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Chen Y, Chen X, Zhang B, Zhang Y, Li S, Liu Z, Gao Y, Zhao Y, Yan L, Li Y, Tian T, Lin Y. DNA framework signal amplification platform-based high-throughput systemic immune monitoring. Signal Transduct Target Ther 2024; 9:28. [PMID: 38320992 PMCID: PMC10847453 DOI: 10.1038/s41392-024-01736-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/14/2023] [Accepted: 01/01/2024] [Indexed: 02/08/2024] Open
Abstract
Systemic immune monitoring is a crucial clinical tool for disease early diagnosis, prognosis and treatment planning by quantitative analysis of immune cells. However, conventional immune monitoring using flow cytometry faces huge challenges in large-scale sample testing, especially in mass health screenings, because of time-consuming, technical-sensitive and high-cost features. However, the lack of high-performance detection platforms hinders the development of high-throughput immune monitoring technology. To address this bottleneck, we constructed a generally applicable DNA framework signal amplification platform (DSAP) based on post-systematic evolution of ligands by exponential enrichment and DNA tetrahedral framework-structured probe design to achieve high-sensitive detection for diverse immune cells, including CD4+, CD8+ T-lymphocytes, and monocytes (down to 1/100 μl). Based on this advanced detection platform, we present a novel high-throughput immune-cell phenotyping system, DSAP, achieving 30-min one-step immune-cell phenotyping without cell washing and subset analysis and showing comparable accuracy with flow cytometry while significantly reducing detection time and cost. As a proof-of-concept, DSAP demonstrates excellent diagnostic accuracy in immunodeficiency staging for 107 HIV patients (AUC > 0.97) within 30 min, which can be applied in HIV infection monitoring and screening. Therefore, we initially introduced promising DSAP to achieve high-throughput immune monitoring and open robust routes for point-of-care device development.
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Affiliation(s)
- Ye Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Xingyu Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Bowen Zhang
- Department of Prosthodontics, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, 300041, PR China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Songhang Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Yang Gao
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Yuxuan Zhao
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Lin Yan
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | - Yi Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China.
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China.
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, PR China.
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, 610041, Sichuan, China.
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Chamorro A, Rossetti M, Bagheri N, Porchetta A. Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:71-106. [PMID: 38273204 DOI: 10.1007/10_2023_235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.
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Affiliation(s)
| | - Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
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Myres GJ, Harris JM. Stable Immobilization of DNA to Silica Surfaces by Sequential Michael Addition Reactions Developed with Insights from Confocal Raman Microscopy. Anal Chem 2023; 95:3499-3506. [PMID: 36718639 DOI: 10.1021/acs.analchem.2c05594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The immobilization of DNA to surfaces is required for numerous biosensing applications related to the capture of target DNA sequences, proteins, or small-molecule analytes from solution. For these applications to be successful, the chemistry of DNA immobilization should be efficient, reproducible, and stable and should allow the immobilized DNA to adopt a secondary structure required for association with its respective target molecule. To develop and characterize surface immobilization chemistry to meet this challenge, it is invaluable to have a quantitative, surface-sensitive method that can report the interfacial chemistry at each step, while also being capable of determining the structure, stability, and activity of the tethered DNA product. In this work, we develop a method to immobilize DNA to silica, glass, or other oxide surfaces by carrying out the reactions in porous silica particles. Due to the high specific surface area of porous silica, the local concentrations of surface-immobilized molecules within the particle are sufficiently high that interfacial chemistry can be monitored at each step of the process with confocal Raman microscopy, providing a unique capability to assess the molecular composition, structure, yield, and surface coverage of these reactions. We employ this methodology to investigate the steps for immobilizing thiolated-DNA to thiol-modified silica surfaces through sequential Michael addition reactions with the cross-linker 1,4-phenylene-bismaleimide. A key advantage of employing a phenyl-bismaleimide over a comparable alkyl coupling reagent is the efficient conversion of the initial phenyl-thiosuccinimide to a more stable succinamic acid thioether linkage. This transformation was confirmed by in situ Raman spectroscopy measurements, and the resulting succinamic acid thioether product exhibited greater than 95% retention of surface-immobilized DNA after 12 days at room temperature in aqueous buffer. Confocal Raman microscopy was also used to assess the conformational freedom of surface-immobilized DNA by comparing the structure of a 23-mer DNA hairpin sequence under duplex-forming and unfolding conditions. We find that the immobilized DNA hairpin can undergo reversible intramolecular duplex formation based on the changes in frequencies and intensities of the phosphate backbone and base-specific vibrational modes that are informative of the hybridization state of DNA.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
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Sensors and the Surface Chemistry Conundrum. ACS Sens 2023; 8:1-2. [PMID: 36704905 DOI: 10.1021/acssensors.3c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Zhou X, Sun Z, Su X, Zheng K, Zou X, Zhang W. Ratiometric Detection of Ochratoxin A Using a Regenerable COF-Au-MB-Apt Signal Probe on a Thermal-Regulated Sensor Module. Anal Chem 2023; 95:1916-1923. [PMID: 36621809 DOI: 10.1021/acs.analchem.2c04031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ochratoxin A (OTA) frequently contaminates grains and consequently threatens human health. Herein, we develop a regenerable signal probe and apply it to a Au-based screen-printed electrode module (SPE) for OTA determination. The signal probe, containing a structural covalent organic framework, gold nanoparticles (AuNPs), indicative methylene blue (MB), and a highly selective aptamer, is synthesized with hydrothermal and self-assembly methods. The SPE is permanently functionalized with Prussian blue (PB), AuNPs, and semicomplementary ssDNA. The signal probe, absorbed onto this SPE via hybridization, is competitively expelled by OTA, providing a ratiometric readout of ΔIMB/IPB. Probe regeneration, to erase expired COF-Au-MB-Apt after each analysis, is established with the synergy of OTA-conducted Apt-ssDNA dissociation and on-chip thermal regulation. This advantage powerfully guarantees reduplicative analyses by avoiding irreversible Apt-OTA combination and accumulation on the sensing interface. Regenerations are performed in repetitive cycles (N = 7) with 98.5% reproduction efficiency, and IMB and IPB fluctuations are calculated as 1.45 and 1.12%. This method shows log-linear OTA response in a wide range from 0.2 pg/mL to 0.6 μg/mL, and the limit of detection is 0.12 pg/mL. During natural OTA determinations, recommended readouts match well with HPLC with less than 4.82% relative error.
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Affiliation(s)
- Xuan Zhou
- College of Photoelectric Engineering, Chongqing University, Chongqing 400044, China
- Department of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zongbao Sun
- Department of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaoyu Su
- Department of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Kaiyi Zheng
- Department of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xiaobo Zou
- Department of Food & Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Wen Zhang
- College of Photoelectric Engineering, Chongqing University, Chongqing 400044, China
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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Manuel BA, Sterling SA, Sanford AA, Heemstra JM. Systematically Modulating Aptamer Affinity and Specificity by Guanosine-to-Inosine Substitution. Anal Chem 2022; 94:6436-6440. [PMID: 35435665 DOI: 10.1021/acs.analchem.2c00422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Aptamers are widely used in small molecule detection applications due to their specificity, stability, and cost effectiveness. One key challenge in utilizing aptamers in sensors is matching the binding affinity of the aptamer to the desired concentration range for analyte detection. The most common methods for modulating affinity have inherent limitations, such as the likelihood of drastic changes in aptamer folding. Here, we propose that substituting guanosine for inosine at specific locations in the aptamer sequence provides a less perturbative approach to modulating affinity. Inosine is a naturally occurring nucleotide that results from hydrolytic deamination of adenosine, and like guanine, it base pairs with cytosine. Using the well-studied cocaine binding aptamer, we systematically replaced guanosine with inosine and were able to generate sequences having a range of binding affinities from 230 nM to 80 μM. Interestingly, we found that these substitutions could also modulate the specificity of the aptamers, leading to a range of binding affinities for structurally related analytes. Analysis of folding stability via melting temperature shows that, as expected, aptamer structure is impacted by guanosine-to-inosine substitutions. The ability to tune binding affinity and specificity through guanosine-to-inosine substitution provides a convenient and reliable approach for rapidly generating aptamers for diverse biosensing applications.
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Affiliation(s)
- Brea A Manuel
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Sierra A Sterling
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aimee A Sanford
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Vandghanooni S, Sanaat Z, Farahzadi R, Eskandani M, Omidian H, Omidi Y. Recent progress in the development of aptasensors for cancer diagnosis: Focusing on aptamers against cancer biomarkers. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Cheng X, Yin W. Probing Biosensing Interfaces With Single Molecule Localization Microscopy (SMLM). Front Chem 2021; 9:655324. [PMID: 33996750 PMCID: PMC8117217 DOI: 10.3389/fchem.2021.655324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 11/23/2022] Open
Abstract
Far field single molecule localization microscopy (SMLM) has been established as a powerful tool to study biological structures with resolution far below the diffraction limit of conventional light microscopy. In recent years, the applications of SMLM have reached beyond traditional cellular imaging. Nanostructured interfaces are enriched with information that determines their function, playing key roles in applications such as chemical catalysis and biological sensing. SMLM enables detailed study of interfaces at an individual molecular level, allowing measurements of reaction kinetics, and detection of rare events not accessible to ensemble measurements. This paper provides an update to the progress made to the use of SMLM in characterizing nanostructured biointerfaces, focusing on practical aspects, recent advances, and emerging opportunities from an analytical chemistry perspective.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory for Modern Optical Instrumentations, National Engineering Research Center of Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Wei Yin
- Core Facilities, School of Medicine, Zhejiang University, Hangzhou, China
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