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Panwar S, Duggirala KS, Yadav P, Debnath N, Yadav AK, Kumar A. Advanced diagnostic methods for identification of bacterial foodborne pathogens: contemporary and upcoming challenges. Crit Rev Biotechnol 2023; 43:982-1000. [PMID: 35994308 DOI: 10.1080/07388551.2022.2095253] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/09/2022] [Indexed: 11/03/2022]
Abstract
It is a public health imperative to have safe food and water across the population. Foodborne infections are one of the primary causes of sickness and mortality in both developed and developing countries. An estimated 100 million foodborne diseases and 120 000 foodborne illness-related fatalities occur each year in India. Several factors affect foodborne illness, such as improper farming methods, poor sanitary and hygienic conditions at all levels of the food supply chain, the lack of preventative measures in the food processing industry, the misuse of food additives, as well as improper storage and handling. In addition, chemical and microbiological combinations also play a key role in disease development. But recent disease outbreaks indicated that microbial pathogens played a major role in the development of foodborne diseases. Therefore, prompt, rapid, and accurate detection of high-risk food pathogens is extremely vital to warrant the safety of the food items. Conventional approaches for identifying foodborne pathogens are labor-intensive and cumbersome. As a result, a range of technologies for the rapid detection of foodborne bacterial pathogens have been developed. Presently, many methods are available for the instantaneous detection, identification, and monitoring of foodborne pathogens, such as nucleic acid-based methods, biosensor-based methods, and immunological-based methods. The goal of this review is to provide a complete evaluation of several existing and emerging strategies for detecting food-borne pathogens. Furthermore, this review outlines innovative methodologies and their uses in food testing, along with their existing limits and future possibilities in the detection of live pathogens in food.
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Affiliation(s)
- Surbhi Panwar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | | | - Pooja Yadav
- Centre for Molecular Biology, Central University of Jammu, Jammu, India
| | - Nabendu Debnath
- Centre for Molecular Biology, Central University of Jammu, Jammu, India
| | - Ashok Kumar Yadav
- Centre for Molecular Biology, Central University of Jammu, Jammu, India
| | - Ashwani Kumar
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, India
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2
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Li W, Zhang P, Liu C, Xu Y, Gan Z, Kang L, Hou Y. Oncogene-targeting nanoprobes for early imaging detection of tumor. J Nanobiotechnology 2023; 21:197. [PMID: 37340418 DOI: 10.1186/s12951-023-01943-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/29/2023] [Indexed: 06/22/2023] Open
Abstract
Malignant tumors have been one of the major reasons for deaths worldwide. Timely and accurate diagnosis as well as effective intervention of tumors play an essential role in the survival of patients. Genomic instability is the important foundation and feature of cancer, hence, in vivo oncogene imaging based on novel probes provides a valuable tool for the diagnosis of cancer at early-stage. However, the in vivo oncogene imaging is confronted with great challenge, due to the extremely low copies of oncogene in tumor cells. By combining with various novel activatable probes, the molecular imaging technologies provide a feasible approach to visualize oncogene in situ, and realize accurate treatment of tumor. This review aims to declare the design of nanoprobes responded to tumor associated DNA or RNA, and summarize their applications in detection and bioimaging for tumors. The significant challenges and prospective of oncogene-targeting nanoprobes towards tumors diagnosis are revealed as well.
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Affiliation(s)
- Wenyue Li
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Peisen Zhang
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China.
| | - Chuang Liu
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Yuping Xu
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Zhihua Gan
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, 100034, China.
| | - Yi Hou
- College of Materials Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 10029, China.
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3
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Prajapati GK, Kumar A, Wany A, Pandey DM. Molecular Beacon Probe (MBP)-Based Real-Time PCR. Methods Mol Biol 2023; 2638:273-287. [PMID: 36781649 DOI: 10.1007/978-1-0716-3024-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,R & D Biologics Division, Promea Therapeutics Pvt Ltd, Sultanpur, Hyderabad, India
| | - Ashutosh Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Aakanksha Wany
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
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Kim SH, Li ITS. Super-Resolution Tension PAINT Imaging with a Molecular Beacon. Angew Chem Int Ed Engl 2023; 62:e202217028. [PMID: 36534951 DOI: 10.1002/anie.202217028] [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: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
DNA-PAINT enabled super-resolution imaging through the transient binding of fluorescently-labelled single-stranded DNA (ssDNA) imagers to target ssDNA. However, its performance is constrained by imager background fluorescence, resulting in relatively long image acquisition and potential artifacts. We designed a molecular beacon (MB) as the PAINT imager. Unbound MB in solution reduces the background fluorescence due to its natively quenched state. They are fluorogenic upon binding to target DNA to create individual fluorescence events. We demonstrate that MB-PAINT provides localization precision similar to traditional linear imager DNA-PAINT. We also show that MB-PAINT is ideally suited for fast super-resolution imaging of molecular tension probes in living cells, eliminating the potential of artifacts from free-diffusing imagers in traditional DNA-PAINT at the cell-substrate interface.
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Affiliation(s)
- Seong Ho Kim
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC V1V 1V7, Canada
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5
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Efficient multiplexing and variant discrimination in reverse-transcription loop-mediated isothermal amplification with sequence-specific hybridization probes. Biotechniques 2022; 73:247-255. [DOI: 10.2144/btn-2022-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) has proven a robust and reliable nucleic acid amplification method that is well suited for simplified and rapid molecular diagnostics. Various approaches have emerged for sequence-specific detection of LAMP products, but with limitations to their widespread utility or applicability for single-nucleotide polymorphism detection and multiplexing. Here we demonstrate the use of simple hybridization probes (as used for qPCR) that enable simple multiplexing and SARS-CoV-2 variant typing in reverse-transcription LAMP. This approach requires no modification to the LAMP primers and is amenable to the detection of single-nucleotide polymorphisms and small sequence changes, which is usually difficult in LAMP. By extending LAMP’s ability to be utilized for multitarget and single-base change detection, we hope to increase its potential to enable more and better molecular diagnostic testing.
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Choijookhuu N, Shibata Y, Ishizuka T, Xu Y, Koji T, Hishikawa Y. An Advanced Detection System for In Situ Hybridization Using a Fluorescence Resonance Energy Transfer-based Molecular Beacon Probe. Acta Histochem Cytochem 2022; 55:119-128. [PMID: 36405552 PMCID: PMC9631986 DOI: 10.1267/ahc.22-00075] [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: 08/10/2022] [Accepted: 08/21/2022] [Indexed: 01/24/2023] Open
Abstract
In situ hybridization (ISH) is a powerful method for detecting specific RNAs at the cellular level. Although conventional ISH using hapten-labeled probes are useful for detecting multiple RNAs, the detection procedures are still complex and required longer time. Therefore, we introduced a new application of fluorescence resonance energy transfer (FRET)-based molecular beacon (MB) probes for ISH. MCF-7 cells and C57BL/6J mouse uterus were used for ISH. MB probes for ERα mRNA and 28S rRNA were labeled with Cy3/BHQ-2 and 6-FAM/DABCYL, and conventional probes were labeled with digoxigenin. Fluorescence measurements revealed that of more-rapid hybridization kinetics compared to conventional probes. In MCF-7 cells, 28S rRNA was detected in nucleolus and cytoplasm of all cells, whereas ERα mRNA was detected in some nucleolus. In the uterus, 28S rRNA was clearly detected using complementary MB probe, but there were no signals in control slides. Moreover, 28S rRNA was detected in all cells, whereas ERα mRNA was detected mainly in the epithelium. Fluorescence intensity of 28S rRNA was decreased significantly in 1 or 2 base-mismatched sequences, that indicates highly specific detection of target RNAs. In conclusion, the FRET-based MB probes are very useful for ISH, providing rapid hybridization, high sensitivity and specificity.
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Affiliation(s)
- Narantsog Choijookhuu
- Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889–1692, Japan
| | - Yasuaki Shibata
- Department of Histology and Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, 1–12–4 Sakamoto, Nagasaki 852–8523, Japan
| | - Takumi Ishizuka
- Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889–1692, Japan
| | - Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889–1692, Japan
| | - Takehiko Koji
- Department of Histology and Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, 1–12–4 Sakamoto, Nagasaki 852–8523, Japan
| | - Yoshitaka Hishikawa
- Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889–1692, Japan,Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889–1692, Japan
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7
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Establishment of a rapid method for skipjack tuna (Katsuwonus pelamis) authentication using molecular beacons in loop-mediated isothermal amplification. Food Chem 2022; 382:132365. [DOI: 10.1016/j.foodchem.2022.132365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022]
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8
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Takehana S, Yang W, Tabata Y. Potential Method of Autophagy Imaging with Cationized Gelatin Nanospheres Incorporating Molecular Beacon. ACS APPLIED BIO MATERIALS 2022; 5:2965-2975. [PMID: 35609115 DOI: 10.1021/acsabm.2c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The objective of this research is to develop an imaging method with cationized gelatin nanospheres incorporating molecular beacon (cGNSMB) to visualize an autophagy activity in living cells. Cationized gelatin nanospheres (cGNS) were prepared by the conventional coacervation method, and then molecular beacon (MB) was incorporated into them. The cGNSMB prepared were internalized into cells at a high efficiency. In this study, a starvation medium of serum and amino acids-free was used to induce autophagy. The autophagy activity was confirmed by an immunofluorescence staining for microtubule-associated proteins light chain 3B (LC3B) of an autophagy specific protein. With the autophagy induction time, the number of LC3 fluorescent dots increased, which indicated an increased autophagy activity. As the autophagy-related genes, sequestosome 1 (SQSTM1) and cathepsin F (CTSF), which up-regulate after autophagy induction, were chosen as the targets of cGNSMB. The fluorescence intensity of cGNSMB targeting to SQSTM1 and CTSF increased with the starvation treatment time, which well corresponded with the gene expression results. When applied to cells in different autophagy conditions, the cGNSMB visualized the autophagy activity corresponding with the autophagy condition of cells. From the results obtained, it was concluded that the cGNSMB provide a promising method to visualize the autophagy of cells. The advantage of cGNSMB visualization is to obtain the temporal and spatial information without destroying sample cells.
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Affiliation(s)
- Sho Takehana
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Wenxuan Yang
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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Dillen A, Lammertyn J. Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms. Analyst 2022; 147:1006-1023. [DOI: 10.1039/d1an02308j] [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
Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
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Carvalho J, Lopes-Nunes J, Figueiredo J, Santos T, Miranda A, Riscado M, Sousa F, Duarte AP, Socorro S, Tomaz CT, Felgueiras M, Teixeira R, Faria C, Cruz C. Molecular Beacon Assay Development for Severe Acute Respiratory Syndrome Coronavirus 2 Detection. SENSORS (BASEL, SWITZERLAND) 2021; 21:7015. [PMID: 34770321 PMCID: PMC8587319 DOI: 10.3390/s21217015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 12/23/2022]
Abstract
The fast spread of SARS-CoV-2 has led to a global pandemic, calling for fast and accurate assays to allow infection diagnosis and prevention of transmission. We aimed to develop a molecular beacon (MB)-based detection assay for SARS-CoV-2, designed to detect the ORF1ab and S genes, proposing a two-stage COVID-19 testing strategy. The novelty of this work lies in the design and optimization of two MBs for detection of SARS-CoV-2, namely, concentration, fluorescence plateaus of hybridization, reaction temperature and real-time results. We also identify putative G-quadruplex (G4) regions in the genome of SARS-CoV-2. A total of 458 nasopharyngeal and throat swab samples (426 positive and 32 negative) were tested with the MB assay and the fluorescence levels compared with the cycle threshold (Ct) values obtained from a commercial RT-PCR test in terms of test duration, sensitivity, and specificity. Our results show that the samples with higher fluorescence levels correspond to those with low Ct values, suggesting a correlation between viral load and increased MB fluorescence. The proposed assay represents a fast (total duration of 2 h 20 min including amplification and fluorescence reading stages) and simple way of detecting SARS-CoV-2 in clinical samples from the upper respiratory tract.
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Affiliation(s)
- Josué Carvalho
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Jéssica Lopes-Nunes
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Joana Figueiredo
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - André Miranda
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Micaela Riscado
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Fani Sousa
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
- C4—Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Ana Paula Duarte
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
- C4—Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Sílvia Socorro
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
| | - Cândida Teixeira Tomaz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
- C4—Cloud Computing Competence Centre, UBIMedical, Universidade da Beira Interior, Estrada Municipal 506, 6200-284 Covilhã, Portugal
| | - Mafalda Felgueiras
- Serviço de Patologia Clínica do Centro Hospitalar Universitário Cova da Beira (CHUCB), 6200-251 Covilhã, Portugal; (M.F.); (R.T.); (C.F.)
| | - Rui Teixeira
- Serviço de Patologia Clínica do Centro Hospitalar Universitário Cova da Beira (CHUCB), 6200-251 Covilhã, Portugal; (M.F.); (R.T.); (C.F.)
| | - Conceição Faria
- Serviço de Patologia Clínica do Centro Hospitalar Universitário Cova da Beira (CHUCB), 6200-251 Covilhã, Portugal; (M.F.); (R.T.); (C.F.)
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; (J.C.); (J.L.-N.); (J.F.); (T.S.); (A.M.); (M.R.); (F.S.); (A.P.D.); (S.S.); (C.T.T.)
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Bidar N, Amini M, Oroojalian F, Baradaran B, Hosseini SS, Shahbazi MA, Hashemzaei M, Mokhtarzadeh A, Hamblin MR, de la Guardia M. Molecular beacon strategies for sensing purpose. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116143] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Mao S, Ying Y, Wu R, Chen AK. Recent Advances in the Molecular Beacon Technology for Live-Cell Single-Molecule Imaging. iScience 2020; 23:101801. [PMID: 33299972 PMCID: PMC7702005 DOI: 10.1016/j.isci.2020.101801] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids, aside from being best known as the carrier of genetic information, are versatile biomaterials for constructing nanoscopic devices for biointerfacing, owing to their unique properties such as specific base pairing and predictable structure. For live-cell analysis of native RNA transcripts, the most widely used nucleic acid-based nanodevice has been the molecular beacon (MB), a class of stem-loop-forming probes that is activated to fluoresce upon hybridization with target RNA. Here, we overview efforts that have been made in developing MB-based bioassays for sensitive intracellular analysis, particularly at the single-molecule level. We also describe challenges that are currently limiting the widespread use of MBs and provide possible solutions. With continued refinement of MBs in terms of labeling specificity and detection accuracy, accompanied by new development in imaging platforms with unprecedented sensitivity, the application of MBs is envisioned to expand in various biological research fields.
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Affiliation(s)
- Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Ruonan Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Antony K. Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
- Corresponding author
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Milliron HYY, Weiland MJ, Kort EJ, Jovinge S. Isolation of Cardiomyocytes Undergoing Mitosis With Complete Cytokinesis. Circ Res 2019; 125:1070-1086. [PMID: 31648614 DOI: 10.1161/circresaha.119.314908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RATIONALE Adult human cardiomyocytes do not complete cytokinesis despite passing through the S-phase of the cell cycle. As a result, polyploidization and multinucleation occur. To get a deeper understanding of the mechanisms surrounding division of cardiomyocytes, there is a crucial need for a technique to isolate cardiomyocytes that complete cell division/cytokinesis. OBJECTIVE Markers of cell cycle progression based on DNA content cannot distinguish between mitotic cardiomyocytes that fail to complete cytokinesis from those cells that undergo true cell division. With the use of molecular beacons (MBs) targeting specific mRNAs, we aimed to identify truly proliferative cardiomyocytes derived from human induced pluripotent stem cells. METHODS AND RESULTS Fluorescence-activated cell sorting combined with MBs was performed to sort cardiomyocyte populations enriched for mitotic cells. Expressions of cell cycle specific genes were confirmed by means of reverse transcription-quantitative polymerase chain reaction and single-cell RNA sequencing (scRNA-seq) combined with gene signatures of cell cycle progression. We characterized the sorted groups by proliferation assays and time-lapse microscopy which confirmed the proliferative advantage of MB-positive cell populations relative to MB-negative and G2/M populations. Gene expression analysis revealed that the MB-positive cardiomyocyte subpopulation exhibited patterns consistent with the processes of nuclear division, chromosome segregation, and transition from M to G1 phase. The use of dual-MBs targeting CDC20 and SPG20 mRNAs enabled the enrichment of cytokinetic events (CDC20highSPG20high). Interestingly, cells that did not complete cytokinesis and remained binucleated were found to be CDC20lowSPG20high while polyploid cardiomyocytes that replicated DNA but failed to complete karyokinesis were found to be CDC20lowSPG20low. CONCLUSIONS This study demonstrates a novel alternative to existing DNA content-based approaches for sorting cardiomyocytes with true mitotic potential that can be used to study the unique dynamics of cardiomyocyte nuclei during mitosis. Our technique for sorting live cardiomyocytes undergoing cytokinesis would provide a basis for future studies to uncover mechanisms underlying the development and regeneration of heart tissue.
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Affiliation(s)
- Hsiao-Yun Y Milliron
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.)
| | - Matthew J Weiland
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.)
| | - Eric J Kort
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.).,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, East Lansing (E.J.K.)
| | - Stefan Jovinge
- From the DeVos Cardiovascular Program, Van Andel Research Institute and Fredrik Meijer Heart and Vascular Institute/Spectrum Health, Grand Rapids, MI (H.Y.M., M.J.W., E.J.K., S.J.).,Cardiovascular Institute, Stanford University, Palo Alto, CA (S.J.)
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14
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Chen C, Chen S, Shiddiky MJA, Chen C, Wu KC. DNA‐Templated Copper Nanoprobes: Overview, Feature, Application, and Current Development in Detection Technologies. CHEM REC 2019; 20:174-186. [DOI: 10.1002/tcr.201900022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/22/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Chung‐An Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Shih‐Chia Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Muhammad J. A. Shiddiky
- School of Environment and Science & Queensland Micro- and Nanotechnology CentreNathan campus, Griffith University 170 Kessels Road QLD 4111 Australia
| | - Chien‐Fu Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Kevin C.‐W. Wu
- Department of Chemical EngineeringNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
- Division of Medical Engineering Research, National Health
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15
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Caputo TM, Battista E, Netti PA, Causa F. Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17147-17156. [PMID: 31021070 DOI: 10.1021/acsami.8b22635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 μL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.
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Affiliation(s)
- Tania M Caputo
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
| | - Edmondo Battista
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Paolo A Netti
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
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16
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Guk K, Hwang SG, Lim J, Son HY, Choi Y, Huh YM, Kang T, Jung J, Lim EK. Fluorescence amplified sensing platforms enabling miRNA detection by self-circulation of a molecular beacon circuit. Chem Commun (Camb) 2019; 55:3457-3460. [PMID: 30735212 DOI: 10.1039/c9cc00351g] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have proposed a novel strategy for miRNA detection through enzyme-free signal amplification by self-circulation of the hybridization between the miRNAs and molecular beacon (MB) circuits. Unlike general MB-based miRNA detection based on the one-to-one (1 : 1) hybridization between MBs and miRNA, our system consists of four species of MBs (MBs A, B, C and D) (MB circuits) and is activated by a hybridization chain reaction. MBs stably coexist as hairpin structures that hardly show fluorescence signals in the absence of target miRNA. After miRNA detection, this MB circuit is able to generate fluorescence signals and amplify the fluorescence signal, contributing to improvement in detection sensitivity under iso-thermal conditions without an enzyme. Furthermore, in vitro and in vivo studies have proven that MB circuits can detect low levels of miRNA with high sensitivity, compared to when only one MB alone is used. Therefore, the MB circuits can provide a useful platform for target miRNA detection.
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Affiliation(s)
- Kyeonghye Guk
- BioNano Technology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
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17
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Qian C, Wang R, Wu C, Wang L, Ye Z, Wu J, Ji F. A fast and visual method for duplex shrimp pathogens detection with high specificity using rapid PCR and molecular beacon. Anal Chim Acta 2018; 1040:105-111. [PMID: 30327099 DOI: 10.1016/j.aca.2018.07.064] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/13/2018] [Accepted: 07/26/2018] [Indexed: 12/26/2022]
Abstract
Molecular diagnosis of genome is one of the major methods for pathogens detection. The commonly used PCR method can realize an exponential amplification of the target gene but is time-consuming. In this work, we proposed a duplex and visual method using rapid PCR combined with molecular beacons to specifically detect two kinds of shrimp pathogens in one reaction tube. We only need to observe the fluorescence change of the reaction tube with naked eye to determine the result. A home-made automatic transfer equipment allows reaction tubes shuttling quickly between two water baths to achieve rapid PCR amplification. A simple device was also designed to present the detection results easily determined with naked eye. This duplex and visual detection method is fast, low-cost and of high specificity. From DNA extraction to results judgment, only 15 min was enough. Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) and Vibrio parahaemolyticus (VP) are two common shrimp pathogens which were chosen as our detection objects. This method may give a possibility to conduct end-point visual duplex detection, which may make a positive influence on the pathogen prevention.
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Affiliation(s)
- Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Rui Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cui Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Liu Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zunzhong Ye
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
| | - Feng Ji
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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18
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Han S, Kang B, Jang E, Ki J, Kim E, Jeong MY, Huh YM, Son HY, Haam S. Convenient Monitoring System of Intracellular microRNA Expression during Adipogenesis via Mechanical Stimulus-Induced Exocytosis of Lipovesicular miRNA Beacon. Adv Healthc Mater 2018; 7. [PMID: 29280320 DOI: 10.1002/adhm.201701019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 11/11/2017] [Indexed: 01/01/2023]
Abstract
Noninvasive investigation of microRNAs (miRNAs) expression, which is deeply related to biological phenomena such as stem cell differentiation, in culture soup is particularly useful for monitoring of stem cell differentiation without phototoxicity of living cells, especially when cell morphologies remain unchanged during differentiation. However, real-time detection of miRNA in culture soup is not recommended because of insufficient miRNA amounts in culture soup. In this study, a convenient method is introduced for real-time assessing intracellular miRNA in culture soup by using lipovesicular miRNA beacon (Lipo-mB) and mechanical stimulus-mediated exocytosis. Pipetting-harvest of culture soup induces exocytosis-secretion of fluorescence signal of Lipo-mB from cytoplasm into culture soup. To demonstrate this method, Lipo-mB is applied for monitoring of adipogenesis by analyzing the expression levels of various intracellular miRNAs, which are related to adipogenesis regulators. The fluorescence intensity profile of the culture soup is correlated with the quantitative reverse-transcription-polymerase chain reaction data and absorbance of Oil Red O staining. These results demonstrate that Lipo-mB can successfully monitor stem cell differentiation by sensing changes in miRNA expression from culture soup of living cells. Lipo-mB can be further developed as an accurate sensing system for analyzing subtle differences in genotype, even when changes in phenotype cannot be observed.
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Affiliation(s)
- Seungmin Han
- Department of Chemical and Biomolecular Engineering; Yonsei University; Seoul 120-749 Republic of Korea
| | - Byunghoon Kang
- Department of Chemical and Biomolecular Engineering; Yonsei University; Seoul 120-749 Republic of Korea
| | - Eunji Jang
- Department of Radiology; College of Medicine; Yonsei University; Seoul 120-752 Republic of Korea
| | - Jisun Ki
- Department of Chemical and Biomolecular Engineering; Yonsei University; Seoul 120-749 Republic of Korea
| | - Eunjung Kim
- Department of Materials; Department of Bioengineering and Institute for Biomedical Engineering; Imperial College London; London SW7 2AZ UK
| | - Mun-Young Jeong
- Department of Radiology; College of Medicine; Yonsei University; Seoul 120-752 Republic of Korea
| | - Yong-Min Huh
- Department of Radiology; College of Medicine; Yonsei University; Seoul 120-752 Republic of Korea
- Severance Biomedical Science Institute; College of Medicine; Yonsei University; Seoul 120-752 Republic of Korea
- YUHS-KRIBB Medical Convergence Research Institute; Seoul 120-752 Republic of Korea
- Brain Korea 21 Project for Medical Science; Yonsei University College of Medicine; Seoul 120-752 Republic of Korea
| | - Hye-Young Son
- Department of Radiology; College of Medicine; Yonsei University; Seoul 120-752 Republic of Korea
- Severance Biomedical Science Institute; College of Medicine; Yonsei University; Seoul 120-752 Republic of Korea
- YUHS-KRIBB Medical Convergence Research Institute; Seoul 120-752 Republic of Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering; Yonsei University; Seoul 120-749 Republic of Korea
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Dembska A, Kierzek E, Juskowiak B. Studying the influence of stem composition in pH-sensitive molecular beacons onto their sensing properties. Anal Chim Acta 2017; 990:157-167. [PMID: 29029739 DOI: 10.1016/j.aca.2017.07.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 06/21/2017] [Accepted: 07/17/2017] [Indexed: 01/04/2023]
Abstract
Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration. Moreover, this conformational transition was accompanied by spectral changes showing developed probes different pyrene excimer-monomer emission ratio triggered by pH changes. The potential of these MBs for intracellular pH sensing is demonstrated on the example of HeLa cells line.
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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20
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Adegoke O, Park EY. Bright luminescent optically engineered core/alloyed shell quantum dots: an ultrasensitive signal transducer for dengue virus RNA via localized surface plasmon resonance-induced hairpin hybridization. J Mater Chem B 2017; 5:3047-3058. [DOI: 10.1039/c7tb00388a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A plasmon-mediated fluorescence molecular beacon biosensor probe has been developed for dengue virus with high sensitivity and specificity.
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Affiliation(s)
- Oluwasesan Adegoke
- Laboratory of Biotechnology
- Research Institute of Green Science and Technology
- Shizuoka University
- Shizuoka 422-8529
- Japan
| | - Enoch Y. Park
- Laboratory of Biotechnology
- Research Institute of Green Science and Technology
- Shizuoka University
- Shizuoka 422-8529
- Japan
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21
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Park J, Song M, Jang W, Chae H, Lee GD, Kim K, Park H, Kim M, Kim Y. Peptide nucleic acid probe-based fluorescence melting curve analysis for rapid screening of common JAK2, MPL, and CALR mutations. Clin Chim Acta 2016; 465:82-90. [PMID: 27939919 DOI: 10.1016/j.cca.2016.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/26/2023]
Abstract
BACKGROUND We developed and evaluated the feasibility of peptide nucleic acid (PNA)-based fluorescence melting curve analysis (FMCA) to detect common mutations in myeloproliferative neoplasms (MPNs). METHODS We have set up two separate reactions of PNA-based FMCA: JAK2 V617F &CALR p.Leu367fs*46 (set A) and MPL W515L/K &CALR p.Lys385fs*47 (set B). Clinical usefulness was validated with allele-specific real-time PCR, fragment analysis, Sanger sequencing in 57 BCR-ABL1-negative MPNs. RESULTS The limit of detection (LOD) of PNA-based FMCA was approximately 10% for each mutation and interference reactions using mixtures of different mutations were not observed. Non-specific amplification was not observed in normal control. PNA-based FMCA was able to detect all JAK2 V617F (n=20), CALR p.Leu367fs*46 (n=10) and p.Lys385fs*47 (n=8). Three of six MPL mutations were detected except three samples with low mutant concentration in out of LOD. JAK2 exon 12 mutations (n=7) were negative without influencing V617F results. Among six variant CALR exon 9 mutations, two were detected by this method owing to invading of probe binding site. CONCLUSIONS PNA-based FMCA for detecting common JAK2, MPL, and CALR mutations is a rapid, simple, and sensitive technique in BCR-ABL1-negative MPNs with >10% mutant allele at the time of initial diagnosis.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Minsik Song
- SeaSun Biomaterials, Daejeon, Republic of Korea
| | - Woori Jang
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | | | | | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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22
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Lim EK, Guk K, Kim H, Chung BH, Jung J. Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon. Chem Commun (Camb) 2016; 52:175-8. [PMID: 26509476 DOI: 10.1039/c5cc05684e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies.
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Affiliation(s)
- Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Kyeonghye Guk
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and Nanobiotechnology Major, School of Engineering, University of Science and Technology (UST), 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea
| | - Hyeran Kim
- BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Bong-Hyun Chung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Juyeon Jung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
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23
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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24
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Abalde-Cela S, Carregal-Romero S, Coelho JP, Guerrero-Martínez A. Recent progress on colloidal metal nanoparticles as signal enhancers in nanosensing. Adv Colloid Interface Sci 2016; 233:255-270. [PMID: 26094082 DOI: 10.1016/j.cis.2015.05.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 11/30/2022]
Abstract
Colloidal metal nanoparticles present very special optical and electromagnetic properties at the nanoscale range. Such plasmonic properties have derived in a huge research field that encompasses the understanding of nanoparticle formation mechanisms for the ultimate goal of developing novel materials for real-life applications. Plasmonic sensing is experiencing a rapid transition by taking advantage of the characteristic properties of colloidal metal nanoparticles. However, a rational design of novel nanoplasmonic substrates, which gathers as much as the required properties for a substrate to be a 'good' sensor is critical through the development of applications that can be effectively transferred as applied technologies. Also, the chosen sensing technique is a key factor when planning the design of a new plasmonic-based sensor. Several factors such as composition, shape, size, particle interactions or stability among others will define the final quality of the nanomaterial as sensing platform. Herein, we review the latest and most promising state-of-the art of nanoplasmonic-based sensors in four differentiated areas regarding the surface-enhanced spectroscopy detection technique being LSPR-, SERS- and SEIRA-, and SEF based platforms.
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Affiliation(s)
- Sara Abalde-Cela
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Susana Carregal-Romero
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain; Oncology Area, Biodonostia Research Institute, Donostia-San Sebastián 20014, Spain
| | - João Paulo Coelho
- Departamento de Química Física I, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Andrés Guerrero-Martínez
- Departamento de Química Física I, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain.
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25
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Kim K, Hong SH, Kim BJ, Kim BR, Lee SY, Kim GN, Shim TS, Kook YH, Kim BJ. Separation of Mycobacterium abscessus into subspecies or genotype level by direct application of peptide nucleic acid multi-probe- real-time PCR method into sputa samples. BMC Infect Dis 2015; 15:325. [PMID: 26259717 PMCID: PMC4531893 DOI: 10.1186/s12879-015-1076-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022] Open
Abstract
Background Recently, we introduced a novel peptide nucleic acid (PNA) multi-probe real time PCR method targeting the hsp65 gene (hsp65 PNA RT-PCR) to distinguish Mycobacterium abscessus groups. Methods Here, we evaluated the usefulness of the hsp65 PNA RT-PCR for the direct identification of the M. abscessus group at the subspecies and genotype levels from sputa samples. The method was applied to total sputa DNA from 60 different patients who were identified as having mycobacterial infections via rpoB PCR restriction analysis of the same cultures. Results The hsp65 PNA RT-PCR method had higher sensitivity than the multi-probe real-time PCR assay targeting hsp65 (HMPRT-PCR) for the detection of M. abscessus from sputum [96.7 % (29/30 samples) vs. 70 % (21/30 samples); 100 % specificity]. Conclusions These results suggest that the PNA-based method is feasible for the detection of M. abscessus members not only from cultures but also directly from sputa. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1076-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea.
| | - Seok-Hyun Hong
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Tae Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
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Dembska A, Juskowiak B. Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:928-933. [PMID: 26123509 DOI: 10.1016/j.saa.2015.06.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023]
Abstract
In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit).
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Affiliation(s)
- Anna Dembska
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland.
| | - Bernard Juskowiak
- Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznan, Poland
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Chang X, Yu C, Wang G, Fan J, Zhang J, Qi Y, Liu K, Fang Y. Constitutional Dynamic Chemistry-based New Concept of Molecular Beacons for High Efficient Development of Fluorescent Probes. J Phys Chem B 2015; 119:6721-9. [PMID: 25985384 DOI: 10.1021/acs.jpcb.5b02664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inspired by the concept of constitutional dynamic chemistry, we propose a new and well-adaptable strategy for developing molecular beacon (MB)-like fluorescent probes. To demonstrate the strategy, we synthesized and used an amino group containing pyrenyl derivative of cholesterol (CP) for the construction of new fluorescent probes with EDTA and sulfuric acid. The probes as created were successfully used for n-hexane purity checking and Ba(2+)and Pb(2+)sensing, respectively.
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Affiliation(s)
- Xingmao Chang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Chunmeng Yu
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Gang Wang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Jiayun Fan
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Jianyun Zhang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Yanyu Qi
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Kaiqiang Liu
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
| | - Yu Fang
- †Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), ‡School of Materials Science and Engineering, and §School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China
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28
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Chowdhury JA, Moriguchi T, Shinozuka K. Pseudo-Dumbbell-Type Molecular Beacon Probes Bearing Modified Deoxyuridine Derivatives and a Silylated Pyrene as a Fluorophore. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jakir Ahmed Chowdhury
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University
| | - Tomohisa Moriguchi
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University
| | - Kazuo Shinozuka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University
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29
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Zhou F, Wang G, Shi D, Sun Y, Sha L, Qiu Y, Zhang X. One-strand oligonucleotide probe for fluorescent label-free “turn-on” detection of T4 polynucleotide kinase activity and its inhibition. Analyst 2015; 140:5650-5. [DOI: 10.1039/c5an00862j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Thioflavin T (ThT), as one of the most exciting fluorogenic molecules, boasts the “molecular-rotor” ability to induce DNA sequences containing guanine repeats to fold into G-quadruplex structures.
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Affiliation(s)
- Fu Zhou
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Guangfeng Wang
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Dongmin Shi
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Yue Sun
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Liang Sha
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Yuwei Qiu
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
| | - Xiaojun Zhang
- Anhui Key Laboratory of Chem-biosensing
- College of Chemistry and Materials Science
- Center for Nanoscience and Nanotechology
- Anhui Normal University
- Wuhu
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30
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Cui Y, Irudayaraj J. Inside single cells: quantitative analysis with advanced optics and nanomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:387-407. [PMID: 25430077 DOI: 10.1002/wnan.1321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 01/08/2023]
Abstract
Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center and Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
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31
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Tan X, Wang Y, Armitage BA, Bruchez MP. Label-free molecular beacons for biomolecular detection. Anal Chem 2014; 86:10864-9. [PMID: 25287123 DOI: 10.1021/ac502986g] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biomolecular detection and imaging methods provide quantitative measurements essential for biological research. In this context, molecular beacon based sensors have emerged as powerful, no-wash imaging agents, providing target-specific fluorescent activation for nucleic acids, proteins, and small molecules. Conventional molecular beacons require double-labeled DNA sequences, which are costly and time-consuming to prepare. To address this issue, we developed DNA based label-free molecular beacons consisting of two regions: a signal-generating region based on human telomeric G-quadruplex sequence that activates Thioflavin T fluorescence and a target recognition sequence designed to interact in a molecular beacon format. We demonstrated the utility of these probes for the selective detection of DNA, RNA, and protein. Multiple probes were applied against a single target to achieve improved brightness in fluorescence detection of nucleic acid targets. This label-free strategy provides a straightforward, cost-effective alternative to fluorescently labeled oligonucleotides in biomolecular detection and imaging.
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Affiliation(s)
- Xiaohong Tan
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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Sun X, Jia M, Guan L, Ji J, Zhang Y, Tang L, Li Z. Multilayer graphene-gold nanocomposite modified stem-loop DNA biosensor for peanut allergen-Ara h1 detection. Food Chem 2014; 172:335-42. [PMID: 25442562 DOI: 10.1016/j.foodchem.2014.09.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 06/20/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022]
Abstract
In this study, we developed an electrochemically-amplified, stem-loop DNA biosensor to detect the peanut allergen Ara h1. Specifically, we electrodeposited a multilayer graphene-gold nanocomposite onto a glassy carbon electrode and then immobilised a thiolated hairpin DNA-biotin probe onto the modified electrode surface. The multilayer graphene-gold composite has good dispersion ability, and can amplify the electrochemical signal due to its high electron-transfer efficiency. The probe was switched to an "off" state in the presence of target DNA. The prepared biosensor demonstrated a linear response ranging from 10(-16) to 10(-13)M, with an ultrasensitive detection limit of 0.041 fM. Moreover, the biosensor showed excellent selectivity, as well as the ability to discriminate between a complementary target and a one-base mismatch or non-complementary sequence. Results show that this prepared DNA biosensor can be successfully used to detect the peanut allergen Ara h1 in a peanut milk beverage. Findings can be applied to the prevention of allergic reactions, thus improving human health and safety.
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Affiliation(s)
- Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Min Jia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lu Guan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yinzhi Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Lili Tang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zaijun Li
- School of Chemical and Material Engineering of Jiangnan University, Wuxi, Jiangsu 214122, China
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33
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Penna A, Galluzzi L. The quantitative real-time PCR applications in the monitoring of marine harmful algal bloom (HAB) species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6851-62. [PMID: 23247526 PMCID: PMC3782655 DOI: 10.1007/s11356-012-1377-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/29/2012] [Indexed: 05/15/2023]
Abstract
In the last decade, various molecular methods (e.g., fluorescent hybridization assay, sandwich hybridization assay, automatized biosensor detection, real-time PCR assay) have been developed and implemented for accurate and specific identification and estimation of marine toxic microalgal species. This review focuses on the recent quantitative real-time PCR (qrt-PCR) technology developed for the control and monitoring of the most important taxonomic phytoplankton groups producing biotoxins with relevant negative impact on human health, the marine environment, and related economic activities. The high specificity and sensitivity of the qrt-PCR methods determined by the adequate choice of the genomic target gene, nucleic acid purification protocol, quantification through the standard curve, and type of chemical detection method make them highly efficient and therefore applicable to harmful algal bloom phenomena. Recent development of qrt-PCR-based assays using the target gene of toxins, such as saxitoxin compounds, has allowed more precise quantification of toxigenic species (i.e., Alexandrium catenella) abundance. These studies focus only on toxin-producing species in the marine environment. Therefore, qrt-PCR technology seems to offer the advantages of understanding the ecology of harmful algal bloom species and facilitating the management of their outbreaks.
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Affiliation(s)
- Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro, Italy,
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34
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Lee JO, Choi JA, Chun KH. Modified Molecular Beacon for Detection of Protein and Its Application for Assay of Streptavidin. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.3.723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Kirsch J, Siltanen C, Zhou Q, Revzin A, Simonian A. Biosensor technology: recent advances in threat agent detection and medicine. Chem Soc Rev 2013; 42:8733-68. [DOI: 10.1039/c3cs60141b] [Citation(s) in RCA: 313] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Use of flow cytometry for rapid, quantitative detection of poliovirus-infected cells via TAT peptide-delivered molecular beacons. Appl Environ Microbiol 2012; 79:696-700. [PMID: 23160127 DOI: 10.1128/aem.02429-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and efficient detection of viral infection is crucial for the prevention of disease spread during an outbreak and for timely clinical management. In this paper, the utility of Tat peptide-modified molecular beacons (MBs) as a rapid diagnostic tool for the detection of virus-infected cells was demonstrated. The rapid intracellular delivery mediated by the Tat peptide enabled the detection of infected cells within 30 s, reaching saturation in signal in 30 min. This rapid detection scheme was coupled with flow cytometry (FC), resulting in an automated, high-throughput method for the identification of virus-infected cells. Because of the 2-order-of-magnitude difference in fluorescence intensity between infected and uninfected cells, as few as 1% infected cells could be detected. Because of its speed and sensitivity, this approach may be adapted for the practical diagnosis of multiple viral infections.
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37
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Design and development of an in-house multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV in plasma samples. IRANIAN JOURNAL OF MICROBIOLOGY 2012; 52:456-63. [PMID: 22783455 DOI: 10.1007/s12088-012-0271-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 04/26/2012] [Indexed: 01/12/2023]
Abstract
BACKGROUND AND OBJECTIVES HIV-1 and HCV infections are life threatening problems in patients who receive blood products. Serological methods have proven useful in detecting these infections, but there are setbacks that make it challenging to detect these infectious agents. By the advent of Nucleic Acid Testing (NAT) methods, especially in multiplex format, more precise detection is possible. MATERIALS AND METHODS We have developed a multiplex RT-PCR assay for simultaneous detection of HIV-1 and HCV. Primers were designed for highly conserved region of genome of each virus. Using these primers and standard plasmids, we determined the limit of detection, clinical and analytical specificity and sensitivity of the assay. Monoplex and multiplex RT-PCR were performed. RESULTS Analytical sensitivity was considered to be 100 and 200 copies/ml for HIV-1 and HCV, respectively. High concentration of one virus had no significant effect on the detection of the other one with low concentration. By analysis of 40 samples, clinical sensitivity of the assay was determined to be 97.5%. Using different viral and human genome samples, the specificity of the assay was evaluated to be 100%. CONCLUSIONS The aim of this study was to develop a reliable, rapid and cost effective method to detect HIV-1 and HCV simultaneously. Results showed that this simple and rapid method is perfectly capable of detecting two viruses in clinical samples.
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Detection of prolactin inducible protein mRNA, a biomarker for breast cancer metastasis, using a molecular beacon-based assay. Anal Bioanal Chem 2012; 404:399-406. [PMID: 22692591 DOI: 10.1007/s00216-012-6162-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 05/24/2012] [Accepted: 05/28/2012] [Indexed: 10/28/2022]
Abstract
Mortality due to breast cancer is increasingly linked to early, undetected metastasis, making methods for earlier detection acutely necessary. We describe the development of an assay based on molecular beacon (MB) chemistry with fluorescence detection to monitor a breast cancer biomarker for the analysis of breast cancer metastasis. The MB assay is based on the complementary base-pairing interactions of the MB nucleic acid with mRNA indicative of breast cancer metastasis. The presence of mRNA is characterized by an increase in the fluorescence intensity of the molecular beacon. The assay gives a linear, reproducible response to prolactin inducible protein mRNA, with a limit of detection in the high picomolar range. This method sensitively and specifically identifies a biomarker directly in serum samples in minimal time and with a straightforward procedure, dramatically reducing the total time for sample analysis over current methods from days to hours. The potential impact of this work in detection and understanding of breast cancer metastasis lies in improvements in simplicity, accuracy, and speed over current methods, which could allow for improved patient treatment and prognoses. Ultimately, additional sample throughput will result in better understanding of disease progression.
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Fabrication of DNA electrochemical biosensor based on gold nanoparticles, locked nucleic acid modified hairpin DNA and enzymatic signal amplification. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.03.143] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Stobiecka M, Molinero AA, Chałupa A, Hepel M. Mercury/homocysteine ligation-induced ON/OFF-switching of a T-T mismatch-based oligonucleotide molecular beacon. Anal Chem 2012; 84:4970-8. [PMID: 22524145 DOI: 10.1021/ac300632u] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A molecular beacon (MB) with stem-loop (hairpin) DNA structure and with attached fluorophore-quencher pair at the ends of the strand has been applied to study the interactions of Hg(2+) ions with a thymine-thymine (T-T) mismatch in Watson-Crick base-pairs and the ligative disassembly of MB·Hg(2+) complex by Hg(2+) sequestration with small biomolecule ligands. In this work, a five base-pair stem with configuration 5'-GGTGG...CCTCC-3' for self-hybridization of MB has been utilized. In this configuration, the four GC base-pair binding energy is not sufficient to hybridize fully at intermediate temperatures and to form a hairpin MB conformation. The T-T mismatch built-in into the stem area can effectively bind Hg(2+) ions creating a bridge, T-Hg-T. We have found that the T-Hg-T bridge strongly enhances the ability of MB to hybridize, as evidenced by an unusually large MB melting temperature shift observed on bridge formation, ΔT(m) = +15.1 ± 0.5 °C, for 100 nM MB in MOPS buffer. The observed ΔT(m) is the largest of the ΔT(m) found for other MBs and dsDNA structures. By fitting the parameters of the proposed model of reversible MB interactions to the experimental data, we have determined the T-Hg-T bridge formation constant at 25 °C, K(1) = 8.92 ± 0.42 × 10(17) M(-1) from mercury(II) titration data and K(1) = 1.04 ± 0.51 × 10(18) M(-1) from the bridge disassembly data; ΔG° = -24.53 ± 0.13 kcal/mol. We have found that the biomarker of oxidative stress and cardiovascular disease, homocysteine (Hcys), can sequester Hg(2+) ions from the T-Hg-T complex and withdraw Hg(2+) ions from MB in the form of stable Hg(Hcys)(2)H(2) complexes. Both the model fitting and independent (1)H NMR results on the thymidine-Hg-Hcys system indicate also the high importance of 1:1 complexes. The high value of K(1) for T-Hg-T bridge formation enables analytical determinations of low concentrations of Hg(2+) (limit of detection LOD = 19 nM or 3.8 ppb, based on 3σ method) and Hcys (LOD = 23 nM, 3σ method). The conditional stability constants for Hg(Hcys)H(2)(2+) and Hg(Hcys)(2)H(2) at 52 °C have been determined, β(112) = 5.37 ± 0.3 × 10(46) M(-3), β(122) = 3.80 ± 0.6 × 10(68) M(-4), respectively.
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Affiliation(s)
- Magdalena Stobiecka
- Department of Chemistry, State University of New York at Potsdam, Potsdam, New York 13676, United States
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41
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He Y, Zhang X, Zhang S, Kris MKL, Man FC, Liu G. Visual detection of single-base mismatches in DNA using hairpin oligonucleotide with double-target DNA binding sequences and gold nanoparticles. Biosens Bioelectron 2012; 34:37-43. [PMID: 22386491 PMCID: PMC4110906 DOI: 10.1016/j.bios.2011.12.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/24/2011] [Accepted: 12/28/2011] [Indexed: 10/14/2022]
Abstract
We describe a hairpin oligonucleotide (HO) with double-target DNA binding sequences in the loop and 11-base in the stem for visual detection of single-base mismatches (SBM) in DNA with highly specificity. The thiol-modified HO was immobilized on gold nanoparticle (Au-NP) surface through a self-assembling process. The strategy of detecting SBM depends on the unique molecular recognition properties of HO to the perfect-matched DNA and SBM to generate different quantities of duplex DNA on the Au-NP surface, which are captured on the test zone of lateral flow test strip via the DNA hybridization reaction between the duplex DNA and preimmobilized DNA probe. Accumulation of Au-NPs produces the characteristic red bands, enabling visual detection of SBM. It was found that the ability of HO to differentiate perfect-matched DNA and SBM was increased dramatically by incorporating double-target DNA binding sequences in the loop of HO. The signal ratio between perfect-matched DNA and SBM was up to 28, which is much higher than that of conventional HO or molecular beacon. The approach was applied to detect the mutation sites, Arg142Cys and Gly529Ile, of transglutaminase 1 gene in autosomal recessive congenital ichthyosis. The results presented here show that the new HO is a potential molecular recognition probe for the future development of nucleic acid-based biosensors and bioassays. The approach can be used for point-of-care diagnosis of genetic diseases and detecting infectious agents or warning against bio-warfare agents.
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Affiliation(s)
- Yuqing He
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou 510095, PR China
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58105
| | - Xibao Zhang
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou 510095, PR China
| | - Sanquan Zhang
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou 510095, PR China
| | - Mak Ka Long Kris
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hongkong
| | - Fong Chi Man
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hongkong
| | - Guodong Liu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58105
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Asanuma H, Akahane M, Kondo N, Osawa T, Kato T, Kashida H. Quencher-free linear probe with multiple fluorophores on an acyclic scaffold. Chem Sci 2012. [DOI: 10.1039/c2sc20732j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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43
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Asanuma H, Osawa T, Kashida H, Fujii T, Liang X, Niwa K, Yoshida Y, Shimada N, Maruyama A. A polycation-chaperoned in-stem molecular beacon system. Chem Commun (Camb) 2012; 48:1760-2. [DOI: 10.1039/c2cc16812j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Zhou S, Acquaah-Harrison G, Jack KD, Bergmeier SC, Hines JV. Ligand-induced changes in T box antiterminator RNA stability. Chem Biol Drug Des 2011; 79:202-8. [PMID: 22117759 DOI: 10.1111/j.1747-0285.2011.01274.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (T(m) ) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.
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Affiliation(s)
- Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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Liu C, Zeng GM, Tang L, Zhang Y, Li YP, Liu YY, Li Z, Wu MS, Luo J. Electrochemical detection of Pseudomonas aeruginosa 16S rRNA using a biosensor based on immobilized stem–loop structured probe. Enzyme Microb Technol 2011; 49:266-71. [DOI: 10.1016/j.enzmictec.2011.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 06/02/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
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46
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Hunt EA, Deo SK. Bioluminescent stem-loop probes for highly sensitive nucleic acid detection. Chem Commun (Camb) 2011; 47:9393-5. [PMID: 21769413 DOI: 10.1039/c1cc13495g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we report the first bioluminescent stem-loop probe, which is 50 times more sensitive and able to achieve a LOD 25 times lower than fluorescent stem-loop probes. Chemical generation of a signal from Renilla luciferase reduces background noise for improved quantitative utility in nucleic acid biomarker detection.
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Affiliation(s)
- Eric A Hunt
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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47
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Sivaraman D, Biswas P, Cella LN, Yates MV, Chen W. Detecting RNA viruses in living mammalian cells by fluorescence microscopy. Trends Biotechnol 2011; 29:307-13. [PMID: 21529975 DOI: 10.1016/j.tibtech.2011.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 02/20/2011] [Accepted: 02/23/2011] [Indexed: 12/29/2022]
Abstract
Traditional methods that rely on viral isolation and culture techniques continue to be the gold standards used for detection of infectious viral particles. However, new techniques that rely on visualization of live cells can shed light on understanding virus-host interaction for early stage detection and potential drug discovery. Live-cell imaging techniques that incorporate fluorescent probes into viral components provide opportunities for understanding mRNA expression, interaction, and virus movement and localization. Other viral replication events inside a host cell can be exploited for non-invasive detection, such as single-virus tracking, which does not inhibit viral infectivity or cellular function. This review highlights some of the recent advances made using these novel approaches for visualization of viral entry and replication in live cells.
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Affiliation(s)
- Divya Sivaraman
- Department of Chemical Engineering, University of Delaware, Newark, DE 19716, USA
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48
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Kumar S, Dagar SS, Mohanty AK, Sirohi SK, Puniya M, Kuhad RC, Sangu KPS, Griffith GW, Puniya AK. Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften 2011; 98:457-72. [PMID: 21475941 DOI: 10.1007/s00114-011-0791-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/19/2011] [Accepted: 03/20/2011] [Indexed: 10/18/2022]
Abstract
Methanogens, the members of domain Archaea are potent contributors in global warming. Being confined to the strict anaerobic environment, their direct cultivation as pure culture is quite difficult. Therefore, a range of culture-independent methods have been developed to investigate their numbers, substrate uptake patterns, and identification in complex microbial communities. Unlike other approaches, fluorescence in situ hybridization (FISH) is not only used for faster quantification and accurate identification but also to reveal the physiological properties and spatiotemporal dynamics of methanogens in their natural environment. Aside from the methodological aspects and application of FISH, this review also focuses on culture-dependent and -independent techniques employed in enumerating methanogens along with associated problems. In addition, the combination of FISH with micro-autoradiography that could also be an important tool in investigating the activities of methanogens is also discussed.
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Affiliation(s)
- Sanjay Kumar
- Dairy Microbiology Division, National Dairy Research Institute, Karnal 132001, India
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49
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Abstract
In this brief review, gold nanoparticles conjugated with functional polymers are described from the viewpoint of application to sensing materials. The optical properties of gold nanoparticles, the synthesis of polymer-functionalized gold nanoparticles, and their analytical applications are discussed. Polymer-functionalized gold nanoparticles are categorized into two classes: biopolymer-conjugated gold nanoparticles and artificial-polymer conjugated gold nanoparticles. Fluorometric and colorimetric sensing using gold nanoparticles are focused; fluorometric detection enables us to exploit sensitive assays for practical use. Furthermore, chemical amplification using gold nanoparticles is also discussed for the sensitive probing.
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Affiliation(s)
- Nobuo Uehara
- Department of Applied Chemistry, Graduate School of Engineering, Utsunomiya University, Tochigi, Japan.
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50
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Li Y, Sun SK, Yang JL, Jiang Y. Label-free DNA hybridization detection and single base-mismatch discrimination using CE-ICP-MS assay. Analyst 2011; 136:5038-45. [DOI: 10.1039/c1an15592j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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