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Yin H, Chu Y, Wang W, Zhang Z, Meng Z, Min Q. Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules. NANOSCALE 2023; 15:2529-2540. [PMID: 36688447 DOI: 10.1039/d2nr06020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.
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Affiliation(s)
- Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Yanxin Chu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhen Meng
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
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2
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Liu M, Miao D, Qin S, Liu H, Bai Y. Mass tags-based mass spectrometric immunoassay and its bioanalysis applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Wang Y, Sun W, Wang J, Wang X, Xu Y, Guo Y, Wang Y, Zhang M, Jiang L, Liu S, Huang J. Ultrasensitive Uracil-DNA Glycosylase Activity Assay and Its Inhibitor Screening Based on Primer Remodeling Jointly via Repair Enzyme and Polymerase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:3868-3875. [PMID: 35298179 DOI: 10.1021/acs.langmuir.2c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of isothermal nucleic acid amplification techniques has great significance for highly sensitive biosensing in modern biology and biomedicine. A facile and robust exponential rolling circle amplification (RCA) strategy is proposed based on primer-remodeling amplification jointly via a repair enzyme and polymerase, and uracil-DNA glycosylase (UDG) is selected as a model analyte. Two kinds of complexes, complex I and complex II, are preprepared by hybridizing a circular template (CT) with a uracil-containing hairpin probe and tetrahydrofuran abasic site mimic (AP site)-embedded fluorescence-quenched probe (AFP), respectively. The target UDG specifically binds to complex I, resulting in the generation of an AP site, followed by cleavage via endonuclease IV (Endo IV) and the successive trimming of unmatched 3' terminus via phi29 DNA polymerase, thus producing a useable primer-CT complex that actuates the primary RCA. Then, numerous complex II anneal with the first-generation RCA product (RP), generating a complex II-RP assembly containing AP sites within the DNA duplex. With the aid of Endo IV and phi29, AFP, as a pre-primer in complex II, is converted into a mature primer to initiate additional rounds of RCA. So, countless AFPs are cleaved, releasing remarkably strong fluorescent signals. The biosensor is demonstrated to enable rapid and accurate detection of the UDG activity with an improved detection limit as low as 4.7 × 10-5 U·mL-1. Moreover, this biosensor is successfully applied for UDG inhibitor screening and complicated biological samples analysis. Compared to the previous exponential RCA methods, our proposed strategy offers additional advantages, including excellent stability, optional design of CT, and simplified operating steps. Therefore, this proposed strategy may create a useful and practical platform for ultrasensitive detection of low levels of analytes in clinical diagnosis and fundamental biomedicine research.
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Affiliation(s)
- Yu Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Wenyu Sun
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Jingfeng Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xu Wang
- Shandong Institute of Metrology and Science, Jinan 250014, P. R. China
| | - Yicheng Xu
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yuanzhen Guo
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Yeru Wang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
| | - Manru Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Long Jiang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Su Liu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, P. R. China
| | - Jiadong Huang
- School of Biological Sciences and Technology, University of Jinan, Jinan 250022, P. R. China
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Gu C, Shan F, Zheng L, Zhou Y, Hu J, Chen G. Towards a protein-selective Raman enhancement by a glycopolymer-based composite surface. J Mater Chem B 2022; 10:1434-1441. [PMID: 35168248 DOI: 10.1039/d1tb02746h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Surface-enhanced Raman scattering (SERS), which is based on the surface plasmon resonance (LSPR) of noble metal nanostructures, is widely used in the biological field due to its advantages of non-damaging samples and detection up to the molecular level. For biological SERS detection, preparation of substrates with biocompatibility and specific adsorption, leading to selective enhancement of the target biomolecules, are important design strategies. Utilizing the specific interaction between a carbohydrate and protein, a glycopolymer-based composite surface is fabricated to realize specific SERS detection of proteins. Herein, we use N-3,4-dihydroxybenzeneethyl methacrylamide (DMA), 2-deoxy-2-(methacrylamido)glucopyranose (MAG) and methacrylic acid (MAA) as monomers in a sunlight-induced RAFT polymerization to synthesize a dopamine-containing glycopolymer. The glycopolymers are used to prepare a SERS substrate. The composite surface shows specific protein adsorption capacity, and the selective Raman enhancement of specific proteins was successfully achieved between the two different proteins Con A and BSA. This provides a feasible approach to design a SERS surface for protein detection and the study of the interaction between sugar and proteins.
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Affiliation(s)
- Chuan Gu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Jiangsu Key Laboratory of Thin Films, Soochow University, Suzhou 215006, P. R. China.
| | - Fangjian Shan
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Jiangsu Key Laboratory of Thin Films, Soochow University, Suzhou 215006, P. R. China.
| | - Lifang Zheng
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Jiangsu Key Laboratory of Thin Films, Soochow University, Suzhou 215006, P. R. China.
| | - Yue Zhou
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Jiangsu Key Laboratory of Thin Films, Soochow University, Suzhou 215006, P. R. China.
| | - Jun Hu
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Jiangsu Key Laboratory of Thin Films, Soochow University, Suzhou 215006, P. R. China.
| | - Gaojian Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Jiangsu Key Laboratory of Thin Films, Soochow University, Suzhou 215006, P. R. China.
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5
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Wang Y, Li B, Tian T, Liu Y, Zhang J, Qian K. Advanced on-site and in vitro signal amplification biosensors for biomolecule analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Ruan Q, Yang J, Zou F, Chen X, Zhang Q, Zhao K, Lin X, Zeng X, Yu X, Wu L, Lin S, Zhu Z, Yang C. Single-Cell Digital Microfluidic Mass Spectrometry Platform for Efficient and Multiplex Genotyping of Circulating Tumor Cells. Anal Chem 2021; 94:1108-1117. [PMID: 34964350 DOI: 10.1021/acs.analchem.1c04194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene mutation profiling of heterogeneous circulating tumor cells (CTCs) offers comprehensive and real-time molecular information of tumors for targeted therapy guidance, but the lack of efficient and multiplex genotyping techniques for single-CTC analysis greatly hinders its development and clinical application. This paper reports a single-CTC mass spectrometry analysis method for efficient and multiplex mutation profiling based on digital microfluidics. Digital microfluidics affords integrated single-CTC manipulation, from single-CTC isolation to high-performance whole genome amplification, via nanoliter droplet-based wettability trapping and hydrodynamic adjustment of cell distribution. Coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, multiplex mutation information of individual CTCs can be efficiently and accurately identified by the inherent mass differences of different DNA sequences. This platform achieves Kirsten rat sarcoma viral oncogene mutation profiling of heterogeneous CTCs at the single-cell level from cancer patient samples, offering new avenues for genotype profiling of single CTCs and cancer therapy guidance.
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Affiliation(s)
- Qingyu Ruan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jian Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fenxiang Zou
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaofeng Chen
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Qianqian Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Kaifeng Zhao
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiaoye Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xi Zeng
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiyuan Yu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuichao Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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7
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Hu J, Liu F, Chen Y, Shangguan G, Ju H. Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules. ACS Sens 2021; 6:3517-3535. [PMID: 34529414 DOI: 10.1021/acssensors.1c01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.
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Affiliation(s)
- Junjie Hu
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Guoqiang Shangguan
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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8
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Xu H, Zhang Z, Wang Y, Lu W, Min Q. Engineering of nanomaterials for mass spectrometry analysis of biomolecules. Analyst 2021; 146:5779-5799. [PMID: 34397044 DOI: 10.1039/d1an00860a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) based analysis has received intense attention in diverse biological fields. However, direct MS interrogation of target biomolecules in complex biological samples is still challenging, due to the extremely low abundance and poor ionization potency of target biological species. Innovations in nanomaterials create new auxiliary tools for deep and comprehensive MS characterization of biomolecules. More recently, growing research interest has been directed to the compositional and structural engineering of nanomaterials for enriching target biomolecules prior to MS analysis, enhancing the ionization efficiency in MS detection and designing biosensing nanoprobes in sensitive MS readout. In this review, we mainly focus on the recent advances in the engineering of nanomaterials towards their applications in sample pre-treatment, desorption/ionization matrices and ion signal amplification for MS profiling of biomolecules. This review will provide a toolbox of nanomaterials for researchers devoted to developing analytical methods and practical applications in the biological MS field.
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Affiliation(s)
- Hongmei Xu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China. and Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Yihan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Weifeng Lu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
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9
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Wang L, Deng Y, Huang Y, Wei J, Ma J, Li G. Template-free multiple signal amplification for highly sensitive detection of cancer cell-derived exosomes. Chem Commun (Camb) 2021; 57:8508-8511. [PMID: 34351331 DOI: 10.1039/d1cc03640h] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work, we have designed a template-free multiple signal amplification method for the highly sensitive detection of cancer cell-derived exosomes. In this design, DNase I serves as a bridge to link the DNA-based amplification approach and terminal deoxynucleotidyl transferase (TdT)-mediated polymerization reaction. Consequently, a detection limit of 10 particles per μL can be achieved, while a complex nucleic acid sequence design can be avoided. This method also exhibits good performance in a complicated matrix and enables the differentiation of healthy individuals from colorectal cancer (CRC) patients.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
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10
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Li J, Yang F, Jiang B, Zhou W, Xiang Y, Yuan R. The synchronization of multiple signal amplifications for label-free and sensitive aptamer-based sensing of a protein biomarker. Analyst 2021; 145:7858-7863. [PMID: 33020770 DOI: 10.1039/d0an01491e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The abnormal variation of the mucin 1 (MUC1) protein level is associated with the development of multiple cancers, and the monitoring of trace MUC1 can be useful for early disease diagnosis. Here, on the basis of the synchronization of DNA-fueled sequence recycling and dual rolling circle amplification (RCA), the establishment of a non-label and highly sensitive fluorescent aptamer-based detection strategy for the MUC1 protein biomarker is described. The target MUC1 binds the aptamer hairpin probe and causes its structure switching to release an ssDNA tail to trigger the recycling of the complex via two toehold-mediated strand displacement reactions under assistance of a fuel DNA. Such a recycling amplification leads to the formation of a partial dsDNA duplex with two primers at both ends, which cooperatively bind the circular DNA ring template to start the dual RCA to produce many G-quadruplex sequences. The protoporphyrin IX dye further associates with the G-quadruplex structures to show a dramatically elevated fluorescent signal for sensitively detecting MUC1 with a low detection limit of 0.5 pM. The established aptamer-based detecting strategy is also highly selective and can realize assay of MUC1 in diluted human serums, highlighting its potential for the detection of different protein biomarkers at low contents.
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Affiliation(s)
- Jin Li
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
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Shi H, Cui J, Sulemana H, Wang W, Gao L. Protein detection based on rolling circle amplification sensors. LUMINESCENCE 2021; 36:842-848. [PMID: 33502072 DOI: 10.1002/bio.4017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/07/2021] [Accepted: 01/17/2021] [Indexed: 12/22/2022]
Abstract
Rolling circle amplification (RCA) is an isothermal process under the action of DNA polymerases. Large-scale DNA templates have been generated using RCA for target detection. Some signal amplification strategies including optical sensors and electrochemical sensors based on RCA have been applied to achieve sensitive detection. Sensors based on RCA have attracted increasing interest. Advances in RCA-based sensors for protein detection are reviewed in this paper. The advantages and detection mechanisms of sensors based on RCA are revealed and discussed. Finally, possible challenges and future perspectives are also outlined.
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Affiliation(s)
- Haixia Shi
- P. E. Department of Jiangsu University, Zhenjiang, China
| | - Jingjie Cui
- School of Automation, Hangzhou Dianzi University, Hangzhou, China
| | | | - Wunian Wang
- P. E. Department of Jiangsu University, Zhenjiang, China
| | - Li Gao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
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12
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Xu H, Huang X, Zhang Z, Zhang X, Min Q, Zhu JJ. Protease-responsive mass barcoded nanotranslators for simultaneously quantifying the intracellular activity of cascaded caspases in apoptosis pathways. Chem Sci 2020; 11:5280-5288. [PMID: 34122985 PMCID: PMC8159337 DOI: 10.1039/d0sc01534b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Quantitatively delineating the activation network of multiple proteases that participate in cellular processes is highly essential for understanding the physiological and pathological states of cells. In this study, protease-responsive mass barcoded nanotranslators (PRMNTs) were engineered for revealing the activity of cascaded caspases in apoptosis in a multiplex and quantitative manner. In the PRMNTs, a series of mass tag-decorated gold nanoparticles (AuNPs) were tethered onto magnetic Fe3O4 nanospheres via a linker containing the substrate peptide of the target protease to form a "one-to-many" core-satellite structure. This nanostructure was internalized into the cells, underwent an enzymatic reaction within the cells, and allowed post-reaction mass spectrometry (MS) interrogation after magnetic separation from the cells. In the presence of intracellular caspases, enzymatic cleavage of the linker could be translated to the decreased ion signals of the mass tags on the remaining AuNPs in the PRMNTs by MS decoding. Benefiting from the multiplexing capability of MS, the intracellular activity of caspase-3, -8 and -9 that orchestrate the apoptotic process was simultaneously quantified at any given time. Kinetic analysis of caspase activity under stimulation of diverse anticancer drugs revealed that programmed cell death followed individual apoptosis pathways, differing in the activation degree and sequence of the caspase cascade. This work represents a modality that interfaces nanotechnology with MS for quantitatively probing the intracellular activity of multiple proteases, which opens up new avenues for revealing the apoptosis mechanism and developing innovative drugs.
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Affiliation(s)
- Hongmei Xu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Xiaodan Huang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Xuemeng Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China
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13
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Zhang Z, Wang S, Ma J, Zhou T, Wang F, Wang X, Zhang G. Rolling Circle Amplification-Based Polyvalent Molecular Beacon Probe-Assisted Signal Amplification Strategies for Sensitive Detection of B16 Cells. ACS Biomater Sci Eng 2020; 6:3114-3121. [PMID: 33463255 DOI: 10.1021/acsbiomaterials.0c00288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We developed a simple and sensitive signal amplification method for the detection of B16 cells based on the combination of rolling circle amplification (RCA) and molecular beacons (MBs). A long-chain structure of DNA synthesized by RCA was used to turn on aptamer-based MBs. Because of the multiple complementary repeat units, the RCA scaffold hybridized tens or hundreds of MBs to form polyvalent aptamer probes. The unfold ability and the fluorescence intensity of MBs were both improved by RCA, as compared to short single chains. The cell experiment results demonstrated that RCA-based polyvalent MBs were significantly more effective than monovalent MBs in targeting B16 cells and signal sensitivity because of their multivalent effects. The establishment of this strategy would provide a powerful platform for early clinical diagnostics of cancer cells.
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Affiliation(s)
- Zhiqing Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Shanshan Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jie Ma
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ting Zhou
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiufeng Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Guodong Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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Zhan Z, Li H, Liu J, Xie G, Xiao F, Wu X, Aguilar ZP, Xu H. A competitive enzyme linked aptasensor with rolling circle amplification (ELARCA) assay for colorimetric detection of Listeria monocytogenes. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106806] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Qi L, Hu Q, Kang Q, Bi Y, Jiang Y, Yu L. Detection of Biomarkers in Blood Using Liquid Crystals Assisted with Aptamer-Target Recognition Triggered in Situ Rolling Circle Amplification on Magnetic Beads. Anal Chem 2019; 91:11653-11660. [PMID: 31430128 DOI: 10.1021/acs.analchem.9b02186] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of biomarkers in body fluids is critical to both diagnosing the life-threatening diseases and optimizing therapeutic interventions. We herein report use of liquid crystals (LCs) to detect biomarkers in blood with high sensitivity and specificity by employing in situ rolling circle amplification (RCA) on magnetic beads (MBs). Specific recognition of cancer biomarkers, such as platelet derived growth factor BB (PDGF-BB) and adenosine, by aptamers leads to formation of a nucleic acid circle on MBs preassembled with ligation DNA, linear padlock DNA, and aptamers, thereby triggering in situ RCA. LCs change from dark to bright appearance after the in situ RCA products being transferred onto the LC interface decorated with octadecy trimethylammonium bromide (OTAB), which is particularly sensitive to the amplified DNA on MBs. Overall, this label-free approach takes advantages of high specificity of aptamer-based assay, efficient enrichment of signaling molecules on MBs, remarkable DNA elongation performance of the RCA reaction, and high sensitivity of LC-based assay. It successfully eliminates the matrix interference on the LC-based sensors and thus achieves at least 4 orders of magnitude improvement in sensitivity for detection of biomarkers compared to other LC-based sensors. In addition, performance of the developed sensor is comparable to that of the commercial ones. Thus, this study provides a simple, powerful, and promising approach to facilitate highly sensitive, specific, and label-free detection of biomarkers in body fluids.
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Affiliation(s)
- Lubin Qi
- Key Laboratory of Colloid and Interface Chemistry , Shandong University, Ministry of Education , Jinan 250100 , China
| | - Qiongzheng Hu
- Shandong Analysis and Test Center , Qilu University of Technology (Shandong Academy of Sciences) , Jinan 250014 , China
| | - Qi Kang
- College of Chemistry, Chemical Engineering and Materials Science , Shandong Normal University , Jinan 250014 , China
| | - Yanhui Bi
- Key Laboratory of Colloid and Interface Chemistry , Shandong University, Ministry of Education , Jinan 250100 , China
| | - Yifei Jiang
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Li Yu
- Key Laboratory of Colloid and Interface Chemistry , Shandong University, Ministry of Education , Jinan 250100 , China
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Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI. Biochem J 2019; 476:1483-1496. [PMID: 31064800 DOI: 10.1042/bcj20190167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/05/2023]
Abstract
Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.
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Li W, Khan M, Li H, Lin L, Mao S, Lin JM. Homogenous deposition of matrix–analyte cocrystals on gold-nanobowl arrays for improving MALDI-MS signal reproducibility. Chem Commun (Camb) 2019; 55:2166-2169. [DOI: 10.1039/c8cc09945f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An Au-nanobowl array was synthesized to utilize its excellent properties to achieve efficient quantitative analysis via MALDI-MS analysis.
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Affiliation(s)
- Weiwei Li
- Department of Chemistry
- Beijing Key Laboratory of Micronalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Mashooq Khan
- Department of Chemistry
- Beijing Key Laboratory of Micronalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Haifang Li
- Department of Chemistry
- Beijing Key Laboratory of Micronalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Ling Lin
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology
- CAS Center for Excellence in Nanoscience
- National Center for Nanoscience and Technology
- Beijing 100190
- P. R. China
| | - Sifeng Mao
- Department of Chemistry
- Beijing Key Laboratory of Micronalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Jin-Ming Lin
- Department of Chemistry
- Beijing Key Laboratory of Micronalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
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