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Chieng A, Wan Z, Wang S. Recent Advances in Real-Time Label-Free Detection of Small Molecules. BIOSENSORS 2024; 14:80. [PMID: 38391999 PMCID: PMC10886562 DOI: 10.3390/bios14020080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
The detection and analysis of small molecules, typically defined as molecules under 1000 Da, is of growing interest ranging from the development of small-molecule drugs and inhibitors to the sensing of toxins and biomarkers. However, due to challenges such as their small size and low mass, many biosensing technologies struggle to have the sensitivity and selectivity for the detection of small molecules. Notably, their small size limits the usage of labeled techniques that can change the properties of small-molecule analytes. Furthermore, the capability of real-time detection is highly desired for small-molecule biosensors' application in diagnostics or screening. This review highlights recent advances in label-free real-time biosensing technologies utilizing different types of transducers to meet the growing demand for small-molecule detection.
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Affiliation(s)
- Andy Chieng
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (A.C.); (Z.W.)
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
| | - Zijian Wan
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (A.C.); (Z.W.)
| | - Shaopeng Wang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; (A.C.); (Z.W.)
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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2
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Li HD, Fang GH, Ye BC, Yin BC. RNase H-Driven crRNA Switch Circuits for Rapid and Sensitive Detection of Various Analytical Targets. Anal Chem 2023; 95:18549-18556. [PMID: 38073045 DOI: 10.1021/acs.analchem.3c04267] [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: 12/20/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR/Cas12a) system has exhibited great promise in the rapid and sensitive molecular diagnostics for its trans-cleavage property. However, most CRISPR/Cas system-based detection methods are designed for nucleic acids and require target preamplification to improve sensitivity and detection limits. Here, we propose a generic crRNA switch circuit-regulated CRISPR/Cas sensor for the sensitive detection of various targets. The crRNA switch is engineered and designed in a blocked state but can be activated in the presence of triggers, which are target-induced association DNA to initiate the trans-cleavage activity of Cas12a for signal reporting. Additionally, RNase H is introduced to specifically hydrolyze RNA duplexed with the DNA trigger, resulting in the regeneration of the trigger to activate more crRNA switches. Such a combination provides a generic and sensitive strategy for the effective sensing of the p53 sequence, thrombin, and adenosine triphosphate. The design is incorporated with nucleic acid nanotechnology and extensively broadens the application scope of the CRISPR technology in biosensing.
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Affiliation(s)
- Hua-Dong Li
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Guan-Hua Fang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang 832000, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang 832000, China
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3
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Gurukandure A, Somasundaram S, Kurian ASN, Khuda N, Easley CJ. Building a Nucleic Acid Nanostructure with DNA-Epitope Conjugates for a Versatile Approach to Electrochemical Protein Detection. Anal Chem 2023; 95:18122-18129. [PMID: 38032341 PMCID: PMC10720615 DOI: 10.1021/acs.analchem.3c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
The recent surge of effort in nucleic-acid-based electrochemical (EC) sensors has been fruitful, yet there remains a need for more generalizable EC platforms for sensing multiple classes of clinically relevant targets. We recently reported a nucleic acid nanostructure for simple, economical, and more generalizable EC readout of a range of analytes, including small molecules, peptides, proteins, and antibodies. The nanostructure is built through on-electrode enzymatic ligation of three oligonucleotides for attachment, binding, and signaling. However, the generalizable detection of larger proteins remains a challenge. Here, we adapted the sensor to quantify larger proteins in a more generic manner through conjugating the protein's minimized antibody-binding epitope to the central DNA strand. This concept was verified using creatine kinase (CK-MM), a biomarker of muscle damage and several disorders for which rapid clinical sensing is important. DNA-epitope conjugates permitted a competitive immunoassay for the CK protein at the electrode via square-wave voltammetry (SWV). Sensing through a signal-off mechanism, the anti-CK antibody limit of detection (LOD) was 5 nM with a response time as low as 3 min. Antibody displacement by native protein analytes gave a signal-on response with the CK sensing range from the LOD of 14 nM up to 100 nM, overlapping with the normal (nonelevated) human clinical range (3-37 nM), and the sensor was validated in 98% human serum. While a need for improved DNA-epitope conjugate purification was identified, overall, this approach allows the quantification of a generic protein- or peptide-binding antibody and should facilitate future quantitative EC readouts of clinically relevant proteins that were previously inaccessible to EC techniques.
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Affiliation(s)
- Asanka Gurukandure
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Subramaniam Somasundaram
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Amanda S. N. Kurian
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Niamat Khuda
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Christopher J. Easley
- Department of Chemistry and
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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4
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Thompson IA, Saunders J, Zheng L, Hariri AA, Maganzini N, Cartwright AP, Pan J, Yee S, Dory C, Eisenstein M, Vuckovic J, Soh HT. An antibody-based molecular switch for continuous small-molecule biosensing. SCIENCE ADVANCES 2023; 9:eadh4978. [PMID: 37738337 PMCID: PMC10516488 DOI: 10.1126/sciadv.adh4978] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
We present a generalizable approach for designing biosensors that can continuously detect small-molecule biomarkers in real time and without sample preparation. This is achieved by converting existing antibodies into target-responsive "antibody-switches" that enable continuous optical biosensing. To engineer these switches, antibodies are linked to a molecular competitor through a DNA scaffold, such that competitive target binding induces scaffold switching and fluorescent signaling of changing target concentrations. As a demonstration, we designed antibody-switches that achieve rapid, sample preparation-free sensing of digoxigenin and cortisol in undiluted plasma. We showed that, by substituting the molecular competitor, we can further modulate the sensitivity of our cortisol switch to achieve detection at concentrations spanning 3.3 nanomolar to 3.3 millimolar. Last, we integrated this switch with a fiber optic sensor to achieve continuous sensing of cortisol in a buffer and blood with <5-min time resolution. We believe that this modular sensor design can enable continuous biosensor development for many biomarkers.
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Affiliation(s)
- Ian A.P. Thompson
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jason Saunders
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Liwei Zheng
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Amani A. Hariri
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alyssa P. Cartwright
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jing Pan
- Department of Mechanical and Aerospace Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Steven Yee
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Constantin Dory
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Michael Eisenstein
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Jelena Vuckovic
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
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5
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Kurian ASN, Gurukandure A, Dovgan I, Kolodych S, Easley CJ. Thermofluorimetric Analysis (TFA) using Probes with Flexible Spacers: Application to Direct Antibody Sensing and to Antibody-Oligonucleotide (AbO) Conjugate Valency Monitoring. Anal Chem 2023; 95:11680-11686. [PMID: 37490525 PMCID: PMC10421636 DOI: 10.1021/acs.analchem.3c01590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Antibodies have long been recognized as clinically relevant biomarkers of disease. The onset of a disease often stimulates antibody production in low quantities, making it crucial to develop sensitive, specific, and easy-to-use antibody assay platforms. Antibodies are also extensively used as probes in bioassays, and there is a need for simpler methods to evaluate specialized probes, such as antibody-oligonucleotide (AbO) conjugates. Previously, we demonstrated that thermofluorimetric analysis (TFA) of analyte-driven DNA assembly can be leveraged to detect protein biomarkers using AbO probes. A key advantage of this technique is its ability to circumvent autofluorescence arising from biological samples, which otherwise hampers homogeneous assays. The analysis of differential DNA melt curves (dF/dT) successfully distinguishes the signal from the background and interferences. Expanding the applicability of TFA further, herein we demonstrate a unique proximity based TFA assay for antibody quantification that is functional in 90% human plasma. We show that the conformational flexibility of the DNA-based proximity probes is critically important for optimal performance in these assays. To promote stable, proximity-induced hybridization of the short DNA strands, substitution of poly(ethylene glycol) (PEG) spacers in place of ssDNA segments led to improved conformational flexibility and sensor performance. Finally, by applying these flexible spacers to study AbO conjugates directly, we validate this modified TFA approach as a novel tool to elucidate the probe valency, clearly distinguishing between monovalent and multivalent AbOs and reducing the reagent amounts by 12-fold.
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Affiliation(s)
- Amanda S. N. Kurian
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849
| | - Asanka Gurukandure
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849
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6
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Wang Y, Peng Y, Li S, Han D, Ren S, Qin K, Zhou H, Han T, Gao Z. The development of a fluorescence/colorimetric biosensor based on the cleavage activity of CRISPR-Cas12a for the detection of non-nucleic acid targets. JOURNAL OF HAZARDOUS MATERIALS 2023; 449:131044. [PMID: 36821893 DOI: 10.1016/j.jhazmat.2023.131044] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Nano-biosensors are of great significance for the analysis and detection of important biological targets. Surprisingly, the CRISPR-Cas12a system not only provides us with excellent gene editing capabilities, it also plays an important role in biosensing due to its high base resolution and high levels of sensitivity. However, most CRISPR-Cas12a-based sensors are limited by their recognition and output modes, are therefore only utilized for the detection of nucleic acids using fluorescence as an output signal. In the present study, we further explored the potential application of CRISPR-Cas12a and developed a CRISPR-Cas12a-based fluorescence/colorimetric biosensor (UCNPs-Cas12a/hydrogel-MOF-Cas12a) that provides an efficient targeting system for small molecules and protein targets. These two sensors yield multiple types of signal outputs by converting the target molecule into a deoxyribonucleic acid (DNA) signal input system using aptamers, amplifying the DNA signal by catalyzed hairpin assembly (CHA), and then combining CRISPR-Cas12a with various nanomaterials. UCNPs-Cas12a/hydrogel-MOF-Cas12a exhibited prominent sensitivity and stability for the detection of estradiol (E2) and prostate-specific antigen (PSA), and was successfully applied for the detection of these targets in milk and serum samples. A major advantage of the hydrogel-MOF-Cas12a system is that the signal output can be observed directly. When combined with aptamers and nanomaterials, CRISPR-Cas12a can be used to target multiple targets, with a diverse array of signal outputs. Our findings create a foundation for the development of CRISPR-Cas12a-based technologies for application in the fields of food safety, environmental monitoring, and clinical diagnosis.
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Affiliation(s)
- Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Kang Qin
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Huanying Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, PR China.
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7
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Meng F, Yu W, Niu M, Tian X, Miao Y, Li X, Zhou Y, Ma L, Zhang X, Qian K, Yu Y, Wang J, Huang L. Ratiometric electrochemical OR gate assay for NSCLC-derived exosomes. J Nanobiotechnology 2023; 21:104. [PMID: 36964516 PMCID: PMC10037838 DOI: 10.1186/s12951-023-01833-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/26/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological type of LC and ranks as the leading cause of cancer deaths. Circulating exosomes have emerged as a valuable biomarker for the diagnosis of NSCLC, while the performance of current electrochemical assays for exosome detection is constrained by unsatisfactory sensitivity and specificity. Here we integrated a ratiometric biosensor with an OR logic gate to form an assay for surface protein profiling of exosomes from clinical serum samples. By using the specific aptamers for recognition of clinically validated biomarkers (EpCAM and CEA), the assay enabled ultrasensitive detection of trace levels of NSCLC-derived exosomes in complex serum samples (15.1 particles μL-1 within a linear range of 102-108 particles μL-1). The assay outperformed the analysis of six serum biomarkers for the accurate diagnosis, staging, and prognosis of NSCLC, displaying a diagnostic sensitivity of 93.3% even at an early stage (Stage I). The assay provides an advanced tool for exosome quantification and facilitates exosome-based liquid biopsies for cancer management in clinics.
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Affiliation(s)
- Fanyu Meng
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Wenjun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Minjia Niu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xvelian Li
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yan Zhou
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lifang Ma
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yongchun Yu
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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8
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Gao H, Wang K, Li H, Fan Y, Sun X, Wang X, Sun H. Recent advances in electrochemical proximity ligation assay. Talanta 2023; 254:124158. [PMID: 36502611 DOI: 10.1016/j.talanta.2022.124158] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Proximity ligation assay (PLA) is a vigorously developed homogeneous immunoassay assisted by DNA combining dual recognition of target protein by pairs of proximity probes, in which the detection of protein is tactfully converted to the detection of DNA. The booming developments in PLA have enabled a variety of ultrasensitive assays for the detection of protein and this concept of PLA is also extended to the detection of nucleic acids and some small molecule. The association between PLA and electrochemical method, defined as electrochemical proximity ligation assay (ECPLA), has gained much interests in disease diagnosis, food safety and environmental assays with the advantages, such as broad range of targets, simplicity, low cost and rapid response. In this review, we took a different perspective to present the history of PLA, the classical ECPLA biosensing methodology as well as the developments of ECPLA based on several key parameters, such as sensitivity, selectivity, reusability and generalization. In addition, the developments of PLA with electrochemiluminescence as readout are also presented. Finally, perspective and some unresolved challenges in ECPLA that can potentially be addressed have also been discussed.
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Affiliation(s)
- Hongfang Gao
- School of Environmental Engineering, Wuxi University, Wuxi, 214105, PR China.
| | - Ke Wang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics & Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Haiyu Li
- School of Environmental Engineering, Wuxi University, Wuxi, 214105, PR China
| | - Yeli Fan
- School of Environmental Engineering, Wuxi University, Wuxi, 214105, PR China
| | - Xiong Sun
- School of Environmental Engineering, Wuxi University, Wuxi, 214105, PR China
| | - Xia Wang
- School of Environmental Engineering, Wuxi University, Wuxi, 214105, PR China
| | - Huiping Sun
- Institute of Materials Science and Devices, Suzhou University of Science and Technology, Suzhou, 215000, PR China
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9
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Khuda N, Somasundaram S, Urgunde AB, Easley CJ. Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors. ACS APPLIED MATERIALS & INTERFACES 2023; 15:5019-5027. [PMID: 36661270 PMCID: PMC10370289 DOI: 10.1021/acsami.2c22741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.
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Affiliation(s)
- Niamat Khuda
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | | | - Ajay B. Urgunde
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
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10
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Wu Y, Wang C, Wang C, Wang P, Chang X, Han L, Zhang Y. Multiple Biomarker Simultaneous Detection in Serum via a Nanomaterial-Functionalized Biosensor for Ovarian Tumor/Cancer Diagnosis. MICROMACHINES 2022; 13:mi13122046. [PMID: 36557345 PMCID: PMC9783278 DOI: 10.3390/mi13122046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/18/2022] [Accepted: 11/19/2022] [Indexed: 06/12/2023]
Abstract
Ovarian tumors/cancers are threatening women's health worldwide, which demands high-performance detection methods and accurate strategies to effectively detect, diagnose and treat them. Here, we report a nanographene oxide particle-functionalized microfluidic fluorescence biosensor to simultaneously detect four biomarkers, CA125, HE4, CEA and APF, for ovarian tumor/cancer diagnosis. The developed biosensor exhibits good selectivity and a large biomarker detection range with a limit of detection of 0.01 U/mL for CA125 and ~1 pg/mL for HE4, CEA and APF. The current results indicate that (1) the proposed biosensor is a promising tool for the simultaneous detection of multiple biomarkers in ovarian tumors/cancer and (2) CA125 and HE4 are strong indicators, AFP may be helpful, and CEA is a weak biomarker for ovarian tumor/cancer diagnosis. The proposed biosensor would be a potential tool, and an analytical approach for the simultaneous detection of multiple biomarkers will provide a new strategy for the early screening, diagnosis and treatment of ovarian tumors/cancers, as well as other cancers.
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Affiliation(s)
- Yu Wu
- Peking University Third Hospital, Haidian District, Beijing 100191, China
| | - Chunhua Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266273, China
| | - Chao Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266273, China
| | - Pan Wang
- Peking University Third Hospital, Haidian District, Beijing 100191, China
| | - Xiaohan Chang
- Peking University Third Hospital, Haidian District, Beijing 100191, China
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao 266273, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250100, China
| | - Yu Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266273, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
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11
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Wang L, Wang X, Chen Z, Liu S. Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System. Anal Chem 2022; 94:8317-8326. [PMID: 35649122 DOI: 10.1021/acs.analchem.2c00800] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge was deployed for the fabrication of a simple and general DNA-based electrochemical sensing platform. It could be harnessed for different signal output behaviors (one signal-off and two signal-on modes) toward a single-step analysis of the target protein. The detection limit toward the target protein could reach about 0.1 nM. Also, it could be used as a streamlined electrochemical workflow for the successive monitoring of protein binding. Furthermore, such an electrochemical sensing platform could be explored for the operation of the concatenated AND logic gates as a molecular keypad lock system. The current sensing platform based on only one duplex DNA scaffold presented features such as simple biosensor design and fabrication, flexible operation for different signal outputs, sensitive and selective protein detection, and expandable logic operation. It thus would pave a broad road toward the development of high-performance biosensors or logic devices to be applied for molecular diagnosis or computing.
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Affiliation(s)
- Li Wang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Xu Wang
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Zhiqiang Chen
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
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12
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Khuda N, Somasundaram S, Easley CJ. Electrochemical Sensing of the Peptide Drug Exendin-4 Using a Versatile Nucleic Acid Nanostructure. ACS Sens 2022; 7:784-789. [PMID: 35180342 PMCID: PMC8985241 DOI: 10.1021/acssensors.1c02336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although endogenous peptides and peptide-based therapeutics are both highly relevant to human health, there are few approaches for sensitive biosensing of this class of molecules with minimized workflow. In this work, we have further expanded on the generalizability of our recently developed DNA nanostructure architecture by applying it to electrochemical (EC) peptide quantification. While DNA-small molecule conjugates were used in a prior work to make sensors for small molecule and protein analytes, here DNA-peptide conjugates were incorporated into the nanostructure at the electrode surfaces, and antibody displacement permitted rapid peptide sensing. Interestingly, multivalent DNA-peptide conjugates were found to be detrimental to the assay readout, yet these effects could be minimized by solution-phase bioconjugation. The final biosensor was validated for quantifying exendin-4 (4.2 kDa)─a human glucagon-like peptide-1 receptor agonist important in diabetes therapy─for the first time using EC methods with minimal workflow. The sensor was functional in 98% human serum, and the low nanomolar assay range lies between the injected dose concentration and the therapeutic range, boding well for future applications in therapeutic drug monitoring.
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13
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Hua X, Fan J, Yang L, Wang J, Wen Y, Su L, Zhang X. Rapid detection of miRNA via development of consecutive adenines (polyA)-based electrochemical biosensors. Biosens Bioelectron 2022; 198:113830. [PMID: 34861526 DOI: 10.1016/j.bios.2021.113830] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/11/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022]
Abstract
Herein, we report rapid electrochemical detection of miRNA let-7a based on a DNA probe consisting of a polyA and Fc-co-labeled harpin structure (the polyA-H probe). The polyA-H probe could be facilely immobilized on Au surfaces through the interactions between polyA and Au, followed by its pre-hybridization with a single strand (S1). The probe's surface density could be optimized for minimizing steric hindrance via changing the polyA block length. The target let-7a could be rapidly amplified via loop-mediated isothermal amplification (LAMP) with four simplified primers, followed by inducing the formation of dimeric i-motif (DIM) structure via H+-induced rapid folding of two C-rich sequences of motif strand 1 and strand 2. It was found that, after introducing the as-formed DIM to hybridize the S1, the immobilized polyA20-H probe could rapidly revert to its hairpin structure, sending out a turn-on electrochemical signal of the Fc. The total time for detecting the let-7a was around 80 min, obviously less than that of most of electrochemical DNA sensors reported previously. The biosensor showed a linear relationship of the current response to the let-7a in the range of 10 fM to 50 nM with a limit of detection (LOD) of 5.1 fM. Our biosensors were further tested using human serum spiked with the let-7a and the extracts of the breast adenocarcinoma cells spiked with and without the let-7a, respectively. Satisfied results were obtained. This study shows a potential promising future of development of electrochemical biosensors for rapid detection of miRNAs in the application of clinical practice.
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Affiliation(s)
- Xiaoyu Hua
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Jingjing Fan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Lingzhi Yang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518037, PR China.
| | - Jun Wang
- Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, 430068, PR China
| | - Yongqiang Wen
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Lei Su
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, PR China.
| | - Xueji Zhang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, PR China
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14
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Fu K, Seo J, Kesler V, Maganzini N, Wilson BD, Eisenstein M, Murmann B, Soh HT. Accelerated Electron Transfer in Nanostructured Electrodes Improves the Sensitivity of Electrochemical Biosensors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102495. [PMID: 34668339 PMCID: PMC8655170 DOI: 10.1002/advs.202102495] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/29/2021] [Indexed: 05/20/2023]
Abstract
Electrochemical biosensors hold the exciting potential to integrate molecular detection with signal processing and wireless communication in a miniaturized, low-cost system. However, as electrochemical biosensors are miniaturized to the micrometer scale, their signal-to-noise ratio degrades and reduces their utility for molecular diagnostics. Studies have reported that nanostructured electrodes can improve electrochemical biosensor signals, but since the underlying mechanism remains poorly understood, it remains difficult to fully exploit this phenomenon to improve biosensor performance. In this work, electrochemical aptamer biosensors on nanoporous electrode are optimized to achieve improved sensitivity by tuning pore size, probe density, and electrochemical measurement parameters. Further, a novel mechanism in which electron transfer is physically accelerated within nanostructured electrodes due to reduced charge screening, resulting in enhanced sensitivity is proposed and experimentally validated. In concert with the increased surface areas achieved with this platform, this newly identified effect can yield an up to 24-fold increase in signal level and nearly fourfold lower limit of detection relative to planar electrodes with the same footprint. Importantly, this strategy can be generalized to virtually any electrochemical aptamer sensor, enabling sensitive detection in applications where miniaturization is a necessity, and should likewise prove broadly applicable for improving electrochemical biosensor performance in general.
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Affiliation(s)
- Kaiyu Fu
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
- Department of RadiologyStanford UniversityStanfordCA94305USA
| | - Ji‐Won Seo
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
- Department of RadiologyStanford UniversityStanfordCA94305USA
| | - Vladimir Kesler
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
| | - Nicolo Maganzini
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
| | - Brandon D. Wilson
- Department of Chemical EngineeringStanford UniversityStanfordCA94305USA
| | - Michael Eisenstein
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
- Department of RadiologyStanford UniversityStanfordCA94305USA
| | - Boris Murmann
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
| | - H. Tom Soh
- Department of Electrical EngineeringStanford UniversityStanfordCA94305USA
- Department of RadiologyStanford UniversityStanfordCA94305USA
- Chan Zuckerberg BiohubSan FranciscoCA94158USA
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15
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Liu J, Liu X, Zhang L, Zhu L, Mei X, Wei J, Li Y. Hand-Held and Integrated Tubular Tip-like Sensing Platform Series: Point-of-care Device for Semi-automated Multiplexed Assay. Anal Chem 2021; 93:15534-15542. [PMID: 34747608 DOI: 10.1021/acs.analchem.1c03717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, most of the electrochemical sensors were prepared based on the planar electrode (PE) and utilized in open circumstance. The accompanying issues include fixed and limited sensing area of PE, insufficient usage of the testing sample, tedious operation, and susceptibility to external environment. Herein, a novel tubular tip-like sensor (TTLS) platform was proposed, where a small tip accommodates all electrodes with a curved surface and also acts as a closed detection chamber. Teaming up with a commercial pipette and potentiostat, the TTLS is able to accomplish the whole assay procedure including sampling, detection, rinsing, and regeneration with a single hand. The electrochemical interface area can be easily tuned to adapting for different scenarios with varied sensitivity request. Moreover, two TTLS-based array systems were derived: one integrates multiple working electrodes in one tip for multicomponent quantification and the other assembles eight independent TTLSs for high-throughput analysis. The admirable sensing performance of the TTLS was fully proved by detecting several liver-related biomarkers in 5 μL of the serum sample. The proposed tubular sensor platform is superior to the traditional electrochemical sensor in the aspects of unique sensing surface, fast and simple operation, good portability, and great compatibility. The TTLS could be used as an ideal analytical tool in point-of-care testing and other fields.
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Affiliation(s)
- Jiang Liu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Science, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China.,Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
| | - Xiaoxue Liu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Science, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
| | - Lu Zhang
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Science, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
| | - Liang Zhu
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Science, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
| | - Xuecui Mei
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Science, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
| | - Jun Wei
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Materials Science and Engineering, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
| | - Yingchun Li
- Shenzhen Key Laboratory of Flexible Printed Electronics Technology and School of Science, Harbin Institute of Technology, Shenzhen 518055, Guangdong, P.R. China
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16
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Ouyang P, Fang C, Han J, Zhang J, Yang Y, Qing Y, Chen Y, Shang W, Du J. A DNA Electrochemical Sensor via Terminal Protection of Small-Molecule-Linked DNA for Highly Sensitive Protein Detection. BIOSENSORS 2021; 11:bios11110451. [PMID: 34821667 PMCID: PMC8615823 DOI: 10.3390/bios11110451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/11/2022]
Abstract
The qualitative and quantitative determination of marker protein is of great significance in the life sciences and in medicine. Here, we developed an electrochemical DNA biosensor for protein detection based on DNA self-assembly and the terminal protecting effects of small-molecule-linked DNA. This strategy is demonstrated using the small molecule biotin and its receptor protein streptavidin (SA). We immobilized DNA with a designed structure and sequence on the surface of the gold electrode, and we named it M1-Biotin DNA. M1-Biotin DNA selectively combines with SA to generate M1-Biotin-SA DNA and protects M1-Biotin DNA from digestion by EXO III; therefore, M1-Biotin DNA remains intact on the electrode surface. M1-Biotin-SA DNA was modified with methylene blue (MB); the MB reporter molecule is located near the surface of the gold electrode, which generates a substantial electrochemical signal during the detection of SA. Through this strategy, we can exploit the presence or absence of an electrochemical signal to provide qualitative target protein determination as well as the strength of the electrochemical signal to quantitatively analyze the target protein concentration. This strategy has been proven to be used for the quantitative analysis of the interaction between biotin and streptavidin (SA). Under optimal conditions, the detection limit of the proposed biosensor is as low as 18.8 pM, and the linear range is from 0.5 nM to 5 μM, showing high sensitivity. The detection ability of this DNA biosensor in complex serum samples has also been studied. At the same time, we detected the folate receptor (FR) to confirm that this strategy can be used to detect other proteins. Therefore, this electrochemical DNA biosensor provides a sensitive, low-cost, and fast target protein detection platform, which may provide a reliable and powerful tool for early disease diagnosis.
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17
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Tian JK, Zhao ML, Song YM, Zhong X, Yuan R, Zhuo Y. MicroRNA-Triggered Deconstruction of Field-Free Spherical Nucleic Acid as an Electrochemiluminescence Biosensing Switch. Anal Chem 2021; 93:13928-13934. [PMID: 34609848 DOI: 10.1021/acs.analchem.1c02965] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Herein, a new field-free and highly ordered spherical nucleic acid (SNA) nanostructure was self-assembled directly by ferrocene (Fc)-labeled DNA tweezers and DNA linkers based on the Watson-Crick base pairing rule, which was employed as an electrochemiluminescence (ECL) quenching switch with improved recognition efficiency due to the high local concentration of the ordered nanostructure. Moreover, with a collaborative strategy combined with the advantages of both self-accelerated approach and pore confinement-enhanced ECL effect, the mesoporous silica nanospheres (mSiO2 NSs) were prepared to be filled with rubrene (Rub) as ECL emitters and Pt nanoparticles (PtNPs) as coreaction accelerators (Rub-Pt@mSiO2 NSs), which demonstrated high ECL response in the aqueous media (dissolved O2 as coreactant). When the SNA nanostructure was immobilized on the Rub-Pt@mSiO2 NSs-modified electrode, it presented a "signal off" state owing to the quenching effect of the Fc molecules. As a proof of concept, the SNA-based ECL switch platform was applied in the detection of microRNA let-7b (let-7b). Impressively, in the presence of the target let-7b, a deconstruction of the SNA nanostructure was actuated, causing the Fc to leave the electrode surface and achieved an extremely high ECL recovery ("signal on" state). Hence, a sensitive determination for let-7b was realized with a low detection limit of 1.8 aM ranging from 10 aM to 1 nM by employing the Rub-Pt@mSiO2 NSs-based ECL platform combined with the target-triggered SNA deconstruction, which also offered an ingenious method for the further applications of biomarker analyses.
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Affiliation(s)
- Jie-Kang Tian
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Mei-Ling Zhao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yu-Meng Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xia Zhong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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18
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Miao P, Tang Y. Cascade Strand Displacement and Bipedal Walking Based DNA Logic System for miRNA Diagnostics. ACS CENTRAL SCIENCE 2021; 7:1036-1044. [PMID: 34235264 PMCID: PMC8228592 DOI: 10.1021/acscentsci.1c00277] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 05/05/2023]
Abstract
DNA logic gated operations empower the highly efficient analysis of multiplex nucleic acid inputs, which have attracted extensive attention. However, the integration of DNA logic gates with abundant computational functions and signal amplification for biomedical diagnosis is far from being fully achieved. Herein, we develop a bipedal DNA walker based amplified electrochemical method for miRNA detection, which is then used as the basic unit for the construction of various logic circuits, enabling the analysis of multiplex miRNAs. In the bipedal walking process, target triggered strand displacement polymerization is able to produce a large number of strands for the fabrication of three-way junction-structured bipedal walkers. The following catalytic hairpin assembly ensures the walking event and the immobilization of signal probes for output. Ultrahigh sensitivity is realized due to the integration of dual signal amplification. In addition, under logic function controls by input triggered cascade strand displacement reactions, NOT, AND, OR, NAND, NOR, XOR, and XNOR logic gates are successfully established. The as-developed DNA logic system can also be extended to multi-input modes, which holds great promise in the fields of DNA computing, multiplex analysis, and clinical diagnosis.
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Affiliation(s)
- Peng Miao
- Suzhou
Institute of Biomedical Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, People’s Republic
of China
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Yuguo Tang
- Suzhou
Institute of Biomedical Engineering and Technology, Chinese Academy
of Sciences, Suzhou 215163, People’s Republic
of China
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19
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Reagentless biomolecular analysis using a molecular pendulum. Nat Chem 2021; 13:428-434. [PMID: 33686229 DOI: 10.1038/s41557-021-00644-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
The development of reagentless sensors that can detect molecular analytes in biological fluids could enable a broad range of applications in personalized health monitoring. However, only a limited set of molecular inputs can currently be detected using reagentless sensors. Here, we report a sensing mechanism that is compatible with the analysis of proteins that are important physiological markers of stress, allergy, cardiovascular health, inflammation and cancer. The sensing method is based on the motion of an inverted molecular pendulum that exhibits field-induced transport modulated by the presence of a bound analyte. We measure the sensor's electric field-mediated transport using the electron-transfer kinetics of an attached reporter molecule. Using time-resolved electrochemical measurements that enable unidirectional motion of our sensor, the presence of an analyte bound to our sensor complex can be tracked continuously in real time. We show that this sensing approach is compatible with making measurements in blood, saliva, urine, tears and sweat and that the sensors can collect data in situ in living animals.
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20
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Chen JY, Yang LY, Liu ZJ, Wei QX, Zhang Y, Wu B, Zhong GX, Fu LX, Lin XH, Weng XH, Xu XW. DNA Nanosieve-Based Regenerative Electrochemical Biosensor Utilizing Nucleic Acid Flexibility for Accurate Allele Typing in Clinical Samples. ACS Sens 2021; 6:1348-1356. [PMID: 33657808 DOI: 10.1021/acssensors.0c02720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, an interface-based DNA nanosieve that has the ability to differentiate ssDNA from dsDNA has been demonstrated for the first time. The DNA nanosieve could be readily built through thiol-DNA's self-assembly on the gold electrode surface, and its cavity size was tunable by varying the concentration of thiol-DNAs. Electrochemical chronocoulometry using [Ru(NH3)6]3+ as redox revealed that the average probe-to-probe separation in the 1 μM thiol-DNA-modified gold electrode was 10.6 ± 0.3 nm so that the rigid dsDNA with a length of ∼17 nm could not permeate the nanosieve, whereas the randomly coiled ssDNA could enter it due to its high flexibility, which has been demonstrated by square wave voltammetry and methylene blue labels through an upside-down hybridization format. After combining the transiently binding characteristic of a short DNA duplex and introducing a regenerative probe (the counterpart of ssDNA), a highly reproducible nanosieve-based E-DNA model was obtained with a relative standard deviation (RSD) as low as 2.7% over seven cycles. Finally, we built a regenerative nanosieve-based E-DNA sensor using a ligation cycle reaction as an ssDNA amplification strategy and realized one-sensor-based continuous measurement to multiple clinical samples with excellent allele-typing performance. This work holds great potential in low-cost and high-throughput analysis between biosensors and biochips and also opens up a new avenue in nucleic acid flexibility-based DNA materials for future applications in DNA origami and molecular logic gates.
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Affiliation(s)
- Jin-Yuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Liang-Yong Yang
- Department of Pharmacy, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Zhou-Jie Liu
- Department of Pharmacy, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Qing-Xia Wei
- Department of Pharmacy, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Ying Zhang
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Bing Wu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Guang-Xian Zhong
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Leng-Xi Fu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiu-Hua Weng
- Department of Pharmacy, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Xiong-Wei Xu
- Department of Pharmacy, The First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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21
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Forrest NT, Vilcapoma J, Alejos K, Halvorsen K, Chandrasekaran AR. Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues. Biochemistry 2021; 60:250-253. [PMID: 33464826 DOI: 10.1021/acs.biochem.0c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nanoscale devices that can respond to external stimuli have potential applications in drug delivery, biosensing, and molecular computation. Construction using DNA has provided many such devices that can respond to cues such as nucleic acids, proteins, pH, light, or temperature. However, simultaneous control of molecular devices is still limited. Here, we present orthogonal control of DNA nanoswitches using physical (light) and biochemical (enzyme and nucleic acid) triggers. Each one of these triggers controls the reconfiguration of specific nanoswitches from locked to open states within a mixture and can be used in parallel to control a combination of nanoswitches. Such dynamic control over nanoscale devices allows the incorporation of tunable portions within larger structures as well as spatiotemporal control of DNA nanostructures.
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Affiliation(s)
- Nathan T Forrest
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Kristina Alejos
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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22
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Bezerra AB, Kurian ASN, Easley CJ. Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques. Anal Chem 2021; 93:198-214. [PMID: 33147015 PMCID: PMC7855502 DOI: 10.1021/acs.analchem.0c04364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Zhang Z, Zhang Y, Yu H, Rong S, Gao H, Meng L, Dai J, Pan H, Chang D. Spherical carrier amplification strategy for electrochemical immunosensor based on polystyrene-gold nanorods @L-cysteine/MoS2 for determination of tacrolimus. Talanta 2020; 220:121321. [DOI: 10.1016/j.talanta.2020.121321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/11/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022]
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24
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Cyclometalated iridium(III) complexes containing an anthracene unit for sensing and imaging singlet oxygen in cellular mitochondria. J Inorg Biochem 2020; 209:111106. [DOI: 10.1016/j.jinorgbio.2020.111106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022]
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25
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Liu ZJ, Yang LY, Wei QX, Ye CL, Xu XW, Zhong GX, Zheng YJ, Chen JY, Lin XH, Liu AL. A novel ligase chain reaction-based electrochemical biosensing strategy for highly sensitive point mutation detection from human whole blood. Talanta 2020; 216:120966. [PMID: 32456905 DOI: 10.1016/j.talanta.2020.120966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 01/15/2023]
Abstract
Challenged by the detection of trace amounts of mutants and disturbance from endogenous substances in clinical samples, herein, we present a novel electrochemical biosensor based on ligase chain reaction (eLCR) via the thermostable ligase with high mutation recognizing ability. The lengthened double-stranded DNAs exponentially generated via LCR were uniformly distributed on a bovine serum albumin-modified gold electrode, in which the phosphate buffer was tactfully added to remove adsorbed uninterested-probes, and thereafter the amperometry current was collected for the specific binding of streptavidin-poly-HRP and subsequent catalysis in the 3, 3', 5, 5'-tetramethylbenzidine substrate that contained hydrogen peroxide. It found that, under optimized conditions, the proposed biosensor exhibited a high selectivity of mutant targets from the 104-fold excess of co-existent wild targets within a detection limit of 0.5 fM. Impressively, without the involvement of pre-PCR, the homozygous mutants were specifically distinguished from the wild genotype of CYP2C19*2 allele in human whole blood samples. Therefore, the proposed eLCR, due to its advantages in simple primer design, operational ease and ease of miniaturization, has demonstrated its considerable potential for point-of-care testing in the diagnosis of point mutation-related diseases and personalized medicine.
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Affiliation(s)
- Zhou-Jie Liu
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Liang-Yong Yang
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Xia Wei
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Guang-Xian Zhong
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yan-Jie Zheng
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China.
| | - Ai-Lin Liu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China.
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One-step electrodeposition of poly(m-aminobenzoic acid) membrane decorated with peptide for antifouling biosensing of Immunoglobulin E. Colloids Surf B Biointerfaces 2020; 186:110706. [DOI: 10.1016/j.colsurfb.2019.110706] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022]
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Xiong Y, Zhang J, Yang Z, Mou Q, Ma Y, Xiong Y, Lu Y. Functional DNA Regulated CRISPR-Cas12a Sensors for Point-of-Care Diagnostics of Non-Nucleic-Acid Targets. J Am Chem Soc 2019; 142:207-213. [PMID: 31800219 DOI: 10.1021/jacs.9b09211] [Citation(s) in RCA: 353] [Impact Index Per Article: 70.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Beyond its extraordinary genome editing ability, the CRISPR-Cas systems have opened a new era of biosensing applications due to its high base resolution and isothermal signal amplification. However, the reported CRISPR-Cas sensors are largely only used for the detection of nucleic acids with limited application for non-nucleic-acid targets. To realize the full potential of the CRISPR-Cas sensors and broaden their applications for detection and quantitation of non-nucleic-acid targets, we herein report CRISPR-Cas12a sensors that are regulated by functional DNA (fDNA) molecules such as aptamers and DNAzymes that are selective for small organic molecule and metal ion detection. The sensors are based on the Cas12a-dependent reporter system consisting of Cas12a, CRISPR RNA (crRNA), and its single-stranded DNA substrate labeled with a fluorophore and quencher at each end (ssDNA-FQ), and fDNA molecules that can lock a DNA activator for Cas12a-crRNA, preventing the ssDNA cleavage function of Cas12a in the absence of the fDNA targets. The presence of fDNA targets can trigger the unlocking of the DNA activator, which can then activate the cleavage of ssDNA-FQ by Cas12a, resulting in an increase of the fluorescent signal detectable by commercially available portable fluorimeters. Using this method, ATP and Na+ have been detected quantitatively under ambient temperature (25 °C) using a simple and fast detection workflow (two steps and <15 min), making the fDNA-regulated CRISPR system suitable for field tests or point-of-care diagnostics. Since fDNAs can be obtained to recognize a wide range of targets, the methods demonstrated here can expand this powerful CRISPR-Cas sensor system significantly to many other targets and thus provide a new toolbox to significantly expand the CRISPR-Cas system into many areas of bioanalytical and biomedical applications.
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Affiliation(s)
- Ying Xiong
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | | | | | | | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology , Nanchang University , Nanchang 330047 , China
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28
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Holtan MD, Somasundaram S, Khuda N, Easley CJ. Nonfaradaic Current Suppression in DNA-Based Electrochemical Assays with a Differential Potentiostat. Anal Chem 2019; 91:15833-15839. [PMID: 31718147 DOI: 10.1021/acs.analchem.9b04149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One of the key factors limiting sensitivity in many electrochemical assays is the nonfaradaic or capacitive current. This is particularly true in modern assay systems based on DNA monolayers at gold electrode surfaces, which have shown great promise for bioanalysis in complex milieu such as whole blood or serum. While various changes in analytical parameters, redox reporter molecules, DNA structures, probe coverage, and electrode surface area have been shown useful, background reduction by hardware subtraction has not yet been explored for these assays. Here, we introduce new electrochemistry hardware that considerably suppresses nonfaradaic currents through real-time analog subtraction during current-to-voltage conversion in the potentiostat. This differential potentiostat (DiffStat) configuration is shown to suppress or remove capacitance currents in chronoamperometry, cyclic voltammetry, and square-wave voltammetry measurements applied to nucleic acid hybridization assays at the electrode surface. The DiffStat makes larger electrodes and higher sensitivity settings accessible to the user, providing order-of-magnitude improvements in sensitivity, and it also significantly simplifies data processing to extract faradaic currents in square-wave voltammetry (SWV). Because two working electrodes are used for differential measurements, unique arrangements are introduced such as converting signal-OFF assays to signal-ON assays or background drift correction in 50% human serum. Overall, this new potentiostat design should be helpful not only in improving the sensitivity of most electrochemical assays, but it should also better support adaptation of assays to the point-of-care by circumventing complex data processing.
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Affiliation(s)
- Mark D Holtan
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Subramaniam Somasundaram
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Niamat Khuda
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
| | - Christopher J Easley
- Department of Chemistry and Biochemistry , Auburn University , Auburn , Alabama 36849 , United States
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