctive nucleic acid technologies are being integrated into modern diagnostic and therapeutic applications
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Affiliation(s)
- Mina Roueinfar
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
| | - Hayley N. Templeton
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Julietta A. Sheng
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Ka Lok Hong
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, Notre Dame of Maryland University, 4701 North Charles Street, Baltimore, MD 21210, USA
- Correspondence: ; Tel.: +1-410-532-5044
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