1
|
Zhang Y, Xu S, Luo M, Chen J, Wang L, Yang F, Ye J, Liu J, He B, Weng L, Li S, Zhang D. Hairpin-Empowered Invasive Reaction Combined with Catalytic Hairpin Assembly Cascade Amplification for the Specific Detection of Single-Nucleotide Polymorphisms. Anal Chem 2024; 96:10283-10293. [PMID: 38864304 DOI: 10.1021/acs.analchem.4c01049] [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: 06/13/2024]
Abstract
Single-nucleotide polymorphism (SNP) is widely used in the study of disease-related genes and in the genetic study of animal and plant strains. Therefore, SNP detection is crucial for biomedical diagnosis and treatment as well as for molecular design breeding of animals and plants. In this regard, this article describes a novel technique for detecting SNP using flap endonuclease 1 (FEN 1) as a specific recognition element and catalytic hairpin assembly (CHA) cascade reaction as a signal amplification strategy. The mutant target (MT) was hybridized with a biotin-modified upstream probe and hairpin-type downstream probe (DP) to form a specific three-base overlapping structure. Then, FEN 1 was employed for three-base overlapping structure-specific recognition, namely, the precise SNP site identification and the 5' flap of DP dissociation. After dissociation, the hybridized probes were magnetically separated by a streptavidin-biotin complex. Especially, the ability to establish such a hairpin-type DP provided a powerful tool that could be used to hide the cut sequence (CS) and avoid false-positive signals. The cleaved CS initiated the CHA reaction and allowed superior fluorescence signal generation. Owing to the high specificity of FEN 1 for single base recognition, only the MT could be distinguished from the wild-type target and mismatched DNA. Owing to the dual signal amplification, as low as 0.36 fM MT and 1% mutation abundance from the mixtures could be detected, respectively. Furthermore, it could accurately identify SNPs from human cancer cells, as well as soybean leaf genome extracts. This strategy paves the way for the development of more precise and sensitive tools for diagnosing early onset diseases as well as molecular design breeding tools.
Collapse
Affiliation(s)
- Yunshan Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shijie Xu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Ma Luo
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Lanyue Wang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Fang Yang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Jing Ye
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jichong Liu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Bingxiao He
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Diming Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| |
Collapse
|
2
|
Li J, Wang C, Zhao S, Qi L, Yu J, Hu X, Chen L, Sun Y, Wang D, Jiang Y, Du Y. Custom-Designed Probes for the Accurate Determination of Epidermal Growth Factor Receptor Mutations and Their Allelic Configuration. Anal Chem 2024; 96:10056-10063. [PMID: 38832555 DOI: 10.1021/acs.analchem.4c01771] [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: 06/05/2024]
Abstract
The identification of single nucleotide polymorphisms (SNPs) is of paramount importance for disease diagnosis and clinical prognostication. In the context of nonsmall cell lung cancer (NSCLC), the emergence of resistance mutations, exemplified by the epidermal growth factor receptor (EGFR) T790 M and C797S, is intricately linked to the therapeutic efficacy of EGFR tyrosine kinase inhibitors (EGFR-TKIs). Herein, a highly efficient and specific SNP detection platform for T790 M and C797S mutations has been engineered through the integration of an asymmetric polymerase chain reaction (PCR) and an ingeniously tailored four-way junction (4WJ) probe. Notably, a molecular beacon (MB) probe was judiciously designed to discern the allelic configuration of these mutations. The administration of first- and third-generation EGFR-TKIs demonstrates therapeutic efficacy solely when the mutations are in the trans configuration, characterized by a low fluorescence signal. In contrast, significant fluorescence by the MB probe is indicative of the C797S mutation being in a cis arrangement with T790M, thereby rendering the cells refractory to the therapeutic interventions of both first- and third-generation EGFR-TKIs. The assay is capable of concurrently detecting two point-mutations and ascertaining their allelic positions in a single test within 1.5 h, enhancing both efficiency and simplicity. It also exhibits high accuracy in the identification of clinical samples, offering promising implications for therapeutic guidelines. By enabling tailored treatment plans based on specific genetic profiles, our approach not only advances the precision of NSCLC treatment strategies but also marks a significant contribution to personalized medicine.
Collapse
Affiliation(s)
- Jiaqi Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Chang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Songchen Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200000, China
| | - Lijuan Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jingyuan Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xintong Hu
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Liguo Chen
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Yi Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Duo Wang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun 130022, China
| | - Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| |
Collapse
|
3
|
Zhao NN, Wang Q, Yang DM, Li DL, Han Y, Zhao S, Zou X, Zhang CY. Elongation and Ligation-Mediated Differential Coding for Label-Free and Locus-Specific Analysis of 8-Oxo-7,8-dihydroguanine in DNA. Anal Chem 2024; 96:5323-5330. [PMID: 38501982 DOI: 10.1021/acs.analchem.4c00387] [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: 03/20/2024]
Abstract
Oxidative DNA damage is closely associated with the occurrence of numerous human diseases and cancers. 8-Oxo-7,8-dihydroguanine (8-oxoG) is the most prevalent form of DNA damage, and it has become not only an oxidative stress biomarker but also a new epigenetic-like biomarker. However, few approaches are available for the locus-specific detection of 8-oxoG because of the low abundance of 8-oxoG damage in DNA and the limited sensitivity of existing assays. Herein, we demonstrate the elongation and ligation-mediated differential coding for label-free and locus-specific analysis of 8-oxoG in DNA. This assay is very simple without the involvement of any specific labeled probes, complicated steps, and large sample consumption. The utilization of Bsu DNA polymerase can specifically initiate a single-base extension reaction to incorporate dATP into the opposite position of 8-oxoG, endowing this assay with excellent selectivity. The introduction of cascade amplification reaction significantly enhances the sensitivity. The proposed method can monitor 8-oxoG with a limit of detection of 8.21 × 10-19 M (0.82 aM), and it can identify as low as 0.001% 8-oxoG damage from a complex mixture with excessive undamaged DNAs. This method can be further applied to measure 8-oxoG levels in the genomic DNA of human cells under diverse oxidative stress, holding prospect potential in the dynamic monitoring of critical 8-oxoG sites, early clinical diagnosis, and gene damage-related biomedical research.
Collapse
Affiliation(s)
- Ning-Ning Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Qian Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Dong-Ming Yang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Dong-Ling Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
4
|
Ma Z, Xu J, Hou W, Lei Z, Li T, Shen W, Yu H, Liu C, Zhang J, Tang S. Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography. Anal Chem 2024; 96:5195-5204. [PMID: 38520334 DOI: 10.1021/acs.analchem.3c05500] [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: 03/25/2024]
Abstract
The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.
Collapse
Affiliation(s)
- Ziyu Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Junjie Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Weilin Hou
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Zi Lei
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Tingting Li
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Hui Yu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438, Jiefang Road, Zhenjiang 212000, Jiangsu, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Jinghui Zhang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
| |
Collapse
|
5
|
Chu Z, Chen J, Zhang J, Xie Q, Zhang F, Wang Q. Cyclic Multiple Primer Generation Rolling Circle Amplification Assisted Capillary Electrophoresis for Simultaneous and Ultrasensitive Detection of Multiple Pathogenic Bacteria. Anal Chem 2024; 96:1781-1788. [PMID: 38214113 DOI: 10.1021/acs.analchem.3c05117] [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: 01/13/2024]
Abstract
Efficient, accurate, and economical detection of pathogenic bacteria is crucial in ensuring food safety and preventing foodborne illnesses. How to fulfill the highly sensitive and simultaneous detection of multiple trace pathogenic bacteria is a big challenge. In this work, capillary electrophoresis coupled with a cyclic multiple primer generation rolling circle amplification (cyclic MPG-RCA) was studied for highly sensitive and simultaneous detection of three kinds of pathogenic bacteria. The cyclic MPG-RCA was based on a carefully designed clover-shaped DNA probe, in which three "leaves" corresponded to three types of aimed pathogenic bacteria: Shigella dysenteriae (S. dysenteriae), Salmonella enterica subsp. enterica serovar Typhi (S. Typhi), and Vibrio parahaemolyticus (V. parahaemolyticus). Under the optimal experimental conditions, the limits of detection (S/N = 3) of this method for bacterial target DNA were 11.4 amol·L-1 (S. dysenteriae), 4.88 amol·L-1 (S. Typhi), and 14.9 amol·L-1 (V. parahaemolyticus), and the conversion concentrations for the target bacteria were 10 colony-forming units (CFU)·mL-1 (S. dysenteriae), 3 CFU·mL-1 (S. Typhi), and 12 CFU·mL-1 (V. parahaemolyticus). This method had been applied to the detection of tap water samples with good results, which proved that it could be used as an effective tool for trace pathogenic bacteria monitoring in foods, environments, and medicines.
Collapse
Affiliation(s)
- Zhaohui Chu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jingyi Chen
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jingzi Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Qihui Xie
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| |
Collapse
|
6
|
Zhang Y, Wang L, Ye J, Chen J, Xu S, Bu S, Deng M, Bian L, Zhao X, Zhang C, Weng L, Zhang D. Rationally Designed Dual Base Pair Mismatch Enables Toehold-Mediated Strand Displacement to Efficiently Recognize Single-Nucleotide Polymorphism without Enzymes. Anal Chem 2024; 96:554-563. [PMID: 38112727 DOI: 10.1021/acs.analchem.3c04778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The efficiency of the enzyme-free toehold-mediated strand displacement (TMSD) technique is often insufficient to detect single-nucleotide polymorphism (SNP) that possesses only single base pair mismatch discrimination. Here, we report a novel dual base pair mismatch strategy enabling TMSD biosensing for SNP detection under enzyme-free conditions when coupled with catalytic hairpin assembly (CHA) and fluorescence resonance energy transfer (FRET). The strategy is based on a competitive strand displacement reaction mechanism, affected by the thermodynamic stability originating from rationally designed dual base pair mismatch, for the specific recognition of mutant-type DNA. In particular, enzyme-free nucleic acid circuits, such as CHA, emerge as a powerful method for signal amplification. Eventually, the signal transduction of this proposed biosensor was determined by FRET between streptavidin-coated 605 nm emission quantum dots (605QDs, donor) and Cy5/biotin hybridization (acceptor, from CHA) when incubated with each other. The proposed biosensor displayed high sensitivity to the mutant target (MT) with a detection concentration down to 4.3 fM and led to high discrimination factors for all types of mismatches in multiple sequence contexts. As such, the application of this proposed biosensor to investigate mechanisms of the competitive strand displacement reaction further illustrates the versatility of our dual base pair mismatch strategy, which can be utilized for the creation of a new class of biosensors.
Collapse
Affiliation(s)
- Yunshan Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lanyue Wang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Jing Ye
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Shijie Xu
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Sisi Bu
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Minxin Deng
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Lina Bian
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| | - Xiaoyu Zhao
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, P. R. China
| | - Chunlong Zhang
- Research Center for Intelligent Robotics, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311121, China
| | - Diming Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| |
Collapse
|
7
|
Wu K, Kong F, Zhang J, Tang Y, Chen Y, Chao L, Nie L, Huang Z. Recent Progress in Single-Nucleotide Polymorphism Biosensors. BIOSENSORS 2023; 13:864. [PMID: 37754098 PMCID: PMC10527258 DOI: 10.3390/bios13090864] [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: 07/19/2023] [Revised: 08/23/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023]
Abstract
Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Libo Nie
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (K.W.); (F.K.); (J.Z.); (Y.T.); (Y.C.); (L.C.)
| | - Zhao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (K.W.); (F.K.); (J.Z.); (Y.T.); (Y.C.); (L.C.)
| |
Collapse
|
8
|
Wu W, Hu Z, Shi C, Xu R, Zhao Y, Ding Y. Construction of CdTe@γ-CD@RBD nanoprobe for Fe 3+-sensing based on FRET mechanism in human serum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 296:122645. [PMID: 37011440 DOI: 10.1016/j.saa.2023.122645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/02/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
A Fe3+ optical sensor (CdTe@γ-CD@RBD) has been developed by using gamma-cyclodextrin (γ-CD) as a bridge to link CdTe quantum dots (QDs) and a Rhodamine B derivative (RBD). The RBD molecule can enter the cavity of the γ-CD anchored onto the surfaces of the QDs. In the presence of Fe3+, the fluorescence resonance energy transfer (FRET) process from QDs to RBD will be initiated, rendering the nanoprobe to display a response to Fe3+. The degree of fluorescence quenching presented a satisfactory linearity between 10 and 60 μΜ with the incremental concentrations of Fe3+, and the calculated limit of detection was 2.51 μΜ. Through sample pretreatment procedures, the probe has been used in the determination of Fe3+ in human serum. The average recoveries in the spiking levels are ranged from 98.60 % to 107.20 % with a relative standard deviation of around 1.43 %-2.96 %. This finding leads to a method for fluorescent detection of Fe3+ with high sensitivity and exceptional selectivity. We believe that this study can give a new insight into the rational design and application of FRET-based nanoprobes.
Collapse
Affiliation(s)
- Wenlu Wu
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, PR China
| | - Zhongfei Hu
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, PR China
| | - Cai Shi
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, PR China
| | - Ruoqian Xu
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, PR China
| | - Yiming Zhao
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, PR China
| | - Yujie Ding
- School of Chemical and Environmental Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, PR China.
| |
Collapse
|
9
|
Darwish GH, Massey M, Daudet G, Alde LG, Algar WR. Tetrameric Antibody Complexes and Affinity Tag Peptides for the Selective Immobilization and Imaging of Single Quantum Dots. Bioconjug Chem 2023. [PMID: 37243625 DOI: 10.1021/acs.bioconjchem.3c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Colloidal semiconductor quantum dots (QDs) are of widespread interest as fluorescent labels for bioanalysis and imaging applications. Single-particle measurements have proven to be a very powerful tool for better understanding the fundamental properties and behaviors of QDs and their bioconjugates; however, a recurring challenge is the immobilization of QDs in a solution-like environment that minimizes interactions with a bulk surface. Immobilization strategies for QD-peptide conjugates are particularly underdeveloped within this context. Here, we present a novel strategy for the selective immobilization of single QD-peptide conjugates using a combination of tetrameric antibody complexes (TACs) and affinity tag peptides. A glass substrate is modified with an adsorbed layer of concanavalin A (ConA) that binds a subsequent layer of dextran that minimizes nonspecific binding. A TAC with anti-dextran and anti-affinity tag antibodies binds to the dextran-coated glass surface and to the affinity tag sequence of QD-peptide conjugates. The result is spontaneous and sequence-selective immobilization of single QDs without any chemical activation or cross-linking. Controlled immobilization of multiple colors of QDs is possible using multiple affinity tag sequences. Experiments confirmed that this approach positions the QD away from the bulk surface. The method supports real-time imaging of binding and dissociation, measurements of Förster resonance energy transfer (FRET), tracking of dye photobleaching, and detection of proteolytic activity. We anticipate that this immobilization strategy will be useful for studies of QD-associated photophysics, biomolecular interactions and processes, and digital assays.
Collapse
Affiliation(s)
- Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Gabrielle Daudet
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Luis G Alde
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| |
Collapse
|
10
|
A protein enzyme-free strategy for fluorescence detection of single nucleotide polymorphisms using asymmetric MNAzymes. Anal Chim Acta 2023; 1243:340811. [PMID: 36697176 DOI: 10.1016/j.aca.2023.340811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/05/2022] [Accepted: 01/06/2023] [Indexed: 01/07/2023]
Abstract
To establish protein enzyme-free and simple approach for sensitive detection of single nucleotide polymorphisms (SNPs), the nucleic acid amplification reactions were developed to reduce the dependence on protein enzymes (polymerase, endonuclease, ligase). These methods, while enabling highly amplified analysis for the short sequences, cannot be generalized to long genomic sequences. Herein, we develop a protein enzyme-free and general SNPs assay based on asymmetric MNAzyme probes. The multi-arm probe (MNAzyme-9M-13) with two asymmetric recognition arms, containing a short (9 nt) and a long (13 nt) arm, is designed to detect EGFR T790 M mutation (MT). Owing to the excellent selectivity of short recognition arm, MNAzyme-9M-13 probe can efficiently avoid interferences from wild-type target (WT) and various single-base mutations. Through a one-pot mixing, MNAzyme-9M-13 probe enables the sensitive detection of MT, without protein enzyme or multi-step operation. The calculated detection limit for MT is 0.59 nM and 0.83%. Moreover, this asymmetric MNAzyme strategy can be applied for SNPs detection in long genomic sequences as well as short microRNAs (miRNAs) only by changing the low-cost unlabeled recognition arms. Therefore, along with simple operation, low-cost, protein enzyme-free and strong versatility, our asymmetric MNAzyme strategy provides a novel solution for SNPs detection and genes analysis.
Collapse
|
11
|
Fan W, Ren W, Liu C. Advances in optical counting and imaging of micro/nano single-entity reactors for biomolecular analysis. Anal Bioanal Chem 2023; 415:97-117. [PMID: 36322160 PMCID: PMC9628437 DOI: 10.1007/s00216-022-04395-8] [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: 09/24/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Ultrasensitive detection of biomarkers is of paramount importance in various fields. Superior to the conventional ensemble measurement-based assays, single-entity assays, especially single-entity detection-based digital assays, not only can reach ultrahigh sensitivity, but also possess the potential to examine the heterogeneities among the individual target molecules within a population. In this review, we summarized the current biomolecular analysis methods that based on optical counting and imaging of the micro/nano-sized single entities that act as the individual reactors (e.g., micro-/nanoparticles, microemulsions, and microwells). We categorize the corresponding techniques as analog and digital single-entity assays and provide detailed information such as the design principles, the analytical performance, and their implementation in biomarker analysis in this work. We have also set critical comments on each technique from these aspects. At last, we reflect on the advantages and limitations of the optical single-entity counting and imaging methods for biomolecular assay and highlight future opportunities in this field.
Collapse
Affiliation(s)
- Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi’an, 710119 Shaanxi Province People’s Republic of China ,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi’an, 710119 Shaanxi Province People’s Republic of China ,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an, 710119 Shaanxi Province People’s Republic of China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi’an, 710119 Shaanxi Province People’s Republic of China ,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi’an, 710119 Shaanxi Province People’s Republic of China ,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an, 710119 Shaanxi Province People’s Republic of China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi’an, 710119 Shaanxi Province People’s Republic of China ,Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi’an, 710119 Shaanxi Province People’s Republic of China ,School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi’an, 710119 Shaanxi Province People’s Republic of China
| |
Collapse
|
12
|
Liu Y, Li B, Liu B, Zhang K. Single-Particle Optical Imaging for Ultrasensitive Bioanalysis. BIOSENSORS 2022; 12:1105. [PMID: 36551072 PMCID: PMC9775667 DOI: 10.3390/bios12121105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.
Collapse
Affiliation(s)
- Yujie Liu
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Kun Zhang
- Shanghai Institute of Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| |
Collapse
|
13
|
Zhao X, Na N, Ouyang J. CRISPR/Cas9-based coronal nanostructures for targeted mitochondria single molecule imaging. Chem Sci 2022; 13:11433-11441. [PMID: 36320584 PMCID: PMC9533423 DOI: 10.1039/d2sc03329a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/07/2022] [Indexed: 02/12/2024] Open
Abstract
The biological state at the subcellular level is highly relevant to many diseases, and the monitoring of organelles such as mitochondria is crucial based on this. However, most DNA and protein based nanoprobes used for the detection of mitochondrial RNAs (mitomiRs) lack spatial selectivity, which leads to inefficiencies in probe delivery and signal turn-on. Herein, we constructed a novel DNA nanoprobe named protein delivery nano-corona (PDNC) to improve the delivery efficiency of Cas protein, for spatially selective imaging of mitomiRs in living cells switched on by a CRISPR/Cas system. Combined with a single-molecule counting method, this strategy enables highly sensitive detection of low-abundance mitomiR. Therefore, the strategy in this work opens up new opportunities for cell identification, early clinical diagnosis, and research in biological behaviour at the subcellular level.
Collapse
Affiliation(s)
- Xuan Zhao
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University Beijing 100875 China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University Beijing 100875 China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University Beijing 100875 China
| |
Collapse
|
14
|
Chan KK, Yap SHK, Giovanni D, Sum TC, Yong KT. Water-stable Perovskite Quantum Dots-based FRET Nanosensor for the Detection of Rhodamine 6G in Water, Food, and Biological Samples. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
15
|
Construction of a magnetic-fluorescent-plasmonic nanosensor for the determination of MMP-2 activity based on SERS-fluorescence dual-mode signals. Biosens Bioelectron 2022; 212:114389. [DOI: 10.1016/j.bios.2022.114389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/09/2022] [Accepted: 05/15/2022] [Indexed: 12/12/2022]
|
16
|
Hao L, Li M, Peng K, Ye T, Wu X, Yuan M, Cao H, Yin F, Gu H, Xu F. Fluorescence Resonance Energy Transfer Aptasensor of Ochratoxin A Constructed Based on Gold Nanorods and DNA Tetrahedrons. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10662-10668. [PMID: 35939804 DOI: 10.1021/acs.jafc.2c03626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Ochratoxin A (OTA) contamination of corn has received significant attention due to the wide distribution and high toxicity of OTA. The maximum residue limit standard of OTA in corn has been established by the Chinese Government and other unions. Nanoparticle-based fluorescence resonance energy transfer (FRET) assays are promising methods for the sensitive and fast detection of OTA. However, satisfactory detection sensitivity is commonly achieved with complicated signal amplification processes or specific nanoparticle morphologies, which means that these assays are not conducive to fast detection. This study proposes a simple and novel strategy to improve the sensitivity of FRET aptasensors. In this strategy, a DNA tetrahedron was first used in gold nanorod-based FRET aptasensors. DNA tetrahedron-modified gold nanorods are used as fluorescent acceptors, and Cy5-modified complementary sequences of the OTA aptamer are used as fluorescent donors. The aptamers of OTA are embedded in the DNA tetrahedrons, and FRET occurs when the aptamers hybridize with the Cy5-modified complementary sequences. The aptamer-integrated DNA tetrahedron modified on the surface of gold nanorods acts as an anchor, thus avoiding the crowding and entanglement of aptamers. Due to the competitive combination between the OTA aptamers and complementary sequences, the greater the amount of OTA, the less the amount of Cy5-modified complementary sequences that bind with the aptamers and the less the amount of Cy5 that is quenched. Thus, the fluorescence intensity is positively related to the OTA concentration. In this study, in the concentration range of 0.01-10 ng/mL, the fluorescence intensity was found to be linearly related to the logarithmic concentration of OTA. The limit of detection was calculated to be 0.005 ng/mL. The specificity of the developed biosensor was demonstrated to be efficient. The accuracy and stability of the developed aptasensor were also tested, and the method exhibited good performance in real samples.
Collapse
Affiliation(s)
- Liling Hao
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Mengqiu Li
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Kaimin Peng
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Tai Ye
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xiuxiu Wu
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Min Yuan
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Hui Cao
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fengqin Yin
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Huajie Gu
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Fei Xu
- School of Health Science and Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| |
Collapse
|
17
|
Wei SH, Liu M, Hu J, Zhang CY. Target-Initiated Cascade Signal Amplification Lights up a G-Quadruplex for a Label-Free Detection of Circular Ribonucleic Acids. Anal Chem 2022; 94:9193-9200. [PMID: 35703015 DOI: 10.1021/acs.analchem.2c01901] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Circular ribonucleic acids (circRNAs) are a type of RNA that originates through back-splicing events from linear primary transcripts. CircRNAs display high structural resistance and tissue specificity. Accurate quantification of the circRNA expression level is of vital importance to disease diagnosis. Herein, we construct a label-free fluorescent biosensor for ultrasensitive analysis of circRNAs based on the integration of target-initiated cascade signal amplification strategy with a light-up G-quadruplex. This assay involves only one assistant probe that targets the circRNA-specific back-splice junction. When circRNA is present, it hybridizes with the assistant probe to initiate the duplex-specific nuclease (DSN)-catalyzed cyclic cleavage reaction, producing abundant triggers with 3'OH termini. Then, terminal deoxynucleotidyl transferase (TdT) catalyzes the addition of dGTP and dATP at the 3'-OH termini of the resultant triggers to obtain abundant long G-rich DNA sequences that can form efficient G-quadruplex products. The addition of Thioflavin T (ThT) can light up G-quadruplex, generating an enhanced fluorescence. This assay may be performed isothermally without the involvement of any nucleic acid templates, exogenous primers, and specific labeled probes. Importantly, this biosensor can discriminate target circRNA from one-base mismatched circRNA and exhibits good performance in human serum. Moreover, it can accurately detect circRNA in cancer cells at a single-cell level and even differentiate the circRNA levels in the tissues of healthy persons and nonsmall cell lung cancer (NSCLC) patients, with promising applications in circRNA-related cancer diagnosis and therapeutics.
Collapse
Affiliation(s)
- Shu-Hua Wei
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| |
Collapse
|
18
|
Wang ZY, Yuan H, Li DL, Hu J, Qiu JG, Zhang CY. Hydroxymethylation-Specific Ligation-Mediated Single Quantum Dot-Based Nanosensors for Sensitive Detection of 5-Hydroxymethylcytosine in Cancer Cells. Anal Chem 2022; 94:9785-9792. [PMID: 35749235 DOI: 10.1021/acs.analchem.2c01495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Hydroxymethylcytosine (5hmC) modification is a key epigenetic regulator of cellular processes in mammalian cells, and its misregulation may lead to various diseases. Herein, we develop a hydroxymethylation-specific ligation-mediated single quantum dot (QD)-based fluorescence resonance energy transfer (FRET) nanosensor for sensitive quantification of 5hmC modification in cancer cells. We design a Cy5-modified signal probe and a biotinylated capture probe for the recognition of specific 5hmC-containing genes. 5hmC in target DNA can be selectively converted by T4 β-glucosyltransferase to produce a glycosyl-modified 5hmC, which cannot be cleaved by methylation-insensitive restriction enzyme MspI. The glycosylated 5hmC DNA may act as a template to ligate a signal probe and a capture probe, initiating hydroxymethylation-specific ligation to generate large amounts of biotin-/Cy5-modified single-stranded DNAs (ssDNAs). The assembly of biotin-/Cy5-modified ssDNAs onto a single QD through streptavidin-biotin interaction results in FRET and consequently the generation of a Cy5 signal. The nanosensor is very simple without the need for bisulfite treatment, radioactive reagents, and 5hmC-specific antibodies. Owing to excellent specificity and high amplification efficiency of hydroxymethylation-specific ligation and near-zero background of a single QD-based FRET, this nanosensor can quantify 5hmC DNA with a limit of detection of 33.61 aM and a wider linear range of 7 orders of magnitude, and it may discriminate the single-nucleotide difference among 5hmC, 5-methylcytosine, and unmodified cytosine. Moreover, this nanosensor can distinguish as low as a 0.001% 5hmC DNA in complex mixtures, and it can monitor the cellular 5hmC level and discriminate cancer cells from normal cells, holding great potential in biomedical research and clinical diagnostics.
Collapse
Affiliation(s)
- Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Huimin Yuan
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Dong-Ling Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Juan Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| |
Collapse
|
19
|
Wang K, Dong E, Fang M, Chen T, Zhu W, Li C. Construction of ratio fluorescence sensor based on CdTe quantum dots and benzocoumarin-3-carboxylic acid for Hg2+ detection. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
20
|
Zhang Z, Wu Y, Lin N, Yin S, Meng Z. Monitoring Clinical-Pathological Grading of Hepatocellular Carcinoma Using MicroRNA-Guided Semiconducting Polymer Dots. ACS APPLIED MATERIALS & INTERFACES 2022; 14:7717-7730. [PMID: 35112844 DOI: 10.1021/acsami.1c24191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNAs involved in nearly all genetic central dogma processes and human biological behavior, which also play a significant role in the pathological activity of tumors, such as gene transcription, protein translation, and exosome secretion. Therefore, through the navigation of certain specific miRNAs, we can trace the specific physiological processes or image some specific tissues. Designing and accurately positioning microRNA (miRNA)-sensitive fluorescent nanoprobes with benign specificity and recognition in cells or tissues are a challenging research field. To solve the difficulties, we introduce four semiconducting polymer dots (Pdots) as nanoprobes linked by specific miRNA antisense sequences for monitoring the pathological grading by the variation in miRNA expression. Based on the base pairing principle, these miRNA-sensitive Pdots could bind to specific miRNAs within the cancerous cells. As impacted by the background of different pathology gradings, the proportions of the four hepatocellular carcinoma (HCC)-specific miRNAs within the cancerous cell are different, and the pathological grading of the patient tissues can be determined by comparing the palette combinations. The short single-stranded RNA-functionalized Pdots, which have excellent microRNA sensitivity, are observed in an experimental cell model and a series of tissue specimens from HCC patients for the first time. Using the Förster (or fluorescence) resonance energy transfer (FRET) model of Pdots and Cy3dt tag to simulate in vivo miRNA detection, the superior sensitivity and specificity of these nanoprobes are verified. The interference of subjective factors in traditional single/bis-dye emission intensity detection is abandoned, and multiple label staining is used to enhance sensitivity further and reduce the false-positive rate. The feasibility exhibited by this novel staining method is verified in normal hepatocellular HCC cell lines and 16 frozen ultrathin tissue sections, which are employed to quantify pathological grading-related color presentation systems for clinical doctors and pathologists' use. The intelligently designed miRNA-guided Pdots will emerge as an ideal platform with promising biological imaging.
Collapse
Affiliation(s)
- Ze Zhang
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Jilin University, No. 126 Xiantai Street, Changchun, Jilin 130000, P. R. China
| | - Yuyang Wu
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Nan Lin
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Shengyan Yin
- State Key Laboratory of Integrated Optoelectronic, College of Electronic Science and Engineering, Jilin University, No. 2699 Qianjin Street, Changchun 130012, P. R. China
| | - Zihui Meng
- Department of Hepatobiliary-Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Jilin University, No. 126 Xiantai Street, Changchun, Jilin 130000, P. R. China
| |
Collapse
|
21
|
|
22
|
Gao YP, Huang KJ, Wang FT, Hou YY, Xu J, Li G. Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications. Analyst 2022; 147:3396-3414. [DOI: 10.1039/d2an00556e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.
Collapse
Affiliation(s)
- Yong-ping Gao
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
- Analysis and Testing Center, Xinyang College, Xinyang 464000, PR China
| | - Ke-Jing Huang
- Key Laboratory of Guangxi Colleges and Universities for Food Safety and Pharmaceutical Analytical Chemistry, School of Chemistry and Chemical and Engineering, Guangxi Minzu University, Nanning 530008, PR China
| | - Fu-Ting Wang
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Yang-Yang Hou
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Jing Xu
- College of Chemistry and Chemical Engineering, Xinyang Normal University, Xinyang 464000, PR China
| | - Guoqiang Li
- International Joint Research Laboratory of New Energy Materials and Devices of Henan Province, School of Physics and Electronics, Henan University, Kaifeng, 475004, PR China
| |
Collapse
|
23
|
Li T, Zou H, Zhang J, Ding H, Li C, Chen X, Li Y, Feng W, Kageyama K. High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms. Analyst 2022; 147:3993-3999. [DOI: 10.1039/d2an01042a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases was developed to assist LR-LAMP for genotyping of SNPs.
Collapse
Affiliation(s)
- Taiwen Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Huayan Zou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Haixia Ding
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Cheng Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Yunzhou Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| |
Collapse
|