1
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Lu X, Zhou X, Song B, Zhang H, Cheng M, Zhu X, Wu Y, Shi H, Chu B, He Y, Wang H, Hong J. Framework Nucleic Acids Combined with 3D Hybridization Chain Reaction Amplifiers for Monitoring Multiple Human Tear Cytokines. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2400622. [PMID: 38489844 DOI: 10.1002/adma.202400622] [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: 01/12/2024] [Revised: 03/04/2024] [Indexed: 03/17/2024]
Abstract
Existing tear sensors are difficult to perform multiplexed assays due to the minute amounts of biomolecules in tears and the tiny volume of tears. Herein, the authors leverage DNA tetrahedral frameworks (DTFs) modified on the wireless portable electrodes to effectively capture 3D hybridization chain reaction (HCR) amplifiers for automatic and sensitive monitoring of multiple cytokines in human tears. The developed sensors allow the sensitive determination of various dry eye syndrome (DES)-associated cytokines in human tears with the limit of detection down to 0.1 pg mL-1, consuming as little as 3 mL of tear fluid. Double-blind testing of clinical DES samples using the developed sensor and commercial ELISA shows no significant difference between them. Compared with single-biomarker diagnosis, the diagnostic accuracy of this sensor based on multiple biomarkers has improved by ≈16%. The developed system offers the potential for tear sensors to enable personalized and accurate diagnosis of various ocular diseases.
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Affiliation(s)
- Xing Lu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Xujiao Zhou
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Bin Song
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Hong Zhang
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Mingrui Cheng
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Xingyu Zhu
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
| | - Yuqi Wu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Haoliang Shi
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Binbin Chu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Yao He
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
- Macao Translatoinal Medicine Center, Macau University of Science and Technology, Taipa, Macau SAR, 999078, China
- Institute of Materials Science and Engineering, Macau University of Science and Technology, Taipa, Macau SAR, 999078, China
| | - Houyu Wang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano & Soft Materials & Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou, 215123, China
| | - Jiaxu Hong
- Department of Ophthalmology and Vision Science, Shanghai Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, 200031, China
- Shanghai Engineering Research Center of Synthetic Immunology, Shanghai, 200032, China
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2
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Tian Z, Shao D, Tang L, Li Z, Chen Q, Song Y, Li T, Simmel FC, Song J. Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems. Nat Commun 2024; 15:4635. [PMID: 38821953 PMCID: PMC11143192 DOI: 10.1038/s41467-024-49021-6] [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] [Received: 10/12/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
Cell-free protein expression (CFE) systems have emerged as a critical platform for synthetic biology research. The vectors for protein expression in CFE systems mainly rely on double-stranded DNA and single-stranded RNA for transcription and translation processing. Here, we introduce a programmable vector - circular single-stranded DNA (CssDNA), which is shown to be processed by DNA and RNA polymerases for gene expression in a yeast-based CFE system. CssDNA is already widely employed in DNA nanotechnology due to its addressability and programmability. To apply above methods in the context of synthetic biology, CssDNA can not only be engineered for gene regulation via the different pathways of sense CssDNA and antisense CssDNA, but also be constructed into several gene regulatory logic gates in CFE systems. Our findings advance the understanding of how CssDNA can be utilized in gene expression and gene regulation, and thus enrich the synthetic biology toolbox.
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Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Dandan Shao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhen Li
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Chen
- College of Forestry, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Yongxiu Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Ningbo institute of Dalian University of Technology, Ningbo, 315016, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui, 230026, China
| | - Friedrich C Simmel
- Department of Bioscience, School of Natural Sciences, Technische Universität München, Garching, Germany
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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3
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Bagheri N, Chamorro A, Idili A, Porchetta A. PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications. Angew Chem Int Ed Engl 2024; 63:e202319677. [PMID: 38284432 DOI: 10.1002/anie.202319677] [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] [Received: 12/19/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
The RNA-programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio-engineering strategies are required to achieve control over Cas12a activity. Here, we show that Toehold Switch DNA hairpins, presenting a rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used to control Cas12a in response to molecular inputs. Reconfiguring the Toehold Switch DNA from a hairpin to a duplex conformation through a strand displacement reaction provides an effective means to modulate the accessibility of the PAM, thereby controlling the binding and cleavage activities of Cas12a. Through this approach, we showcase the potential to trigger downstream Cas12a activity by leveraging proximity-based strand displacement reactions in response to target binding. By utilizing the trans-cleavage activity of Cas12a as a signal transduction method, we demonstrate the versatility of our approach for sensing applications. Our system enables rapid, one-pot detection of IgG antibodies and small molecules with high sensitivity and specificity even within complex matrices. Besides the bioanalytical applications, the switchable PAM-engineered Toehold Switches serve as programmable tools capable of regulating Cas12a-based targeting and DNA processing in response to molecular inputs and hold promise for a wide array of biotechnological applications.
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Affiliation(s)
- Neda Bagheri
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alejandro Chamorro
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Andrea Idili
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Sciences and Chemical Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
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4
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Sorrentino D, Ranallo S, Nakamura E, Franco E, Ricci F. Synthetic Genes For Dynamic Regulation Of DNA-Based Receptors. Angew Chem Int Ed Engl 2024; 63:e202319382. [PMID: 38457363 DOI: 10.1002/anie.202319382] [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] [Received: 12/15/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
We present a strategy to control dynamically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be cotranscriptionally regulated (activated or inhibited) through specific RNA molecules produced by rationally designed synthetic genes. The kinetics of our DNA sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling.
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Affiliation(s)
- Daniela Sorrentino
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Eiji Nakamura
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering and of Bioengineering, University of California at Los Angeles, 420 Westwood Plaza, Los Angeles, California, 90095, United States
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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5
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Tan W, Zhang C, Cheng S, Hu X, Wang M, Xian Y. DNA Gate-Based CRISPR-Cas Exponential Amplification System for Ultrasensitive Small Extracellular Vesicle Detection to Enhance Breast Cancer Diagnosis. Anal Chem 2024; 96:1328-1335. [PMID: 38190500 DOI: 10.1021/acs.analchem.3c04873] [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: 01/10/2024]
Abstract
Tumor-derived small extracellular vesicles (tEVs) as potential biomarkers possess abundant surface proteins closely related to parent cells, which are crucial for noninvasive cancer diagnosis. However, tEVs exhibit phenotype heterogeneity and low abundance, posing a significant challenge for multiplex detection with a high sensitivity. Herein, we developed a DNA gate-based exponential amplification CRISPR-Cas (DGEAC) system for accurate and ultrasensitive detection of tEVs, which can greatly improve the accuracy of breast cancer (BC) diagnosis. Based on the coexpression of CD63 and vascular endothelial growth factor (VEGF) on BC-derived tEVs, we developed a dual-aptamer-based AND gate fluorescent probe by proximity hybridization. By integrating the target recognition and trans-cleavage activity of Cas12a, an autocatalysis-driven exponential amplification circuit was developed for ultrasensitive detection of CD63 and VEGF proteins on tEVs, which could avoid false negative signals from single protein or other interfering proteins. We achieved highly sensitive detection of tEVs over a linear range from 1.75 × 103 to 3.5 × 108 particles/mL with a detection limit as low as 1.02 × 103 particles/mL. Furthermore, the DGEAC system can distinguish tEVs from tEVs derived from different BC cell lines, including MDA-MB-231, MCF-7, SKBR3, and MCF-10A. Compared to linear amplification (AUC 90.0%), the DGEAC system effectively differentiates BC in different stages (AUC 98.3%).
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Affiliation(s)
- Wenqiao Tan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Cuiling Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Shasha Cheng
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Xinyu Hu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Man Wang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yuezhong Xian
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
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6
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Steinkühler J, Peruzzi JA, Krüger A, Villaseñor CG, Jacobs ML, Jewett MC, Kamat NP. Improving Cell-Free Expression of Model Membrane Proteins by Tuning Ribosome Cotranslational Membrane Association and Nascent Chain Aggregation. ACS Synth Biol 2024; 13:129-140. [PMID: 38150067 DOI: 10.1021/acssynbio.3c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Cell-free gene expression (CFE) systems are powerful tools for transcribing and translating genes outside of a living cell. Synthesis of membrane proteins is of particular interest, but their yield in CFE is substantially lower than that for soluble proteins. In this paper, we study the CFE of membrane proteins and develop a quantitative kinetic model. We identify that ribosome stalling during the translation of membrane proteins is a strong predictor of membrane protein synthesis due to aggregation between the ribosome nascent chains. Synthesis can be improved by the addition of lipid membranes, which incorporate protein nascent chains and, therefore, kinetically compete with aggregation. We show that the balance between peptide-membrane association and peptide aggregation rates determines the yield of the synthesized membrane protein. We define a membrane protein expression score that can be used to rationalize the engineering of lipid composition and the N-terminal domain of a native and computationally designed membrane proteins produced through CFE.
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Affiliation(s)
- Jan Steinkühler
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Bio-Inspired Computation, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - Justin A Peruzzi
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Citlayi G Villaseñor
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
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7
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Díaz-Fernández A, Ranallo S, Ricci F. Enzyme-Linked DNA Displacement (ELIDIS) Assay for Ultrasensitive Electrochemical Detection of Antibodies. Angew Chem Int Ed Engl 2024; 63:e202314818. [PMID: 37994381 DOI: 10.1002/anie.202314818] [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] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/24/2023]
Abstract
Here we report the development of a method for the electrochemical ultrasensitive detection of antibodies that couples the programmability and versatility of DNA-based systems with the sensitivity provided by enzymatic amplification. The platform, termed Enzyme-Linked DNA Displacement (ELIDIS), is based on the use of antigen-DNA conjugates that, upon the bivalent binding of a specific target antibody, induce the release of an enzyme-DNA hybrid strand from a preformed duplex. Such enzyme-DNA hybrid strand can then be electrochemically detected with a disposable electrode with high sensitivity. We applied ELIDIS to demonstrate the sensitive (limit of detection in the picomolar range), specific and multiplexed detection of five different antibodies including three clinically relevant ones. ELIDIS is also rapid (it only requires two reaction steps), works well in complex media (serum) and is cost-effective. A direct comparison with a commercial ELISA kit for the detection of Cetuximab demonstrates the promising features of ELIDIS as a point-of-care platform for antibodies detection.
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Affiliation(s)
- Ana Díaz-Fernández
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - Simona Ranallo
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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8
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Brannetti S, Gentile S, Chamorro-Garcia A, Barbero L, Del Grosso E, Ricci F. Decorated DNA-Based Scaffolds as Lateral Flow Biosensors. Angew Chem Int Ed Engl 2023; 62:e202313243. [PMID: 37804080 DOI: 10.1002/anie.202313243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA-based structures decorated with reporter tags and recognition elements. We have rationally re-engineered tile-based DNA tubular structures that can act as scaffolds and can be decorated with recognition elements of different nature (i.e. antigens, aptamers or proteins) and with orthogonal fluorescent dyes. As a proof-of-principle we have developed sandwich and competitive multiplex lateral flow platforms for the detection of several targets, ranging from small molecules (digoxigenin, Dig and dinitrophenol, DNP), to antibodies (Anti-Dig, Anti-DNP and Anti-MUC1/EGFR bispecific antibodies) and proteins (thrombin). Coupling the advantages of functional DNA-based scaffolds together with the simplicity of LFAs, our approach offers the opportunity to detect a wide range of targets with nanomolar sensitivity and high specificity.
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Affiliation(s)
- Simone Brannetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Serena Gentile
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alejandro Chamorro-Garcia
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Luca Barbero
- RBM-Merck an affiliate of Merck KGaA, Via Ribes 1, 10010, Turin, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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9
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Yu M, Ye R, Zeng T, Tan L, Zhao Z, Gao W, Chen X, Lian Z, Ma Y, Li A, Hu J. Constructing an Ultra-Rapid Nanoconfinement-Enhanced Fluorescence Clinical Detection Platform by Using Machine Learning and Tunable DNA Xerogel "Probe". Anal Chem 2023; 95:15690-15699. [PMID: 37830461 DOI: 10.1021/acs.analchem.3c02955] [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: 10/14/2023]
Abstract
Low mass transfer efficiency and unavoidable matrix effects seriously limit the development of rapid and accurate determination of biosensing systems. Herein, we have successfully constructed an ultra-rapid nanoconfinement-enhanced fluorescence clinical detection platform based on machine learning (ML) and DNA xerogel "probe", which was performed by detecting neutrophil gelatinase-associated lipocalin (NGAL, protein biomarker of acute kidney injury). By regulating pore sizes of the xerogels, the transfer of NGAL in xerogels can approximate that in homogeneous solution. Due to electrostatic attraction of the pore entrances, NGAL rapidly enriches on the surface and inside the xerogels. The reaction rate of NGAL and aptamer cross-linked in xerogels is also accelerated because of the nanoconfinement effect-induced increasing reactant concentration and the enhanced affinity constant KD between reactants, which can be promoted by ∼667-fold than that in bulk solution, thus achieving ultra-rapid detection (ca. 5 min) of human urine. The platform could realize one-step detection without sample pretreatments due to the antiligand exchange effect on the surface of N-doped carbon quantum dots (N-CQDs) in xerogels, in which ligand exchange between -COOH and underlying interfering ions in urine will be inhibited due to higher adsorption energy of -COOH on the N-CQD surface relative to the interfering ions. Based on the ML-extended program, the real-time analysis of the urine fluorescence spectra can be completed within 2 s. Interestingly, by changing DNA, aptamer sequences, or xerogel fluorescence intensities, the detection platform can be customized for targeted diseases.
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Affiliation(s)
- Meng Yu
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Rongkai Ye
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Tao Zeng
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Li Tan
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ziyu Zhao
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Wenjing Gao
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Xin Chen
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ziqi Lian
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Ying Ma
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
| | - Aiqing Li
- Division of Nephrology, Nanfang Hospital, National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou 510515, China
| | - Jianqiang Hu
- School of Chemistry and Chemical Engineering, Key Lab of Fuel Cell Technology of Guangdong Province, South China University of Technology, Guangzhou 510641, China
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10
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Wan J, Liang Y, Hu Q, Liang Z, Feng W, Tian Y, Li S, Ye Z, Hong M, Han D, Niu L. Amplification-Free Ratiometric Electrochemical Aptasensor for Point-of-Care Detection of Therapeutic Monoclonal Antibodies. Anal Chem 2023; 95:14094-14100. [PMID: 37672684 DOI: 10.1021/acs.analchem.3c03052] [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: 09/08/2023]
Abstract
The rapid quantification of therapeutic monoclonal antibodies (mAbs) is of great significance to their pharmacokinetics/pharmacodynamics (PK/PD) research and the personalized medication for disease treatment. Taking advantage of the direct decoration of tens of redox tags to the target of interest, we illustrate herein an amplification-free ratiometric electrochemical aptasensor for the point-of-care (POC) detection of trace amounts of therapeutic mAbs. The POC detection of therapeutic mAbs involved the use of the methylene blue (MB)-conjugated aptamer as the affinity element and the decoration of therapeutic mAbs with ferrocene (Fc) tags via the boronate crosslinking, in which the MB-derived peak current was used as the reference signal, and the peak current of the Fc tag was used as the output signal. As each therapeutic mAb carries tens of diol sites for the site-specific decoration of the Fc output tags, the boronate crosslinking enabled the amplification-free detection, which is cost-effective and quite simple in operation. In the presence of bevacizumab (BevMab) as the target, the resulting ratiometric signal (i.e., the IFc/IMB value) exhibited a good linear response over the range of 0.025-2.5 μg/mL, and the limit of detection (LOD) of the electrochemical aptasensor was 6.5 ng/mL. Results indicated that the aptamer-based affinity recognition endowed the detection of therapeutic mAbs with high selectivity, while the ratiometric readout exhibited satisfactory reproducibility and robustness. Moreover, the ratiometric electrochemical aptasensor is applicable to the detection of therapeutic mAbs in serum samples. Taking together, the amplification-free ratiometric electrochemical aptasensor holds great promise in the POC detection of therapeutic mAbs.
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Affiliation(s)
- Jianwen Wan
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yiyi Liang
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Qiong Hu
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Zhiwen Liang
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Wenxing Feng
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yiyan Tian
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Shiqi Li
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Zhuojun Ye
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Mingru Hong
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Dongxue Han
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Li Niu
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, P. R. China
- Center for Advanced Analytical Science, Guangzhou Key Laboratory of Sensing Materials and Devices, Guangdong Engineering Technology Research Center for Sensing Materials and Devices, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
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Zhang C, Paluzzi VE, Sha R, Jonoska N, Mao C. Implementing Logic Gates by DNA Crystal Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302345. [PMID: 37220213 DOI: 10.1002/adma.202302345] [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: 03/13/2023] [Revised: 05/03/2023] [Indexed: 05/25/2023]
Abstract
DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Natasha Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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Ranallo S, Bracaglia S, Sorrentino D, Ricci F. Synthetic Antigen-Conjugated DNA Systems for Antibody Detection and Characterization. ACS Sens 2023. [PMID: 37463359 PMCID: PMC10391708 DOI: 10.1021/acssensors.3c00564] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Antibodies are among the most relevant biomolecular targets for diagnostic and clinical applications. In this Perspective, we provide a critical overview of recent research efforts focused on the development and characterization of devices, switches, and reactions based on the use of synthetic antigen-conjugated DNA strands designed to be responsive to specific antibodies. These systems can find applications in sensing, drug-delivery, and antibody-antigen binding characterization. The examples described here demonstrate how the programmability and chemical versatility of synthetic nucleic acids can be used to create innovative analytical tools and target-responsive systems with promising potentials.
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Affiliation(s)
- Simona Ranallo
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Sara Bracaglia
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Daniela Sorrentino
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
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