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Meng X, Petrou L, Kenaan A, Khan D, O'Hare D, Ladame S. Pitfalls and challenges of peptide nucleic acid immobilisation on carbon surfaces for sequence-specific capturing of nucleic acid biomarkers. Biosens Bioelectron 2024; 264:116634. [PMID: 39154509 DOI: 10.1016/j.bios.2024.116634] [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: 06/07/2024] [Revised: 07/25/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
Nucleic acid sensors based on a peptide nucleic acid (PNA) probe have seen a surge in interest since their discovery in the 1990s, and after the patent protecting them expired in 2013. The appeal of PNA as capture and/or sensing probes as an alternative to standard DNA or RNA oligonucleotides originates from their superior chemical stability and affinity for complementary oligonucleotides, as well as their increased responsiveness to single base mismatches. The implementation of PNA probes onto optical and electrochemical sensors has showed great promise although progress has been hampered by issues mostly associated with surface chemistry, probe accessibility and non-specific binding. Herein, we report on a systematic comparison between various PNA immobilisation strategies on carbon substrates based on both covalent and non-covalent chemistries. Besides the use of standard electrochemical techniques to characterise the extent of surface modification, the ability of immobilised PNAs to engage in chemical interactions with freely diffusing molecules was also investigated. Using original chemical tags, this study provides a unique insight into the impact of immobilisation chemistries on PNA's (bio)availability. Rapid immobilisation of biotinylated PNA oligomers on screen-printed carbon electrode (SPCE) coated with adsorbed polystreptavidin (pSA) demonstrated highest efficiency and ease in the preparation process. An original nucleic acid sensor using this immobilisation chemistry is reported that is based on a sandwich assay between a surface bound PNA capture probe and a freely diffusing electrochemically active PNA sensing probe.
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Affiliation(s)
- Xiaotong Meng
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom; School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua university, Beijing 100084, China
| | - Loukia Petrou
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ahmad Kenaan
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Daanyaal Khan
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom.
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2
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Dong L, Zhang Y, Fu B, Swart C, Jiang H, Liu Y, Huggett J, Wielgosz R, Niu C, Li Q, Zhang Y, Park SR, Sui Z, Yu L, Liu Y, Xie Q, Zhang H, Yang Y, Dai X, Shi L, Yin Y, Fang X. Reliable biological and multi-omics research through biometrology. Anal Bioanal Chem 2024; 416:3645-3663. [PMID: 38507042 DOI: 10.1007/s00216-024-05239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/22/2024]
Abstract
Metrology is the science of measurement and its applications, whereas biometrology is the science of biological measurement and its applications. Biometrology aims to achieve accuracy and consistency of biological measurements by focusing on the development of metrological traceability, biological reference measurement procedures, and reference materials. Irreproducibility of biological and multi-omics research results from different laboratories, platforms, and analysis methods is hampering the translation of research into clinical uses and can often be attributed to the lack of biologists' attention to the general principles of metrology. In this paper, the progresses of biometrology including metrology on nucleic acid, protein, and cell measurements and its impacts on the improvement of reliability and comparability in biological research are reviewed. Challenges in obtaining more reliable biological and multi-omics measurements due to the lack of primary reference measurement procedures and new standards for biological reference materials faced by biometrology are discussed. In the future, in addition to establishing reliable reference measurement procedures, developing reference materials from single or multiple parameters to multi-omics scale should be emphasized. Thinking in way of biometrology is warranted for facilitating the translation of high-throughput omics research into clinical practices.
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Affiliation(s)
- Lianhua Dong
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Yu Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Boqiang Fu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Claudia Swart
- Physikalisch-Technische Bundesanstalt, 38116, Braunschweig, Germany
| | | | - Yahui Liu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Jim Huggett
- National Measurement Laboratory at LGC (NML), Teddington, Middlesex, UK
| | - Robert Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Chunyan Niu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Qianyi Li
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yongzhuo Zhang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Sang-Ryoul Park
- Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Zhiwei Sui
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | - Lianchao Yu
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China
| | | | - Qing Xie
- BGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongfu Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xinhua Dai
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Ye Yin
- BGI, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Xiang Fang
- Center for Advanced Measurement of Science, National Institute of Metrology, Beijing, 100029, China.
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3
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Zhao Z, Jiang M, He C, Yin W, Feng Y, Wang P, Ying L, Fu T, Su D, Peng R, Tan W. Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues. ACS NANO 2024; 18:9958-9968. [PMID: 38547522 DOI: 10.1021/acsnano.3c10216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.
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Affiliation(s)
- Zeyin Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Mengyuan Jiang
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chen He
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Wenjuan Yin
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yawei Feng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Peng Wang
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lisha Ying
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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4
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Nakano Y, Isobe K, Yoshizawa T, Urabe N, Homma S, Kishi K. Upregulation of long non‑coding RNA LINC00460 in EGFR‑mutant lung cancer indicates a poor prognosis in patients treated with osimertinib. Oncol Lett 2023; 26:380. [PMID: 37559586 PMCID: PMC10407845 DOI: 10.3892/ol.2023.13966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/30/2023] [Indexed: 08/11/2023] Open
Abstract
The long non-coding RNA (lncRNA) LINC00460 is involved in tumor growth, metastasis and drug resistance. The present study investigated the clinical significance of LINC00460 expression in patients with epidermal growth factor receptor (EGFR) mutation-positive lung cancer treated with osimertinib. Osimertinib-resistant cells we derived from EGFR-mutant non-small-cell lung cancer (NSCLC) cell lines, after which, small interfering RNA (siRNA)-mediated silencing and in vitro-transcribed (IVT), synthetic LINC00460 RNA transfection were used to investigate the effects of LINC00460 expression on acquired resistance to osimertinib. Reverse transcription-quantitative polymerase chain reaction was performed to evaluate LINC00460 expression in 54 samples (RNA extracted from the tumor tissues of 30 cases and cell-free RNA from 24 cases) obtained from patients with EGFR mutation-positive lung cancer who had received osimertinib as the initial treatment. The acquisition of osimertinib resistance increased the expression of LINC00460 in the EGFR-mutant NSCLC cell lines. By contrast, knockdown of LINC00460 in osimertinib-resistant cell lines increased their sensitivity to osimertinib, whereas treatment of NSCLC cells with IVT LINC00460 RNA decreased their sensitivity to osimertinib. The present study examined LINC00460 expression at the primary tumor site and demonstrated that compared with in the low-expression group (n=24), the high-expression group (n=6) had a significantly lower best overall response rate to osimertinib (16.6% vs. 60.0%; P=0.044), significantly shorter median progression-free survival (PFS; 224 days vs. 669 days; P=0.001) and significantly shorter median overall survival (724 days vs. not reached; P=0.011). Moreover, following osimertinib therapy, PFS was significantly shorter for patients with high LINC00460 expression in plasma cell-free RNA (n=12) than for those with low LINC00460 expression (n=12) (median PFS: 655 days vs. 210 days; P=0.020). In conclusion, the upregulation of LINC00460, the expression of which is implicated in osimertinib resistance, in the primary site and plasma of patients with EGFR mutation-positive lung cancer may be associated with a poor prognosis in those treated with osimertinib.
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Affiliation(s)
- Yuta Nakano
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143-8541, Japan
- Pharmaceutical & ADMET Research Development, Daiichi Sankyo RD Novare Co., Ltd, Tokyo 134-8630, Japan
| | - Kazutoshi Isobe
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143-8541, Japan
| | - Takahiro Yoshizawa
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143-8541, Japan
| | - Naohisa Urabe
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143-8541, Japan
| | - Sakae Homma
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143-8541, Japan
| | - Kazuma Kishi
- Department of Respiratory Medicine, Toho University School of Medicine, Tokyo 143-8541, Japan
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5
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Zhang Z, Shang C, Hu C, Liu Y, Han J. Branched DNA-Based Electrochemical Biosensor for Sensitive Nucleic Acids Analysis with Gold Nanoparticles as Amplifier. Int J Mol Sci 2023; 24:12565. [PMID: 37628745 PMCID: PMC10454004 DOI: 10.3390/ijms241612565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
A branched DNA-based electrochemical biosensor was designed to sensitively detect specific nucleic acids. On this platform, novel a branched DNA with three sticky ends could be used as a biosensor to sensitively and specifically detect nucleic acids. Meanwhile, we also employed branched DNA-modified AuNPs as a signal amplifier to further improve the sensitivity. Branched DNA sensors, target DNA, and DNA-modified AuNPs formed a sandwich structure to produce an electronic signal for target DNA detection. The reaction primarily involved DNA hybridization without bulky thermal cyclers and enzymes. We proved that the hybridization reaction easily occurred under different conditions, such as the NaCl concentration, reaction time, pH, and temperature, except for a pH lower than 4. The limit of detection could go as low as 0.09 pM (S/N = 3) with excellent specificity and selectivity. There was a correlation curve relationship between the peak current and the logarithm of the target DNA concentration (0.10 pM to 10 nM). The correlation coefficient reached 0.987. The electrochemical platform enables a branched DNA nanostructure to determine nucleic acids for disease diagnosis.
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Affiliation(s)
- Zhikun Zhang
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | | | | | | | - Jilong Han
- School of Chemical and Pharmaceutical Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
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6
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You H, Wang M, Wang S, Xu J, Hu S, Li T, Yu Z, Tang D, Gan N. Ultrasensitive and Specific Phage@DNAzyme Probe-Triggered Fluorescent Click Chemistry for On-Site Detection of Foodborne Pathogens Using a Smartphone. Anal Chem 2023. [PMID: 37471313 DOI: 10.1021/acs.analchem.3c00603] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Rapid, specific, and on-site detection of virulent foodborne pathogenic strains plays a key role in controlling food safety. In this work, an ultrasensitive and specific Phage@DNAzyme signal probe was designed to detect foodborne pathogens. The proposed sensing probe was composed of the selected phage and functionalized DNAzyme, which realized the specific recognition of target foodborne pathogens at the strain level and the efficient catalysis of copper(II) based azide-alkyne cycloaddition (CuAAC) click reaction with fluorescent signal, respectively. As a proof of concept, the virulent Escherichia coli O157:H7 (E. coli O157:H7) as the representative analyte was first enriched and purified from the complex food samples by a 4-mercaptophenylboronic acid-modified gold slide. Following, the Phage@DNAzyme probes were specifically combined with the captured E. coli O157: H7 and catalyzed the click reaction between 3-azido-7-hydroxycoumarin and 3-butyn-1-ol with the assistance of Cu(II) to generate a visual fluorescent signal. Finally, the corresponding fluorescent signals were measured by a smartphone to quantify the target concentrations. Under optimized conditions, the bioassay exhibited a wide linear range from 102 to 108 CFU/mL and the detection limit was 50 CFU/mL (S/N = 3). It was further extended to the detection of another foodborne pathogen Salmonella typhimurium with satisfying sensing performances. This work gives a new path for developing rapid, specific, and on-site detection methods for trace levels of pathogenic strains in foods.
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Affiliation(s)
- Hang You
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Ming Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Shuai Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Jie Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Shuhao Hu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Tianhua Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Zhenzhong Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350116, China
| | - Ning Gan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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7
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Zhang Z, Zhang L, Liu Y, Hu C, Liu Q. Sensitive DNA Detection using a Branched DNA as a Sensor Coupled with Hybridization Chain Reaction. ChemistrySelect 2022. [DOI: 10.1002/slct.202201891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Zhikun Zhang
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Liu Zhang
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Yumin Liu
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Cuixia Hu
- School of Chemical and Pharmaceutical Engineering Hebei University of Science and Technology Shijiazhuang 050018 China
| | - Qingju Liu
- Beijing Research Center for Agriculture Standards and Testing Beijing Academy of Agriculture and Forestry Sciences Beijing 100097 China
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Zhang H, Laššáková S, Yan Z, Wang X, Šenkyřík P, Gaňová M, Chang H, Korabecna M, Neuzil P. Digital polymerase chain reaction duplexing method in a single fluorescence channel. Anal Chim Acta 2022; 1238:340243. [DOI: 10.1016/j.aca.2022.340243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022]
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9
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Role of Förster Resonance Energy Transfer in Graphene-Based Nanomaterials for Sensing. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Förster resonance energy transfer (FRET)-based fluorescence sensing of various target analytes has been of growing interest in the environmental, bioimaging, and diagnosis fields. Graphene-based zero- (0D) to two-dimensional (2D) nanomaterials, such as graphene quantum dots (GQDs), graphene oxide (GO), reduced graphene oxide (rGO), and graphdiyne (GD), can potentially be employed as donors/acceptors in FRET-based sensing approaches because of their unique electronic and photoluminescent properties. In this review, we discuss the basics of FRET, as well as the role of graphene-based nanomaterials (GQDs, GO, rGO, and GD) for sensing various analytes, including cations, amino acids, explosives, pesticides, biomolecules, bacteria, and viruses. In addition, the graphene-based nanomaterial sensing strategy could be applied in environmental sample analyses, and the reason for the lower detection ranges (micro- to pico-molar concentration) could also be explained in detail. Challenges and future directions for designing nanomaterials with a new sensing approach and better sensing performance will also be highlighted.
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10
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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11
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Dai P, Zhu X, Pei Y, Chen P, Li J, Gao Z, Liang Y, Kong X. Evaluation of optical genome mapping for detecting chromosomal translocation in clinical cytogenetics. Mol Genet Genomic Med 2022; 10:e1936. [PMID: 35384386 PMCID: PMC9184658 DOI: 10.1002/mgg3.1936] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background Balanced reciprocal translocation is one of the most common chromosomal abnormalities in humans that may lead to infertility, recurrent pregnancy loss, or having children with physical or mental abnormalities. Karyotyping and FISH are traditional detection approaches with a low resolution. Bionano optical genome mapping (OGM) developed in recent years can be used to analyze chromosomal abnormalities at a higher resolution, providing the possibility of more in‐depth analyses of balanced chromosome translocations. Methods To evaluate the feasibility of OGM to detect chromosome balanced translocations, 10 genetic outpatients were collected and detected simultaneously by karyotype analysis, FISH, CNV‐seq, and Bionano OGM in this study. Results The results showed that the karyotypes of the patients were detected by karyotype analysis, FISH, and Bionano OGM, but one patient with karyotype t(Y,19) was not correctly detected by OGM. There were not find any chromosome abnormality by CNV‐seq. More importantly, OGM allowed the location of the mutation to the gene level, which is important for aiding diagnoses, compared to karyotype analysis, and FISH. Conclusions This study shows that OGM can be a high adjunctive diagnostic method for detecting balanced chromosome translocations, but the accuracy and precision of OGM detecting mutations need to be gradually improved in telomere and centromere regions.
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Affiliation(s)
- Peng Dai
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaofan Zhu
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Peng Chen
- Department of Neurology, The First Hospital of Yulin, Yulin, China
| | | | - Zhi Gao
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Liang
- GrandOmics Diagnostic, Wuhan, China
| | - Xiangdong Kong
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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12
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Drandi D, Decruyenaere P, Ferrante M, Offner F, Vandesompele J, Ferrero S. Nucleic Acid Biomarkers in Waldenström Macroglobulinemia and IgM-MGUS: Current Insights and Clinical Relevance. Diagnostics (Basel) 2022; 12:diagnostics12040969. [PMID: 35454017 PMCID: PMC9028641 DOI: 10.3390/diagnostics12040969] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 12/13/2022] Open
Abstract
Waldenström Macroglobulinemia (WM) is an indolent lymphoplasmacytic lymphoma, characterized by the production of excess immunoglobulin M monoclonal protein. WM belongs to the spectrum of IgM gammopathies, ranging from asymptomatic IgM monoclonal gammopathy of undetermined significance (IgM-MGUS), through IgM-related disorders and asymptomatic WM to symptomatic WM. In recent years, its complex genomic and transcriptomic landscape has been extensively explored, hereby elucidating the biological mechanisms underlying disease onset, progression and therapy response. An increasing number of mutations, cytogenetic abnormalities, and molecular signatures have been described that have diagnostic, phenotype defining or prognostic implications. Moreover, cell-free nucleic acid biomarkers are increasingly being investigated, benefiting the patient in a minimally invasive way. This review aims to provide an extensive overview of molecular biomarkers in WM and IgM-MGUS, considering current shortcomings, as well as potential future applications in a precision medicine approach.
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Affiliation(s)
- Daniela Drandi
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, 10126 Torino, Italy; (M.F.); (S.F.)
- Correspondence: (D.D.); (P.D.)
| | - Philippe Decruyenaere
- Department of Hematology, Ghent University Hospital, 9000 Ghent, Belgium;
- OncoRNALab, Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium;
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Correspondence: (D.D.); (P.D.)
| | - Martina Ferrante
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, 10126 Torino, Italy; (M.F.); (S.F.)
| | - Fritz Offner
- Department of Hematology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium;
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Simone Ferrero
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, 10126 Torino, Italy; (M.F.); (S.F.)
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13
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Bodulev OL, Sakharov IY. A Microtiter-Plate Chemiluminescence Method for the Determination of MicroRNA-141 Based on the Application of Catalytic Hairpin Assembly and a Streptavidin–Polyperoxidase Conjugate. JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1134/s1061934822040050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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van Kooten XF, Rozevsky Y, Marom Y, Ben Sadeh E, Meller A. Purely electrical SARS-CoV-2 sensing based on single-molecule counting. NANOSCALE 2022; 14:4977-4986. [PMID: 35258059 PMCID: PMC8969453 DOI: 10.1039/d1nr07787b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/03/2022] [Indexed: 05/23/2023]
Abstract
The majority of RNA based COVID-19 diagnostics employ enzymatic amplification to achieve high sensitivity, but this relies on arbitrary thresholding, which complicates the comparison of test results and may lead to false outcomes. Here we introduce solid-state nanopore sensing for label-free quantification of SARS-CoV-2 RNA in clinical nasal swab samples. This PCR-free method involves reverse transcribing a target gene on the viral RNA before enzymatically digesting all but the resulting dsDNA. Ratiometric quantification of RNA abundance is achieved by single-molecule counting and length-based nanopore identification of dsDNA from a SARS-CoV-2 gene and a human reference gene. We graded nasal swab samples from >15 subjects and find that the SARS-CoV-2 ratiometric nanopore index correlates well with the reported RT-qPCR threshold cycle for positive classified samples. Remarkably, nanopore analysis also reports quantitative positive outcomes for clinical samples classified as negative by RT-qPCR, suggesting that the method may be used to diagnose COVID-19 in samples that may evade detection. We show that the sample preparation workflow can be implemented using a compact microfluidic device with integrated thermal control for semi-automated processing of extremely small sample volumes, offering a viable route towards automated, fast and affordable RNA quantification in a small and portable device.
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Affiliation(s)
| | - Yana Rozevsky
- Department of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel.
| | - Yulia Marom
- Department of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel.
| | - Efrat Ben Sadeh
- Department of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel.
| | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa 32000, Israel.
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15
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Mukunda DC, Rodrigues J, Joshi VK, Raghushaker CR, Mahato KK. A comprehensive review on LED-induced fluorescence in diagnostic pathology. Biosens Bioelectron 2022; 209:114230. [PMID: 35421670 DOI: 10.1016/j.bios.2022.114230] [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: 09/23/2021] [Revised: 03/19/2022] [Accepted: 03/25/2022] [Indexed: 11/02/2022]
Abstract
Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.
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Affiliation(s)
| | - Jackson Rodrigues
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Vijay Kumar Joshi
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Chandavalli Ramappa Raghushaker
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India
| | - Krishna Kishore Mahato
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka-576104, India.
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16
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Khanna K, Mandal S, Blanchard AT, Tewari M, Johnson-Buck A, Walter NG. Rapid kinetic fingerprinting of single nucleic acid molecules by a FRET-based dynamic nanosensor. Biosens Bioelectron 2021; 190:113433. [PMID: 34171818 PMCID: PMC8295208 DOI: 10.1016/j.bios.2021.113433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 01/05/2023]
Abstract
Biofluid-derived cell-free nucleic acids such as microRNAs (miRNAs) and circulating tumor-derived DNAs (ctDNAs) have emerged as promising disease biomarkers. Conventional detection of these biomarkers by digital PCR and next generation sequencing, although highly sensitive, requires time-consuming extraction and amplification steps that also increase the risk of sample loss and cross-contamination. To achieve the direct, rapid, and amplification-free detection of miRNAs and ctDNAs with near-perfect specificity and single-molecule level sensitivity, we herein designed a single-molecule kinetic fingerprinting assay, termed intramolecular single-molecule recognition through equilibrium Poisson sampling (iSiMREPS). iSiMREPS exploits a dynamic DNA nanosensor comprising a surface anchor and a pair of fluorescent detection probes: one probe captures a target molecule onto the surface, while the other transiently interrogates the target to generate kinetic fingerprints by intramolecular single-molecule Förster resonance energy transfer (smFRET) that are recorded by single-molecule fluorescence microscopy and identify the target after kinetic filtering and data analysis. We optimize the sensor design, use formamide to further accelerate the fingerprinting kinetics, and maximize sensitivity by removing non-target-bound probes using toehold-mediated strand displacement to reduce background. We show that iSiMREPS can detect, in as little as 10 s, two distinct, promising cancer biomarkers-miR-141 and a common EGFR exon 19 deletion-reaching a limit of detection (LOD) of ~3 fM and a mutant allele fraction among excess wild-type as low as 1 in 1 million, or 0.0001%. We anticipate that iSiMREPS will find utility in research and clinical diagnostics based on its features of rapid detection, high specificity, sensitivity, and generalizability.
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Affiliation(s)
- Kunal Khanna
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Shankar Mandal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Aaron T Blanchard
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, United States; Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109, United States
| | - Muneesh Tewari
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, United States; Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, 48109, United States; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, United States; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States; Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, 48109, United States; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, United States.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, United States; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, 48109, United States; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, United States.
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17
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Yim Y, Shin H, Ahn SM, Min DH. Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery. Chem Commun (Camb) 2021; 57:9820-9833. [PMID: 34494621 DOI: 10.1039/d1cc02157e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.
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Affiliation(s)
- Yeajee Yim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seong Min Ahn
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 06683, Republic of Korea
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18
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Zhang H, Xia C, Feng G, Fang J. Hospitals and Laboratories on Paper-Based Sensors: A Mini Review. SENSORS 2021; 21:s21185998. [PMID: 34577205 PMCID: PMC8472957 DOI: 10.3390/s21185998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 02/07/2023]
Abstract
With characters of low cost, portability, easy disposal, and high accuracy, as well as bulky reduced laboratory equipment, paper-based sensors are getting increasing attention for reliable indoor/outdoor onsite detection with nonexpert operation. They have become powerful analysis tools in trace detection with ultra-low detection limits and extremely high accuracy, resulting in their great popularity in medical detection, environmental inspection, and other applications. Herein, we summarize and generalize the recently reported paper-based sensors based on their application for mechanics, biomolecules, food safety, and environmental inspection. Based on the biological, physical, and chemical analytes-sensitive electrical or optical signals, extensive detections of a large number of factors such as humidity, pressure, nucleic acid, protein, sugar, biomarkers, metal ions, and organic/inorganic chemical substances have been reported via paper-based sensors. Challenges faced by the current paper-based sensors from the fundamental problems and practical applications are subsequently analyzed; thus, the future directions of paper-based sensors are specified for their rapid handheld testing.
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19
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Rahman M, Sampad MJN, Hawkins A, Schmidt H. Recent advances in integrated solid-state nanopore sensors. LAB ON A CHIP 2021; 21:3030-3052. [PMID: 34137407 PMCID: PMC8372664 DOI: 10.1039/d1lc00294e] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The advent of single-molecule probing techniques has revolutionized the biomedical and life science fields and has spurred the development of a new class of labs-on-chip based on powerful biosensors. Nanopores represent one of the most recent and most promising single molecule sensing paradigms that is seeing increased chip-scale integration for improved convenience and performance. Due to their physical structure, nanopores are highly sensitive, require low sample volume, and offer label-free, amplification-free, high-throughput real-time detection and identification of biomolecules. Over the last 25 years, nanopores have been extensively employed to detect a variety of biomolecules with a growing range of applicatons ranging from nucleic acid sequencing to ultrasensitive diagnostics to single-molecule biophysics. Nanopores, in particular those in solid-state membranes, also have the potential for integration with other technologies such as optics, plasmonics, microfluidics, and optofluidics to perform more complex tasks for an ever-expanding demand. A number of breakthrough results using integrated nanopore platforms have already been reported, and more can be expected as nanopores remain the focus of innovative research and are finding their way into commercial instruments. This review provides an overview of different aspects and challenges of nanopore technology with a focus on chip-scale integration of solid-state nanopores for biosensing and bioanalytical applications.
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Affiliation(s)
- Mahmudur Rahman
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA. and Dhaka University of Engineering & Technology, Gazipur, Bangladesh
| | | | - Aaron Hawkins
- ECEn Department, Brigham Young University, 459 Clyde Building, Provo, UT, 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064 USA.
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20
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Plasmonic Biosensors for Single-Molecule Biomedical Analysis. BIOSENSORS-BASEL 2021; 11:bios11040123. [PMID: 33921010 PMCID: PMC8071374 DOI: 10.3390/bios11040123] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022]
Abstract
The rapid spread of epidemic diseases (i.e., coronavirus disease 2019 (COVID-19)) has contributed to focus global attention on the diagnosis of medical conditions by ultrasensitive detection methods. To overcome this challenge, increasing efforts have been driven towards the development of single-molecule analytical platforms. In this context, recent progress in plasmonic biosensing has enabled the design of novel detection strategies capable of targeting individual molecules while evaluating their binding affinity and biological interactions. This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level. Functional applications are discussed according to plasmonic sensing modes based on either nanoapertures or nanoparticle approaches. A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses). The utility of plasmonic-based single-molecule analysis for personalized medicine, considering technological limitations and future prospects, is also overviewed.
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21
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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22
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23
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Zhang Y, Nunoura T, Nishiura D, Hirai M, Shimamura S, Kurosawa K, Ishiwata C, Deguchi S. A single-molecule counting approach for convenient and ultrasensitive measurement of restriction digest efficiencies. PLoS One 2020; 15:e0244464. [PMID: 33382779 PMCID: PMC7775078 DOI: 10.1371/journal.pone.0244464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Restriction endonucleases play a central role in the microbial immune system against viruses and are widely used in DNA specific cleavage, which is called restriction digestion, for genetic engineering. Herein, we applied digital cell-free protein synthesis as an easy-to-use orthogonal readout means to assess the restriction digest efficiency, a new application of digital bioassays. The digital counting principle enabled an unprecedentedly sensitive trace analysis of undigested DNA at the single-molecule level in a PCR-free manner. Our approach can quantify the template DNA of much lower concentrations that cannot be detected by ensemble-based methods such as gold-standard DNA electrophoresis techniques. The sensitive and quantitative measurements revealed a considerable variation in the digest efficiency among restriction endonucleases, from less than 70% to more than 99%. Intriguingly, none of them showed truly complete digestion within reasonably long periods of reaction time. The same rationale was extended to a multiplexed assay and applicable to any DNA-degrading or genome-editing enzymes. The enzyme kinetic parameters and the flanking sequence-dependent digest efficiency can also be interrogated with the proposed digital counting method. The absolute number of residual intact DNA molecules per microliter was concluded to be at least 107, drawing attention to the residual issue of genetic materials associated with the interpretation of nucleases' behaviors and functions in daily genetic engineering experiments.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Daisuke Nishiura
- Center for Mathematical Science and Advanced Technology, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Miho Hirai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Chieko Ishiwata
- Center for Mathematical Science and Advanced Technology, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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24
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Cohen L, Cui N, Cai Y, Garden PM, Li X, Weitz DA, Walt DR. Single Molecule Protein Detection with Attomolar Sensitivity Using Droplet Digital Enzyme-Linked Immunosorbent Assay. ACS NANO 2020; 14:9491-9501. [PMID: 32589401 DOI: 10.1021/acsnano.0c02378] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Many proteins are present at low concentrations in biological samples, and therefore, techniques for ultrasensitive protein detection are necessary. To overcome challenges with sensitivity, the digital enzyme-linked immunosorbent assay (ELISA) was developed, which is 1000× more sensitive than conventional ELISA and allows sub-femtomolar protein detection. However, this sensitivity is still not sufficient to measure many proteins in various biological samples, thereby limiting our ability to detect and discover biomarkers. To overcome this limitation, we developed droplet digital ELISA (ddELISA), a simple approach for detecting low protein levels using digital ELISA and droplet microfluidics. ddELISA achieves maximal sensitivity by improving the sampling efficiency and counting more target molecules. ddELISA can detect proteins in the low attomolar range and is up to 25-fold more sensitive than digital ELISA using Single Molecule Arrays (Simoa), the current gold standard tool for ultrasensitive protein detection. Using ddELISA, we measured the LINE1/ORF1 protein, a potential cancer biomarker that has not been previously measured in serum. Additionally, due to the simplicity of our device design, ddELISA is promising for point-of-care applications. Thus, ddELISA will facilitate the discovery of biomarkers that have never been measured before for various clinical applications.
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Affiliation(s)
- Limor Cohen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemical Biology, Harvard University, Boston, Massachusetts 02115, United States
| | - Naiwen Cui
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yamei Cai
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Padric M Garden
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Xiang Li
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David A Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - David R Walt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Chemical Biology, Harvard University, Boston, Massachusetts 02115, United States
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25
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Inukai R, Takao H, Shimokawa F, Terao K. Capture and elongation of single chromosomal DNA molecules using optically driven microchopsticks. BIOMICROFLUIDICS 2020; 14:044114. [PMID: 32831987 PMCID: PMC7428348 DOI: 10.1063/5.0017727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/05/2020] [Indexed: 05/11/2023]
Abstract
DNA analysis based on the observation of single DNA molecules has been a key technology in molecular biology. Several techniques for manipulating single DNA molecules have been proposed for this purpose; however, these techniques have limits on the manipulatable DNA. To overcome this, we demonstrate a method of DNA manipulation using microstructures captured by optical tweezers that allow the manipulation of a chromosomal DNA molecule. For proper DNA handling, we developed microstructures analogous to chopsticks to capture and elongate single DNA molecules under an optical microscope. Two microstructures (i.e., microchopsticks) were captured by two focused laser beams to pinch a single yeast chromosomal DNA molecule between them and thereby manipulate it. The experiments demonstrated successful DNA manipulation and revealed that the size and geometry of the microchopsticks are important factors for effective DNA handling. This technique allows a high degree of freedom in handling single DNA molecules, potentially leading to applications in the study of chromosomal DNA.
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Affiliation(s)
- Ryo Inukai
- Department of Intelligent Mechanical Systems Engineering, Kagawa University, Takamatsu 761-0396, Japan
| | | | | | - Kyohei Terao
- Author to whom correspondence should be addressed:. Tel.: +81 (87) 864-2346
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