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Abstract
DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.
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Affiliation(s)
- Stefen Stangherlin
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, ON, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, ON, N2L 3G1, Canada.
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Labas SR, Liu J. Interactions between Caffeine, Theophylline and Derivatives with Gold Nanoparticles and Implications for Aptamer-Based Label-Free Colorimetric Detection. Chempluschem 2022; 87:e202200265. [PMID: 36356981 DOI: 10.1002/cplu.202200265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/11/2022] [Indexed: 01/31/2023]
Abstract
Caffeine, theophylline, and other methylxanthines have interesting biological activities and are consumed in high quantities globally, causing health and environmental concerns. Gold nanoparticles (AuNPs) have excellent optical properties for biosensor development, although little is known about the adsorption of these xanthine derivatives to AuNPs. In this work, interactions of these compounds with AuNPs were studied. Caffeine, theophylline and theobromine are adsorbed in a manner that affords protection against salt-induced aggregation, whereas xanthine and paraxanthine are adsorbed to destabilize and thus aggregate the AuNPs. Caffeine and theophylline are able to protect AuNPs starting at concentrations as low as 6.3 μM. Xanthine and paraxanthine induce significant AuNP aggregation at 5 μM. Adsorption was also confirmed by surface-enhanced Raman scattering (SERS). Using two recently selected DNA aptamers for caffeine and theophylline, the label-free colorimetric sensing method was tested; our results indicated that due to adsorption of these target molecules, this method cannot be directly used for their detection. The adsorption of these compounds to AuNPs may enable various detection methods such as SERS, but at the same time, it may complicate other detection methods.
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Affiliation(s)
- Sarah R Labas
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2 L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2 L 3G1, Canada
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3
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Target-induced gold nanoparticles colorimetric sensing coupled with aptamer for rapid and high-sensitivity detecting kanamycin. Anal Chim Acta 2022; 1230:340377. [DOI: 10.1016/j.aca.2022.340377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/23/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022]
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4
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Polymer-assisted Au@PDA nanoparticles lyophilized powder with high stability and low adsorption and its application in colorimetric biosensing. Anal Chim Acta 2022; 1220:339995. [DOI: 10.1016/j.aca.2022.339995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/27/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
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5
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Peng B, Liu Z, Jiang Y. Aggregation of DNA-Grafted Nanoparticles in Water: The Critical Role of Sequence-Dependent Conformation of DNA Coating. J Phys Chem B 2022; 126:847-857. [DOI: 10.1021/acs.jpcb.1c09450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bo Peng
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Zhu Liu
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Yi Jiang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
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Kong L, Wang X, Ma C, Zhou S, Sun X, Jiang D, Wang T, Wan H, Wang P. A robust colorimetric aptasensor for the label-free detection of marine toxins based on tyrosine-capped gold nanoparticles. Analyst 2022; 147:5314-5323. [DOI: 10.1039/d2an01394k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tyrosine-capped AuNPs decrease the interaction between targets and AuNPs, presenting better robustness than traditional Cit-AuNPs. Utilizing the superior features, a label-free aptasensor is developed for marine toxin detection for the first time.
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Affiliation(s)
- Liubing Kong
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xinyi Wang
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Chiyu Ma
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Shuqi Zhou
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xianyou Sun
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Deming Jiang
- Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
| | - Tianxing Wang
- Zhejiang, e-Linkcare Meditech co., LTD, No.30 Baita Tongjiang Road, Taizhou, Zhejiang, 310011, China
| | - Hao Wan
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
| | - Ping Wang
- Biosensor National Special Laboratory, Key Laboratory of Biomedical Engineering of Ministry of Education, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
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8
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Monitoring fiber-like aggregation of collagen using gold nanoparticles as probes. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01935-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zhang F, Liu J. Interactions of the Cocaine and Quinine Aptamer with Gold Nanoparticles under the Dilute Biosensor and Concentrated NMR Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11939-11947. [PMID: 34591480 DOI: 10.1021/acs.langmuir.1c02239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The cocaine aptamer was later found to bind quinine with an even higher affinity. In this work, we used a fluorescently labeled aptamer named MN4 to study its adsorption by gold nanoparticles (AuNPs), and the subsequent displacement by the nonlabeled aptamer and by quinine. Without washing, 14% of the preadsorbed MN4 strands were displaced by 4000-fold excess of free MN4, whereas no displacement was observed after washing, suggesting that washing removed weakly adsorbed aptamers. In a previous paper, rapid exchange was observed with NMR by directly mixing AuNPs and concentrated MN4, and our work has unified the dilute and concentrated aptamer conditions. The difference is attributable to the conformation of the adsorbed aptamer, where dilute aptamers are adsorbed in a collapsed state with a much higher affinity to AuNPs. In addition, the preadsorbed MN4 aptamer cannot be desorbed by adding quinine, indicating that direct desorption-based fluorescent sensors cannot be made. Finally, based on the similar color responses to both the aptamer and its nonbinding mutants, the label-free colorimetric detection method cannot be directly applied for the detection of quinine. This work indicated that different experimental conditions need to be carefully compared to have a unified understanding of aptamer/AuNP systems.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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Zara L, Achilli S, Chovelon B, Fiore E, Toulmé JJ, Peyrin E, Ravelet C. Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants. Anal Chim Acta 2021; 1159:338382. [PMID: 33867041 DOI: 10.1016/j.aca.2021.338382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/28/2023]
Abstract
Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.
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Affiliation(s)
- Lorena Zara
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Novaptech, 2 Allée Du Doyen Georges Brus, 33600, Pessac, France
| | - Silvia Achilli
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | - Benoît Chovelon
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Service de Biochimie, Biologie Moléculaire, Toxicologie Environnementale, CHU de Grenoble-Alpes Site Nord- Institut de Biologie et de Pathologie, La Tronche, France
| | | | | | - Eric Peyrin
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France.
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Wang Y, Bi Y, Wang R, Wang L, Qu H, Zheng L. DNA-Gated Graphene Field-Effect Transistors for Specific Detection of Arsenic(III) in Rice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1398-1404. [PMID: 33433214 DOI: 10.1021/acs.jafc.0c07052] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
As one of the most toxic forms of arsenic, inorganic As(III) is easy to accumulate in rice, leading to severe public health problems. Effective control of As(III) requires the development of fast analytical methods for its detection with high sensitivity and specificity. Toward this end, in this work, we report the fabrication of an As(III) electrochemical sensor based on a solution-gated graphene transistor (SGGT) platform with a novel sensing mechanism. The gold gate electrode of the SGGT was modified with DNA probes and then blocked with bovine serum albumin (BSA). The specific interaction between As(III) and gold disrupted the adsorption states of DNA probes, redistributing surface charges on the gate electrode, further leading to potential drop changes at the interfaces of the gate electrode and graphene active layer. This new mechanism based on DNA-charge-redistribution-induced SGGT current responses (denoted as "DNA-SGGT") was found to greatly improve the selectivity of the sensor: the response of DNA-SGGT to As(III) was effectively enhanced fourfold, while to other interfering cations, it was significantly reduced. The optimized sensor showed a detection limit as low as 5 nM with superior selectivity to As(III). The as-prepared DNA-SGGT-based sensor has also been successfully applied to the detection of As(III) in practical rice samples with a high recovery rate, showing great potential for heavy metal detection in many types of food samples.
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Affiliation(s)
- Yuhong Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yulong Bi
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Rongrong Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
- Intelligent Interconnected Systems Laboratory of Anhui Province, Hefei University of Technology, Hefei 230009, China
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Li Y, Liu J. Nanozyme's catching up: activity, specificity, reaction conditions and reaction types. MATERIALS HORIZONS 2021; 8:336-350. [PMID: 34821258 DOI: 10.1039/d0mh01393e] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Nanozymes aim to mimic enzyme activities. In addition to catalytic activity, nanozymes also need to have specificity and catalyze biologically relevant reactions under physiological conditions to fit in the definition of enzyme and to set nanozymes apart from typical inorganic catalysts. Previous discussions in the nanozyme field mainly focused on the types of reactions or certain analytical, biomedical or environmental applications. In this article, we discuss efforts made to mimic enzymes. First, the catalytic cycles are compared, where a key difference is specific substrate binding by enzymes versus non-specific substrate adsorption by nanozymes. We then reviewed efforts to engineer and surface-modify nanomaterials to accelerate reaction rates, strategies to graft affinity ligands and molecularly imprinted polymers to achieve specific catalysis, and methods to bring nanozyme reactions to neutral pH and ambient temperature. Most of the current nanozyme reactions used a few model chromogenic substrates of no biological relevance. Therefore, we also reviewed efforts to catalyze the conversion of biomolecules and biopolymers using nanozymes. By the efforts to close the gaps between nanozymes and enzymes, we believe nanozymes are catching up rapidly. Still, challenges exist in materials design to further improve nanozymes as true enzyme mimics and achieve impactful applications.
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Affiliation(s)
- Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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Yang Y, Li W, Liu J. Review of recent progress on DNA-based biosensors for Pb 2+ detection. Anal Chim Acta 2020; 1147:124-143. [PMID: 33485571 DOI: 10.1016/j.aca.2020.12.056] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/12/2020] [Accepted: 12/25/2020] [Indexed: 02/08/2023]
Abstract
Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb2+ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb2+ has become a rapidly growing topic in the analytical community. Pb2+ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb2+ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb2+ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb2+ sensing. In this article, these Pb2+ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.
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Affiliation(s)
- Yongjie Yang
- Department of Food and Biological Sciences, College of Agriculture, Yanbian University, Yanji, 133002, China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Weixuan Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada; Water Institute, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
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Zhang F, Liu J. Label‐Free Colorimetric Biosensors Based on Aptamers and Gold Nanoparticles: A Critical Review. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/anse.202000023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering Fuzhou University Fuzhou 350108 People's Republic of China
- Department of Chemistry Waterloo Institute for Nanotechnology University of Waterloo Waterloo N2 L 3G1 Ontario Canada
| | - Juewen Liu
- Department of Chemistry Waterloo Institute for Nanotechnology University of Waterloo Waterloo N2 L 3G1 Ontario Canada
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Detection of chloramphenicol with an aptamer-based colorimetric assay: critical evaluation of specific and unspecific binding of analyte molecules. Mikrochim Acta 2020; 187:668. [PMID: 33215333 DOI: 10.1007/s00604-020-04644-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
A chloramphenicol (CAP)-binding aptamer of 80 nucleotides (nt) was reported in 2011. In 2014, it was truncated to 40 nt and has since been used by most researchers, although a careful binding study is still lacking. In this work, binding assays using isothermal titration calorimetry and various DNA-staining dyes were performed. By comparing the truncated aptamer with three control sequences, no specific binding of CAP was observed in each case. The secondary structures of the original and truncated aptamers were analyzed, and it was shown that the likelihood of the truncated aptamer to retain the same binding mechanism as the original sequence is low. We further examined gold nanoparticle (AuNP)-based label-free colorimetric assays. By quantifying the extinction ratio at 620 nm over that at 520 nm, a similar color response was observed regardless of the sequence of DNA, suggesting the color change mainly reflected other events such as the adsorption of CAP by the AuNPs, instead of aptamer binding to CAP. Salt-induced aggregation experiments suggested direct adsorption of CAP on AuNPs. CAP only weakly inhibited DNA adsorption by AuNPs but did not displace pre-adsorbed DNA. Therefore, CAP adsorption by AuNPs needs to be considered when designing related sensors, for example, by using non-aptamer sequences as controls. This work calls for careful confirmation of aptamer binding and control experiments for designing aptamer and AuNP-based biosensors.
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Chang Y, Gao S, Liu M, Liu J. Designing signal-on sensors by regulating nanozyme activity. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4708-4723. [PMID: 32990706 DOI: 10.1039/d0ay01625j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanozymes are nanomaterials with enzyme-like activities. Compared to natural enzymes, nanozymes are more stable and cost-effective, and they have unique properties due to their nanoscale size and surface chemistry. In this review, we summarize 'signal-on' nanozyme-based sensors for detecting metal ions, anions, small molecules and proteins. Since protein-based enzymes are already highly active, they were used to detect their inhibitors, resulting in 'signal-off' sensors. On the other hand, for nanozymes, target molecules were detected either as a promotor of nanozyme activity or for its ability to selectively remove nanozyme inhibitors. In both cases, 'signal-on' detection was achieved. We classify the commonly used nanozymes based on their composition such as metal oxide, gold nanoparticles and other nanomaterials, most of which belong to the oxidase, peroxidase and catalase mimics. The nanozymes can catalyze the oxidation of colorless or non-fluorescent substrates to produce a visual or fluorescent signal. Based on this, this article presents some typical 'turn-on' and 'turn-off-on' sensors, and we critically review their design principles. At the end, further perspectives for the nanozyme-based sensors are outlined.
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Affiliation(s)
- Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China.
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Zhou J, Li Y, Wang W, Lu Z, Han H, Liu J. Kanamycin Adsorption on Gold Nanoparticles Dominates Its Label-Free Colorimetric Sensing with Its Aptamer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11490-11498. [PMID: 32907335 DOI: 10.1021/acs.langmuir.0c01786] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A short kanamycin-binding aptamer has been widely used for detecting kanamycin. One of the popular signaling methods is based on the color change of gold nanoparticles (AuNPs) to develop label-free colorimetric biosensors. The general perception was that aptamer binding to its target would inhibit aptamer adsorption by the AuNPs. This inhibited adsorption results in the aggregation of the AuNPs and a color change upon addition of salt. However, the potential adsorption of kanamycin was ignored. Herein, we carefully studied the adsorption of kanamycin on AuNPs and performed a comprehensive analysis using two mutated aptamers and a randomly sequenced DNA which were not supposed to bind kanamycin. In addition, a total of six antibiotics were studied over a wide concentration range. As low as 90 nM kanamycin can induce the aggregation of 3 nM citrate-capped AuNPs, indicating very strong adsorption of kanamycin. The color change was independent of DNA sequence, and all the tested sequences showed a similar color response, regardless of aptamer. Among the different antibiotics, kanamycin and streptomycin induced a color change but not the other four. Our results support an alternative mechanism that kanamycin and streptomycin adsorption by the AuNPs was the main reason for the color change instead of aptamer binding.
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Affiliation(s)
- Jiaojiao Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yuqing Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | | | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Zhang F, Huang PJJ, Liu J. Sensing Adenosine and ATP by Aptamers and Gold Nanoparticles: Opposite Trends of Color Change from Domination of Target Adsorption Instead of Aptamer Binding. ACS Sens 2020; 5:2885-2893. [PMID: 32847353 DOI: 10.1021/acssensors.0c01169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The 27 mer DNA aptamer for adenosine and adenosine 5'-triphosphate (ATP) is a popular model system for designing biosensors. Various strategies have been reported for label-free colorimetric detection using gold nanoparticles (AuNPs). It is generally accepted that free aptamers can protect AuNPs against salt-induced aggregation, whereas target-bound aptamers cannot. However, these studies only considered the aptamer binding to its target, and the adsorption of the aptamer on AuNPs, but none considered the adsorption of target molecules by AuNPs. We herein report that the adsorption of adenosine destabilized citrate-capped AuNPs with an apparent Kd of just 7.7 μM adenosine, whereas that of ATP stabilized the AuNPs because of the negative charges from the triphosphate group. The adsorbed ATP inhibited the adsorption of DNA. Using the aptamer and a nonbinding mutant, ATP and guanosine 5'-triphosphate (GTP) had the same colorimetric response, and so did adenosine and guanosine, regardless of the DNA sequence, indicating that the color change mainly reflected the adsorption of the nucleosides and nucleotides instead of aptamer binding. The related literature examples using this aptamer were classified into three types and individually analyzed, where the reported color changes can all be explained by the adsorption of target analytes.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People’s Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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Hu S, Huang PJJ, Wang J, Liu J. Dissecting the Effect of Salt for More Sensitive Label-Free Colorimetric Detection of DNA Using Gold Nanoparticles. Anal Chem 2020; 92:13354-13360. [PMID: 32856891 DOI: 10.1021/acs.analchem.0c02688] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Taking advantage of the protection effect of single-stranded DNA oligonucleotides, gold nanoparticles (AuNPs) remain dispersed and retain a red color with the addition of a low concentration of salt, while AuNPs would aggregate in the presence of double-stranded DNA. This difference has been used to design label-free colorimetric sensors for DNA detection. NaCl is the most commonly used salt to induce the aggregation of AuNPs. In this work, we aimed to test if other salts can provide even better sensor performance and to understand the effects of the cations and anions in salts. We first studied the effect of anions, including halides (NaF, NaCl, NaBr, and NaI), and other common salts (NaNO3, NaClO4, Na2SO4, Na2S2O3, sodium phosphate, and sodium citrate). Among them, weakly adsorbing ones such as F-, citrate, and phosphate appeared to yield better sensitivity than Cl-. Anions can directly adsorb on the AuNPs and affect DNA adsorption. We then tested cations, and only group 1A metals (LiCl, NaCl, KCl, RbCl, and CsCl) can signal DNA adsorption, while divalent metals (MgCl2, CaCl2, MnCl2, and NiCl2) barely showed the effect of DNA. CsCl only works for strongly adsorbing DNA, such as A15, but not weakly adsorbing T15. Overall, NaF is a better salt than NaCl by having a 2.3-fold higher sensitivity, which was confirmed in a DNA sensing assay. This work has identified a better salt yielding higher sensitivity, and sensing work relying on the change of the aggregation state of AuNPs can benefit from this study.
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Affiliation(s)
- Shengqiang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jianxiu Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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20
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Tao X, Wang X, Liu B, Liu J. Conjugation of antibodies and aptamers on nanozymes for developing biosensors. Biosens Bioelectron 2020; 168:112537. [PMID: 32882473 DOI: 10.1016/j.bios.2020.112537] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Nanozymes are engineered nanomaterials with enzyme-like activities. Over the past decade, impressive progresses on nanozymes in biosensing have been made due to their unique advantages of high stability, low cost, and easy modification compared to natural enzymes. For many biosensors, it is critical to conjugate nanozymes to affinity ligands such as antibodies and aptamers. Since different nanomaterials have different surface properties, conjugation methods need to be compatible with these properties. In addition, the effect of biomolecules on nanozyme activity needs to be considered. In this review, we first categorized nanozyme-based biosensors into four parts, respectively describing noncovalent and covalent modifications with antibodies and aptamers. Meanwhile, recent advances in antibody and aptamer labeled nanozyme biosensors are summarized, and the methods of their conjugation are further illustrated. Finally, conclusions and future perspectives for the development and application of nanozyme bioconjugates are discussed.
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Affiliation(s)
- Xiaoqi Tao
- College of Food Science, Southwest University, Chongqing, 400715, China; Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Xin Wang
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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21
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Díaz-Amaya S, Zhao M, Allebach JP, Chiu GTC, Stanciu LA. Ionic Strength Influences on Biofunctional Au-Decorated Microparticles for Enhanced Performance in Multiplexed Colorimetric Sensors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:32397-32409. [PMID: 32645268 DOI: 10.1021/acsami.0c07636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The rising development of biosensors offers a great potential for health, food, and environmental monitoring. However, in many colorimetric platforms, there is a performance limitation stemming from the tendency of traditional Au nanoparticles toward nonspecific aggregation in response to changing ionic strength (salt concentration). This work puts forward a new type of colorimetric aptamer-functionalized labeling of microparticles, which allows to leverage an increase in ionic strength as a positive driver of enhanced detection performance of analytical targets. The resulting device is a cost-effective, instrument-free, portable, and reliable aptasensor that serves as basis for the fabrication of universal paper-based colorimetric platforms with the capability of multiplex, multireplicates and provides quantitative colorimetric detection. A controlled fabrication process was demonstrated by keeping 90% of the signal obtained from the as-fabricated devices (n = 40) within ± 1 standard deviation (SD) (relative SD = 5.69%) and following a mesokurtic normal-like distribution (p = 0.385). We propose for the first time a salt-induced aggregation mechanism for highly stable multilayered label particles (ssDNA-PEI-Au-PS) as the basis of the detection scheme. The use of DNA aptamers as capture biomolecules and PEI as an encapsulating agent allows for a sensitive and highly specific colorimetric response. As a proof of concept, multiplexed detection of mercury (Hg2+) and arsenic (As3+) was demonstrated. In addition, we introduced a robust image analysis algorithm for testing zone segmentation and color signal quantification that allowed for analytical detection, reaching a limit of detection of 1 ppm for both targeted analytes, with enough evidence (p > 0.05) to prove the high specificity of the fabricated device versus a pool of possible interferent ions.
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Affiliation(s)
- Susana Díaz-Amaya
- Department of Materials Engineering, Purdue University. West Lafayette, Indiana 47907, United States
- Birck Nanotechnology Center, Purdue University. West Lafayette, Indiana 47907, United States
| | - Min Zhao
- School of Electrical and Computer Engineering, Purdue University. West Lafayette, Indiana 47907, United States
| | - Jan P Allebach
- School of Electrical and Computer Engineering, Purdue University. West Lafayette, Indiana 47907, United States
| | - George T-C Chiu
- School of Electrical and Computer Engineering, Purdue University. West Lafayette, Indiana 47907, United States
- School of Mechanical Engineering, Purdue University. West Lafayette, Indiana 47907, United States
| | - Lia A Stanciu
- Department of Materials Engineering, Purdue University. West Lafayette, Indiana 47907, United States
- Birck Nanotechnology Center, Purdue University. West Lafayette, Indiana 47907, United States
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22
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Liu X, He F, Zhang F, Zhang Z, Huang Z, Liu J. Dopamine and Melamine Binding to Gold Nanoparticles Dominates Their Aptamer-Based Label-Free Colorimetric Sensing. Anal Chem 2020; 92:9370-9378. [PMID: 32515584 DOI: 10.1021/acs.analchem.0c01773] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Target-directed aptamer adsorption by gold nanoparticles (AuNPs) has been widely used to develop label-free colorimetric biosensors. However, the potential interactions between target molecules and AuNPs have not been considered, which may lead to misinterpretation of analytical results. In this work, the detection of dopamine, melamine, and K+ was studied as model systems to address this problem. First, dopamine and two control molecules all induced the aggregation of citrate-capped AuNPs with apparent Kd's of 5.8 μM dopamine, 51.6 μM norepinephrine, and 142 μM tyramine. Isothermal titration calorimetry measured the aptamer Kd to be 1.9 μM dopamine and 16.8 μM norepinephrine, whereas tyramine cannot bind. Surface enhanced Raman spectroscopy confirmed direct adsorption of dopamine, and the adsorbed dopamine inhibited the adsorption of DNA. Using a typical salt-induced colorimetric detection protocol, a similar color response was observed regardless of the sequence of DNA, indicating the observed color change reflected the adsorption of dopamine by the AuNPs instead of the binding of dopamine by the aptamer. For this label-free sensor to work, the interaction between the target molecule and AuNPs should be very weak, while dopamine represents an example of strong interactions. For the other two systems, the melamine detection did not reflect aptamer binding either but the K+ detection did, suggesting melamine also strongly interacted with AuNPs, whereas K+ had very weak interactions with AuNPs. Since each target molecule is different, such target/AuNP interactions need to be studied case-by-case to ensure the sensing mechanism.
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Affiliation(s)
- Xixia Liu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei 425002, China.,Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Fan He
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,College of Food Science, Guangdong Provincial Key Laboratory of Food Quality and Safety, South China Agricultural University, Guangzhou 510642, Guangdong P. R. China
| | - Fang Zhang
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
| | - Zijie Zhang
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Zhicheng Huang
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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23
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Jimmy Huang PJ, Yang J, Chong K, Ma Q, Li M, Zhang F, Moon WJ, Zhang G, Liu J. Good's buffers have various affinities to gold nanoparticles regulating fluorescent and colorimetric DNA sensing. Chem Sci 2020; 11:6795-6804. [PMID: 34094129 PMCID: PMC8159396 DOI: 10.1039/d0sc01080d] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Citrate-capped gold nanoparticles (AuNPs) are highly important for sensing, drug delivery, and materials design. Many of their reactions take place in various buffers such as phosphate and Good's buffers. The effect of buffer on the surface properties of AuNPs is critical, yet this topic has not been systematically explored. Herein, we used halides such as fluoride, chloride, and bromide as probes to measure the relative adsorption strength of six common buffers. Among them, HEPES had the highest adsorption affinity, while MES, citrate and phosphate were weakly adsorbed with an overall ranking of HEPES > PIPES > MOPS > MES > citrate, phosphate. The adsorption strength was reflected from the inhibited adsorption of DNA and from the displacement of pre-adsorbed DNA. This conclusion is also supported by surface enhanced Raman spectroscopy. Furthermore, some buffer molecules did not get adsorbed instantaneously, and the MOPS buffer took up to 1 h to reach equilibrium. Finally, a classic label-free AuNP-based colorimetric sensor was tested. Its sensitivity increased by 15.7-fold when performed in a MES buffer compared to a HEPES buffer. This study has articulated the importance of buffer for AuNP-based studies and how it can improve sensors and yield more reproducible experimental systems. Aside from maintaining pH, Good's buffers can be adsorbed on gold nanoparticles with different affinities, affecting the stability and its fluorescent and colorimetric sensing performance.![]()
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada
| | - Jeffy Yang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada
| | - Kellie Chong
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada
| | - Qianyi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada
| | - Miao Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada .,School of Chemistry and Chemical Engineering, Shanxi University Taiyuan 030006 China
| | - Fang Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada .,College of Biological Science and Engineering, Fuzhou University Fuzhou 350108 China
| | - Woohyun J Moon
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada
| | - Guomei Zhang
- School of Chemistry and Chemical Engineering, Shanxi University Taiyuan 030006 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo Waterloo ON N2L 3G1 Canada
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24
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McConnell EM, Nguyen J, Li Y. Aptamer-Based Biosensors for Environmental Monitoring. Front Chem 2020; 8:434. [PMID: 32548090 PMCID: PMC7272472 DOI: 10.3389/fchem.2020.00434] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022] Open
Abstract
Due to their relative synthetic and chemical simplicity compared to antibodies, aptamers afford enhanced stability and functionality for the detection of environmental contaminants and for use in environmental monitoring. Furthermore, nucleic acid aptamers can be selected for toxic targets which may prove difficult for antibody development. Of particular relevance, aptamers have been selected and used to develop biosensors for environmental contaminants such as heavy metals, small-molecule agricultural toxins, and water-borne bacterial pathogens. This review will focus on recent aptamer-based developments for the detection of diverse environmental contaminants. Within this domain, aptamers have been combined with other technologies to develop biosensors with various signal outputs. The goal of much of this work is to develop cost-effective, user-friendly detection methods that can complement or replace traditional environmental monitoring strategies. This review will highlight recent examples in this area. Additionally, with innovative developments such as wearable devices, sentinel materials, and lab-on-a-chip designs, there exists significant potential for the development of multifunctional aptamer-based biosensors for environmental monitoring. Examples of these technologies will also be highlighted. Finally, a critical perspective on the field, and thoughts on future research directions will be offered.
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Affiliation(s)
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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25
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Wu R, Peng H, Zhu JJ, Jiang LP, Liu J. Attaching DNA to Gold Nanoparticles With a Protein Corona. Front Chem 2020; 8:121. [PMID: 32161750 PMCID: PMC7052371 DOI: 10.3389/fchem.2020.00121] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/10/2020] [Indexed: 12/24/2022] Open
Abstract
DNA-functionalized gold nanoparticles (AuNPs) have been widely used in directed assembly of materials, biosensors, and drug delivery. This conjugate may encounter proteins in these applications and proteins may affect not only DNA adsorption but also the function of the attached DNA. Bovine serum albumin (BSA) with many cysteine residues can strongly adsorb on AuNPs and this conjugate showed high colloidal stability against salt, acid and base. Similar protection effects were also observed with a few other common proteins including catalase, hemoglobin, glucose oxidase, and horseradish peroxidase. DNA oligonucleotides without a thiol label can hardly displace adsorbed BSA, and BSA cannot displace pre-adsorbed DNA either, indicating a strongly kinetically controlled system. Thiolated DNA can be attached at a low density on the AuNPs with a BSA corona. The BSA corona did not facilitate the hybridization of the conjugated DNA, while a smaller peptide, glutathione allowed faster hybridization. Overall, proteins increase the colloidal stability of AuNPs, and they do not perturb the gold-thiol bond in the DNA conjugate, although a large protein corona may inhibit the hybridization function of DNA.
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Affiliation(s)
- Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Huaping Peng
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada.,Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
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26
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Chang Y, Liu B, Huang Z, Liu Y, Liu M, Liu J. Yttrium Oxide as a Strongly Adsorbing but Nonquenching Surface for DNA Oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1034-1042. [PMID: 31935105 DOI: 10.1021/acs.langmuir.9b02743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A large number of nanomaterials can strongly adsorb DNA and quench fluorescence, such as graphene oxide, gold nanoparticles, and most metal oxides. On the other hand, noncationic nanomaterials that adsorb DNA but cannot quench fluorescence are less known. These materials are attractive for studying the mechanism of DNA-based surface reactions. Y2O3 was found to have this property. Herein, we used fluorescently labeled oligonucleotides as probes to study the mechanism of DNA adsorption. The fluorescence was quenched at low concentrations of Y2O3 and then recovered and even enhanced with higher Y2O3 concentrations. The reason was attributed to the intermolecular quenching by the DNA bases of the neighboring strands. The fluorescence enhancement was due to breaking of the intramolecular fluorophore/DNA interactions, and the most enhancement was observed with a Cy3-labeled DNA. DNA adsorption followed the Langmuir isotherm on Y2O3. Desorption experiments suggested that DNA was adsorbed through the phosphate backbone, with FAM-G15 and FAM-C15 adsorbed more strongly than the other two DNA homopolymers. With a high salt concentration, no fluorescence change was observed, suggesting that the DNA adsorbed in a folded state reducing intermolecular quenching. Overall, Y2O3 might be useful as a model surface for investigating DNA hybridization on a surface.
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Affiliation(s)
- Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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27
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Duan J, Liu B, Liu J. Interactions between gold, thiol and As(iii) for colorimetric sensing. Analyst 2020; 145:5166-5173. [DOI: 10.1039/d0an00946f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Arsenite cannot crosslink glutathione-capped gold nanoparticles but a high concentration of arsenite can displace adsorbed glutathione, indicating that any two species from gold, thiol and arsenite can react.
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Affiliation(s)
- Junling Duan
- College of Chemistry and Material Science
- Shandong Agricultural University
- Tai'an
- P.R. China
- Department of Chemistry
| | - Biwu Liu
- Department of Chemistry
- Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
| | - Juewen Liu
- Department of Chemistry
- Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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28
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Chia HL, Mayorga-Martinez CC, Gusmão R, Novotny F, Webster RD, Pumera M. A highly sensitive enzyme-less glucose sensor based on pnictogens and silver shell–gold core nanorod composites. Chem Commun (Camb) 2020; 56:7909-7912. [DOI: 10.1039/d0cc02770g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel pnictogen-based composite, pnictogen–Au@AgNRs, for the development of a highly sensitive non-enzymatic glucose sensor.
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Affiliation(s)
- Hui Ling Chia
- NTU Institute for Health Technologies
- Interdisciplinary Graduate School
- Nanyang Technological University
- Singapore 637335
- Singapore
| | - Carmen C. Mayorga-Martinez
- Center for Advanced Functional Nanorobots
- Department of Inorganic Chemistry
- Faculty of Chemical Technology
- University of Chemistry and Technology Prague
- Dejvice
| | - Rui Gusmão
- Center for Advanced Functional Nanorobots
- Department of Inorganic Chemistry
- Faculty of Chemical Technology
- University of Chemistry and Technology Prague
- Dejvice
| | - Filip Novotny
- Center for Advanced Functional Nanorobots
- Department of Inorganic Chemistry
- Faculty of Chemical Technology
- University of Chemistry and Technology Prague
- Dejvice
| | - Richard D. Webster
- Division of Chemistry and Biological Chemistry
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Martin Pumera
- Center for Advanced Functional Nanorobots
- Department of Inorganic Chemistry
- Faculty of Chemical Technology
- University of Chemistry and Technology Prague
- Dejvice
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29
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Zhang X, Fan X, Wang Y, Lei F, Li L, Liu J, Wu P. Highly Stable Colorimetric Sensing by Assembly of Gold Nanoparticles with SYBR Green I: From Charge Screening to Charge Neutralization. Anal Chem 2019; 92:1455-1462. [DOI: 10.1021/acs.analchem.9b04660] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario N2L 3G1, Canada
| | - Xiaoya Fan
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yanying Wang
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
| | - Fengjie Lei
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Lin Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Ontario N2L 3G1, Canada
| | - Peng Wu
- Analytical & Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
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30
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Zhang F, Wang S, Liu J. Gold Nanoparticles Adsorb DNA and Aptamer Probes Too Strongly and a Comparison with Graphene Oxide for Biosensing. Anal Chem 2019; 91:14743-14750. [PMID: 31675214 DOI: 10.1021/acs.analchem.9b04142] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Using fluorescently labeled DNA oligonucleotides and nanomaterials for developing biosensors has been extensively reported for gold nanoparticles (AuNPs) and graphene oxide (GO) among others. These materials have vastly different affinities and mechanisms for interacting with DNA, and their analytical performance is likely to be different. In this work, we used several DNA sequences and, respectively, adsorbed them on AuNPs and GO to quench fluorescence. Different from previous work, we used KCN to fully dissolve the AuNPs to calculate the percentage of the desorbed DNA due to the complementary DNA (cDNA) and aptamer target. The desorbed probe DNA from the AuNPs was less than 5% for all of the targets including DNA, adenosine, Hg2+, and lysozyme, indicating a very strong DNA adsorption affinity. Desorption of DNA was achieved by adding HEPES buffer, NaCl, and As(III), but such desorption was attributed to the adsorption of these molecules or ions by the AuNPs instead of their interaction with the adsorbed DNA. For GO, more probes desorbed with addition of target analytes but so did nonspecific desorption by random DNA and proteins. In summary, AuNPs are unlikely to be a good surface for developing biosensors relying solely on the desorption of probe DNA, while for GO the main problem is nonspecific desorption.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering , Fuzhou University , Fuzhou 350108 , People's Republic of China.,Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Shaoyun Wang
- College of Biological Science and Engineering , Fuzhou University , Fuzhou 350108 , People's Republic of China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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31
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Wu R, Jiang LP, Zhu JJ, Liu J. Effects of Small Molecules on DNA Adsorption by Gold Nanoparticles and a Case Study of Tris(2-carboxyethyl)phosphine (TCEP). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13461-13468. [PMID: 31536371 DOI: 10.1021/acs.langmuir.9b02652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA-functionalized gold nanoparticles (AuNPs) often encounter various small molecules and ions such as backfilling agents, bifunctional cross-linkers, stabilizers, and molecules from biological fluids both during and after the DNA conjugation process. Small molecules and ions can influence the stability and property of the conjugate, but such interactions are yet to be fully explored. In this work, eight important molecules were studied and compared, including tris(2-carboxyethyl)phosphine hydrochloride (TCEP), 3-(2-pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP), 4-maleimidobutyric acid N-hydroxysuccinimide ester (GMBS), 6-hydroxy-1-hexanethiol (MCH), l-glutathione (GSH), bromide (Br-), bis(p-sulfonatophenyl)phenylphosphine (BSPP), and thiocyanate (SCN-). Depending on the size, charge, and adsorption affinity on the AuNPs, they can either stabilize or destabilize the AuNPs. Their ability to displace thiolated DNA from AuNPs follows the order of MCH > SPDP > GSH > SCN- > TCEP > Br- > BSPP > GMBS. BSPP has the best stabilization effect for the colloidal stability of AuNPs, while it does not displace the adsorbed DNA. TCEP can be adsorbed on AuNPs and enhance the adsorption of A/C rich DNA in low-salt conditions. This work indicates that the effects of small molecules and ions cannot be ignored when studying the DNA-functionalized AuNPs, which ensures optimal applications and correct interpretation of the data.
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Affiliation(s)
- Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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32
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Zong C, Liu J. The Arsenic-Binding Aptamer Cannot Bind Arsenic: Critical Evaluation of Aptamer Selection and Binding. Anal Chem 2019; 91:10887-10893. [PMID: 31340640 DOI: 10.1021/acs.analchem.9b02789] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An arsenic-binding aptamer named Ars-3 was reported in 2009, and it has been used for detection of As(III) in more than two dozen papers. In this work, we performed extensive binding assays using isothermal titration calorimetry, various DNA-staining dyes, and gold nanoparticles. By carefully comparing Ars-3 and a few random control DNA sequences, no specific binding of As(III) was observed in each case. Therefore, we conclude that Ars-3 cannot bind As(III). Possible reasons for some of the previously reported binding and detection were speculated to be related to the adsorption of As(III) onto gold surfaces, which were used in many related sensor designs, and As(III)/Au interactions were not considered before. The selection data in the original paper were then analyzed in terms of sequence alignment, secondary structure prediction, and dissociation constant measurement. These steps need rigorous testing before confirming specific binding of newly selected aptamers. This study calls for attention to the gap between aptamer selection and biosensor design, and the gap needs to be filled by careful binding assays to further the growth of the aptamer field.
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Affiliation(s)
- Chenghua Zong
- Department of Chemistry and Materials Science, Jiangsu Key Laboratory of Green Synthesis for Functional Materials , Jiangsu Normal University , Xuzhou , Jiangsu 221116 , P.R. China.,Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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