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Hussain A, Wang M, Yu D, Zhang J, Naseer QA, Ullah A, Milon Essola J, Zhang X. Medical and molecular biophysical techniques as substantial tools in the era of mRNA-based vaccine technology. Biomater Sci 2024. [PMID: 39016519 DOI: 10.1039/d4bm00561a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The COVID-19 pandemic prompted the advancement of vaccine technology using mRNA delivery into the host cells. Consequently, mRNA-based vaccines have emerged as a practical approach against SARS-CoV-2 owing to their inherent properties, such as cost-effectiveness, rapid manufacturing, and preservation. These features are vital, especially in resource-constrained regions. Nevertheless, the design of mRNA-based vaccines is intricately intertwined with the refinement of biophysical technologies, thereby establishing their high potential. The preparation of mRNA-based vaccines involves a sequence of phases combining medical and molecular biophysical technologies. Furthermore, their efficiency depends on the capability to optimize their positive attributes, thus paving the way for their subsequent preclinical and clinical evaluations. Using biophysical techniques, the characterization of nucleic acids extends from their initial formulation to their cellular internalization abilities and encapsulation in biomolecule complexes, such as lipid nanoparticles (LNPs), for designing mRNA-based LNPs. Furthermore, nanoparticles are subjected to a series of careful screening steps to assess their physical and chemical characteristics before achieving an optimum formulation suitable for preclinical and clinical studies. This review provides a comprehensive understanding of the fundamental role of biophysical techniques in the complex development of mRNA-based vaccines and their role in the recent success during the COVID-19 pandemic.
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Affiliation(s)
- Abid Hussain
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Maoye Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Dan Yu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Jiahui Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Qais Ahmad Naseer
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Aftab Ullah
- School of Medicine, Huaqiao University, No. 269 Chenghua North Rd., Quanzhou, Fujian 362021, China.
| | - Julien Milon Essola
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Centre for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, P.R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
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2
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Yang J, Dong C, Zhang A, Ren J. Quantification of mRNA in Single Cells Based on Dimerization-Induced Photoluminescence Nonblinking of Quantum Dots. Anal Chem 2022; 94:12407-12415. [PMID: 36050288 DOI: 10.1021/acs.analchem.2c02209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoluminescence (PL) intermittency (or "blinking") is a unique characteristic of single quantum dot (QD) emission. Here, we report a novel single-molecule detection strategy for the intracellular mRNA of interest using the mRNA-induced nonblinking QD dimers as probes. The working principle of the method is that the DNA hybrid of the target DNA (or mRNA) with a biotin-modified ssDNA probe can induce two blinking streptavidin-modified QDs (SAV-QDs) conjugated. The formed QD dimer as a bright spot showed a nonblinking emission property, observed with total inner reflection fluorescence microscopy (TIRFM). In theory, one nonblinking spot indicated a target DNA (or mRNA). The experimental results from single-spot fluorescence trajectory analysis and single-particle brightness analysis based on TIRFM and fluorescence correlation spectroscopy (FCS) techniques verified this dimerization process of QDs or its induced nonblinking emission. Employing a target DNA with the same base sequences to Survivin mRNA as a model, the detection strategy was used to detect the target DNA concentration based on the linear relationship between the percentage of the nonblinking spots and the target DNA concentration. This single-molecule detection strategy was also successfully used for determining Survivin mRNA in a single HeLa cell. The method can simplify the hybridization steps, eliminate self-quenching and photobleaching of fluorophores, and reduce the influence of unspecific binding on the detection.
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Affiliation(s)
- Jie Yang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Aidi Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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3
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Zhao Y, Tong RJ, Xia F, Peng Y. Current status of optical fiber biosensor based on surface plasmon resonance. Biosens Bioelectron 2019; 142:111505. [DOI: 10.1016/j.bios.2019.111505] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023]
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4
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Ostromohov N, Huber D, Bercovici M, Kaigala GV. Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics. Anal Chem 2018; 90:11470-11477. [DOI: 10.1021/acs.analchem.8b02630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nadya Ostromohov
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Deborah Huber
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Govind V. Kaigala
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
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5
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A Label-free and Functional Fluorescent Oligonucleotide Probe Based on a G-Quadruplex Molecular Beacon for the Detection of Kanamycin. Chem Res Chin Univ 2018. [DOI: 10.1007/s40242-018-7366-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Zhang Y, Ai J, Gu Q, Gao Q, Qi H, Zhang C. Determination of mutated genes in the presence of wild-type DNA by using molecular beacons as probe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:286-290. [PMID: 27960142 DOI: 10.1016/j.saa.2016.11.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 11/24/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA. The ligand formed hydrogen bonds with unpaired bases and stabilized the unpaired base-containing dsDNA if target DNA is mutated one. As a result, more MBs were opened by the mutant genes in the presence of the ligand and a further increase in the fluorescence intensity was obtained. By contrast, fluorescence intensity did not change if target DNA is wild-type one. Consequent increase in the fluorescence intensity of the MB was regarded as a signal derived from mutant genes. The proposed method was applied in synthetic template systems to determine point mutation in DNA obtained from PCR analysis. The method also allows rapid and simple discrimination of a signal if it is originated in the presence of mutant gene or alternatively by a lower concentration of wild gene.
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Affiliation(s)
- Yonghua Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; School of Chemistry and Chemical Engineer, Luoyang Normal University, Luoyang 471022, China
| | - Junjie Ai
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Qiaorong Gu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Qiang Gao
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Honglan Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Chengxiao Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
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7
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Shigeto H, Nakatsuka K, Ikeda T, Hirota R, Kuroda A, Funabashi H. Continuous Monitoring of Specific mRNA Expression Responses with a Fluorescence Resonance Energy Transfer-Based DNA Nano-tweezer Technique That Does Not Require Gene Recombination. Anal Chem 2016; 88:7894-8. [DOI: 10.1021/acs.analchem.6b02710] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hajime Shigeto
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Keisuke Nakatsuka
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
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8
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Almlie CK, Hsiao A, Burrows SM. Dye-Specific Wavelength Offsets to Resolve Spectrally Overlapping and Co-Localized Two-Photon Induced Fluorescence. Anal Chem 2016; 88:1462-7. [DOI: 10.1021/acs.analchem.5b04476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- C. Kyle Almlie
- Chemistry Department, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Austen Hsiao
- Chemistry Department, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Sean M. Burrows
- Chemistry Department, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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9
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Cao Q, Teng Y, Yang X, Wang J, Wang E. A label-free fluorescent molecular beacon based on DNA-Ag nanoclusters for the construction of versatile Biosensors. Biosens Bioelectron 2015; 74:318-21. [DOI: 10.1016/j.bios.2015.06.044] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 01/21/2023]
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10
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Funabashi H, Shigeto H, Nakatsuka K, Kuroda A. A FRET-based DNA nano-tweezer technique for the imaging analysis of specific mRNA. Analyst 2015; 140:999-1003. [PMID: 25529369 DOI: 10.1039/c4an02064b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A DNA nano-tweezer (DNA-NT) structure-based target mRNA detection probe, which uses fluorescence resonance energy transfer (FRET) as a detection signal and works as a single molecule, has been developed. This FRET-paired fluorescent dye-modified DNA-NT, self-assembled from three single-stranded DNAs, alters its structure from open to closed states and produces a FRET signal in response to in vitro transcripts of Hes-1 mRNA. Our results showed that the FRET-based DNA-NT detected both GLUT1 mRNA as a pre-fixed target mRNA model and Hes-1 mRNA as a model expressed inside a living cell. These results confirm the feasibility of using the FRET-based DNA-NT for imaging analysis of target mRNA.
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Affiliation(s)
- Hisakage Funabashi
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan.
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11
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Hairpin DNA probe-based fluorescence assay for detecting palindrome cleavage activity of HIV-1 integrase. Anal Biochem 2014; 460:36-8. [DOI: 10.1016/j.ab.2014.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/05/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
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12
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Real-time imaging of the epithelial-mesenchymal transition using microRNA-200a sequence-based molecular beacon-conjugated magnetic nanoparticles. PLoS One 2014; 9:e102164. [PMID: 25048580 PMCID: PMC4105468 DOI: 10.1371/journal.pone.0102164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/16/2014] [Indexed: 12/30/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) plays important roles in tumor progression to metastasis. Thus, the development of an imaging probe that can monitor transient periods of the EMT process in live cells is required for a better understanding of metastatic process. Inspired by the fact that the mRNA expression levels of zinc finger E-box-binding homeobox 1 (ZEB1) increase when cells adopt mesenchyme characteristics and that microRNA-200a (miR-200a) can bind to ZEB1 mRNA, we conjugated molecular beacon (MB) mimicking mature miR-200a to magnetic nanoparticles (miR-200a-MB-MNPs) and devised an imaging method to observe transitional changes in the cells during EMT. Transforming growth factor-β1 treated epithelial cells and breast cancer cell lines representing both epithelial and mesenchymal phenotypes were used for the validation of miR-200a-MB-MNPs as an EMT imaging probe. The real-time imaging of live cells acquired with the induction of EMT revealed an increase in fluorescence signals by miR-200a-MB-MNPs, cell morphology alterations, and the loss of cell-cell adhesion. Our results suggest that miR-200a-MB-MNPs can be used as an imaging probe for the real-time monitoring of the EMT process in live cells.
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13
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Heuer-Jungemann A, Harimech PK, Brown T, Kanaras AG. Gold nanoparticles and fluorescently-labelled DNA as a platform for biological sensing. NANOSCALE 2013; 5:9503-9510. [PMID: 23982570 DOI: 10.1039/c3nr03707j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the past decade gold nanoparticle-nucleic acid conjugates became progressively important for biomedical applications. Fluorophores attached to nucleic acid-gold nanoparticle conjugates have opened up a new era of biological sensing. The most promising advancement in this field was the invention of the so-called 'nano-flare' systems. These systems are capable of detecting specific endocellular targets such as mRNAs, microRNAs or small molecules in real time. In this minireview, we discuss the current progress in the field of DNA-nanoparticles as sensors, their properties, stability, cellular uptake and cytotoxicity.
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Affiliation(s)
- Amelie Heuer-Jungemann
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK.
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14
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Riahi R, Dean Z, Wu TH, Teitell MA, Chiou PY, Zhang DD, Wong PK. Detection of mRNA in living cells by double-stranded locked nucleic acid probes. Analyst 2013; 138:4777-85. [PMID: 23772441 PMCID: PMC3736730 DOI: 10.1039/c3an00722g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Double-stranded probes are homogeneous biosensors for rapid detection of specific nucleotide sequences. These double-stranded probes have been applied in various molecular sensing applications, such as real-time polymerase chain reaction and detection of bacterial 16S rRNA. In this study, we present the design and optimization of double-stranded probes for single-cell gene expression analysis in living cells. With alternating DNA/LNA monomers for optimizing the stability and specificity, we show that the probe is stable in living cells for over 72 hours post-transfection and is capable of detecting changes in gene expression induced by external stimuli. The probes can be delivered to a large number of cells simultaneously by cationic liposomal transfection or to individual cells selectively by photothermal delivery. We also demonstrate that the probe quantifies intracellular mRNA in living cells through the use of an equilibrium analysis. With its effectiveness and performance, the double-stranded probe represents a broadly applicable approach for large-scale single-cell gene expression analysis toward numerous biomedical applications, such as systems biology, cancer, and drug screening.
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Affiliation(s)
- Reza Riahi
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721-0119, USA
| | - Zachary Dean
- Biomedical Engineering Interdisciplinary Program, The University of Arizona, Tucson, AZ 85721-0119, USA
| | - Ting-Hsiang Wu
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095-1597, USA
| | - Michael A. Teitell
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA, 90095
| | - Pei-Yu Chiou
- Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA 90095-1597, USA
| | - Donna D. Zhang
- Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ 85721-0119, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721-0119, USA
| | - Pak Kin Wong
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, AZ 85721-0119, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721-0119, USA
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15
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Wu C, Chen T, Han D, You M, Peng L, Cansiz S, Zhu G, Li C, Xiong X, Jimenez E, Yang CJ, Tan W. Engineering of switchable aptamer micelle flares for molecular imaging in living cells. ACS NANO 2013; 7:5724-31. [PMID: 23746078 PMCID: PMC3789376 DOI: 10.1021/nn402517v] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Simultaneous monitoring of the expression, distribution, and dynamics of biological molecules in living cells is one of the most challenging tasks in the analytical sciences. The key to effective and successful intracellular imaging is the development of delivery platforms with high efficiency and ultrasensitive molecular probes for specific targets of interest. To achieve these goals, many nanomaterials are widely used as carriers to introduce nucleic acid probes into living cells for real-time imaging of biomolecules. However, limitations on their use include issues of cytotoxicity and delivery efficiency. Herein, we propose a switchable aptamer micelle flare (SAMF), formed by self-assembly of an aptamer switch probe-diacyllipid chimera, to monitor ATP molecules inside living cells. Similarity of hydrophobic composition between diacyllipids in the micelle flares and phospholipid bilayers in the dynamic membranes of living cells allows SAMFs to be uptaken by living cells more efficiently than aptamer switch probes without external auxiliary. Switchable aptamers were found to bind target ATP molecules with high selectivity and specificity, resulting in restoration of the fluorescence signal from "OFF" to "ON" state, thus indicating the presence of the analyte. These switchable aptamer micelle flares, which exhibit cell permeability and nanoscale controllability, show exceptional promise for molecular imaging in bioanalysis, disease diagnosis, and drug delivery.
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Affiliation(s)
- Cuichen Wu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Tao Chen
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Da Han
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, People's Republic of China
| | - Mingxu You
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Lu Peng
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Sena Cansiz
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Guizhi Zhu
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, People's Republic of China
| | - Chunmei Li
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Xiangling Xiong
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, People's Republic of China
| | - Elizabeth Jimenez
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Chaoyong James Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Department of Chemical Biology, Key Laboratory of Analytical Science, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Weihong Tan
- Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, People's Republic of China
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16
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Oligonucleotide optical switches for intracellular sensing. Anal Bioanal Chem 2013; 405:6181-96. [PMID: 23793395 DOI: 10.1007/s00216-013-7086-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 12/16/2022]
Abstract
Fluorescence imaging coupled with nanotechnology is making possible the development of powerful tools in the biological field for applications such as cellular imaging and intracellular messenger RNA monitoring and detection. The delivery of fluorescent probes into cells and tissues is currently receiving growing interest because such molecules, often coupled to nanodimensional materials, can conveniently allow the preparation of small tools to spy on cellular mechanisms with high specificity and sensitivity. The purpose of this review is to provide an exhaustive overview of current research in oligonucleotide optical switches for intracellular sensing with a focus on the engineering methods adopted for these oligonucleotides and the more recent and fascinating techniques for their internalization into living cells. Oligonucleotide optical switches can be defined as specifically designed short nucleic acid molecules capable of turning on or modifying their light emission on molecular interaction with well-defined molecular targets. Molecular beacons, aptamer beacons, hybrid molecular probes, and simpler linear oligonucleotide switches are the most promising optical nanosensors proposed in recent years. The intracellular targets which have been considered for sensing are a plethora of messenger-RNA-expressing cellular proteins and enzymes, or, directly, proteins or small molecules in the case of sensing through aptamer-based switches. Engineering methods, including modification of the oligonucleotide itself with locked nucleic acids, peptide nucleic acids, or L-DNA nucleotides, have been proposed to enhance the stability of nucleases and to prevent false-negative and high background optical signals. Conventional delivery techniques are treated here together with more innovative methods based on the coupling of the switches with nano-objects.
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17
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Li Z, Sun S, Yang Z, Zhang S, Zhang H, Hu M, Cao J, Wang J, Liu F, Song F, Fan J, Peng X. The use of a near-infrared RNA fluorescent probe with a large Stokes shift for imaging living cells assisted by the macrocyclic molecule CB7. Biomaterials 2013; 34:6473-81. [PMID: 23755836 DOI: 10.1016/j.biomaterials.2013.05.020] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 05/13/2013] [Indexed: 11/29/2022]
Abstract
A near-infrared fluorescent dye Hsd was designed and synthesized, which absorbed as hemicyane and emitted as Cy7 and therefore produced a Stokes shift as large as 224 nm. Quantum chemistry calculation demonstrated that the large Stokes shift was produced by the combination of intramolecular charge transfer (ICT) and internal conversion. Significantly, Hsd showed selectively response to RNA in aqueous solution and fixed cells. Moreover, Hsd could be uptaken into the cells under the assistance of cucurbit[7]uril (CB7) and selectively stain RNA in living cells. The introducing of CB7 provides a platform to amplify the application of some cell-impermeant fluorescent stains through the supramolecular chemistry methods.
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Affiliation(s)
- Zhiyong Li
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Hi-tech Zone, Dalian 116024, PR China
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18
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El-Yazbi AF, Loppnow GR. Chimeric RNA–DNA Molecular Beacons for Quantification of Nucleic Acids, Single Nucleotide Polymophisms, and Nucleic Acid Damage. Anal Chem 2013; 85:4321-7. [DOI: 10.1021/ac301669y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
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19
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Han SX, Jia X, Ma JL, Zhu Q. Molecular beacons: a novel optical diagnostic tool. Arch Immunol Ther Exp (Warsz) 2013; 61:139-48. [PMID: 23292078 PMCID: PMC7079750 DOI: 10.1007/s00005-012-0209-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/20/2012] [Indexed: 12/31/2022]
Abstract
As a result of the efforts of the Human Genome Project and the rise in demand for molecular diagnostic assays, the development and optimization of novel hybridization probes have focused on speed, reliability, and accuracy in the identification of nucleic acids. Molecular beacons (MBs) are single-stranded, fluorophore-labeled nucleic acid probes that are capable of generating a fluorescent signal in the presence of target, but are dark in the absence of target. Because of the high specificity and sensitivity characteristics, MBs have been used in variety of fields. In this review, MBs are introduced and discussed as diagnostic tools in four sections: several technologies of MBs will be illustrated primarily; the limitation of MBs next; the third part is new fashions of MBs; and the last one is to present the application of MBs in disease diagnosis.
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Affiliation(s)
- Su-Xia Han
- Department of Oncology, The First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi 710061, People's Republic of China
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20
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Yoshimura H, Inaguma A, Yamada T, Ozawa T. Fluorescent probes for imaging endogenous β-actin mRNA in living cells using fluorescent protein-tagged pumilio. ACS Chem Biol 2012; 7:999-1005. [PMID: 22387832 DOI: 10.1021/cb200474a] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subcellular localization and dynamics of mRNAs control various physiological functions in living cells. A novel technique for visualizing endogenous mRNAs in living cells is necessary for investigation of the spatiotemporal movement of mRNAs. A pumilio homology domain of human pumilio 1 (PUM-HD) is a useful RNA binding protein as a tool for mRNA recognition because the domain can be modified to bind a specific 8-base sequence of target mRNA. In this study, we designed PUM-HD to match the sequence of β-actin mRNA and developed an mRNA probe consisting of two PUM-HD mutants flanking full-length enhanced green fluorescent protein (EGFP). Fluorescence microscopy with the probe in living cells revealed that the probe was labeled precisely with the β-actin mRNA in cytosol. Fluorescent spots from the probe were colocalized with microtubules and moved directionally in living cells. The PUM-HD mutants conjugated with full-length EGFP can enable visualization of β-actin mRNA localization and dynamics in living cells.
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Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School
of Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asumi Inaguma
- The Department of Structural
Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193,
Japan
| | - Toshimichi Yamada
- Department of Chemistry, School
of Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School
of Science, The University of Tokyo, 7-3-1
Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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21
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Wu MS, Qian GS, Xu JJ, Chen HY. Sensitive electrochemiluminescence detection of c-Myc mRNA in breast cancer cells on a wireless bipolar electrode. Anal Chem 2012; 84:5407-14. [PMID: 22612343 DOI: 10.1021/ac3009912] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report an ultrasensitive wireless electrochemiluminescence (ECL) protocol for the detection of a nucleic acid target in tumor cells on an indium tin oxide bipolar electrode (BPE) in a poly(dimethylsiloxane) microchannel. The approach is based on the modification of the anodic pole of the BPE with antisense DNA as the recognition element, Ru(bpy)(3)(2+)-conjugated silica nanoparticles (RuSi@Ru(bpy)(3)(2+)) as the signal amplification tag, and reporter DNA as a reference standard. It employs the hybridization-induced changes of RuSi@Ru(bpy)(3)(2+) ECL efficiency for the specific detection of reporter DNA released from tumor cells. Prior to ECL detection, tumor cells are transfected with CdSe@ZnS quantum dot (QD)-antisense DNA/reporter DNA conjugates. Upon the selective binding of antisense DNA probes to intracellular target mRNA, reporter DNA will be released from the QDs, which indicates the amount of the target mRNA. The proof of concept is demonstrated using a proto-oncogene c-Myc mRNA in MCF-7 cells (breast cancer cell line) as a model target. The wireless ECL biosensor exhibited excellent ECL signals which showed a good linear range over 2 × 10(-16) to 1 × 10(-11) M toward the reporter DNA detection and could accurately quantify c-Myc mRNA copy numbers in living cells. C-Myc mRNA in each MCF-7 cell and LO2 cell was estimated to be 2203 and 13 copies, respectively. This wireless ECL strategy provides great promise in a miniaturized device and may facilitate the achievement of point of care testing.
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Affiliation(s)
- Mei-Sheng Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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22
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Kam Y, Rubinstein A, Nissan A, Halle D, Yavin E. Detection of endogenous K-ras mRNA in living cells at a single base resolution by a PNA molecular beacon. Mol Pharm 2012; 9:685-93. [PMID: 22289057 DOI: 10.1021/mp200505k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detection of mRNA alterations is a promising approach for identifying biomarkers as means of differentiating benign from malignant lesions. By choosing the KRAS oncogene as a target gene, two types of molecular beacons (MBs) based on either phosphothioated DNA (PS-DNA-MB) or peptide nucleic acid (TO-PNA-MB, where TO = thiazole orange) were synthesized and compared in vitro and in vivo. Their specificity was examined in wild-type KRAS (HT29) or codon 12 point mutation (Panc-1, SW480) cells. Incubation of both beacons with total RNA extracted from the Panc-1 cell line (fully complementary sequence) showed a fluorescent signal for both beacons. Major differences were observed, however, for single mismatch mRNA transcripts in cell lines HT29 and SW480. PS-DNA-MB weakly discriminated such single mismatches in comparison to TO-PNA-MB, which was profoundly more sensitive. Cell transfection of TO-PNA-MB with the aid of PEI resulted in fluorescence in cells expressing the fully complementary RNA transcript (Panc-1) but undetectable fluorescence in cells expressing the K-ras mRNA that has a single mismatch to the designed TO-PNA-MB (HT29). A weaker fluorescent signal was also detected in SW480 cells; however, these cells express approximately one-fifth of the target mRNA of the designed TO-PNA-MB. In contrast, PS-DNA-MB showed no fluorescence in all cell lines tested post PEI transfection. Based on the fast hybridization kinetics and on the single mismatch discrimination found for TO-PNA-MB we believe that such molecular beacons are promising for in vivo real-time imaging of endogenous mRNA with single nucleotide polymorphism (SNP) resolution.
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Affiliation(s)
- Yossi Kam
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, PO Box 12065, Jerusalem 91120, Israel
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23
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Alexander JC, Pandit A, Bao G, Connolly D, Rochev Y. Monitoring mRNA in living cells in a 3D in vitro model using TAT-peptide linked molecular beacons. LAB ON A CHIP 2011; 11:3908-3914. [PMID: 21952477 DOI: 10.1039/c1lc20447e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
There is a growing need for the development of in vitro 3D cell culture models for assessing newer therapeutics for clinical applications and mechanisms of human pathology. Molecular beacons have been successfully delivered in two-dimensional (2D) systems to monitor, detect, and localize specific mRNA expression in living cells at the single cell level. However, to date the use of molecular beacons in three-dimensional (3D) systems has not been reported. To translate this technology into specific clinical targeted applications, it is critical to develop and demonstrate efficacy in a 3D system. For the first time the use of TAT-peptide conjugated molecular beacons to monitor mRNA in a 3D in vitro system has been reported.
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Affiliation(s)
- Jennifer Claire Alexander
- Network of Excellence for Functional Biomaterials (NFB), National University of Ireland, Galway, Ireland
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24
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Monroy-Contreras R, Vaca L. Molecular beacons: powerful tools for imaging RNA in living cells. J Nucleic Acids 2011; 2011:741723. [PMID: 21876785 PMCID: PMC3163130 DOI: 10.4061/2011/741723] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 06/14/2011] [Accepted: 06/22/2011] [Indexed: 12/25/2022] Open
Abstract
Recent advances in RNA functional studies highlights the pivotal role of these molecules in cell physiology. Diverse methods have been implemented to measure the expression levels of various RNA species, using either purified RNA or fixed cells. Despite the fact that fixed cells offer the possibility to observe the spatial distribution of RNA, assays with capability to real-time monitoring RNA transport into living cells are needed to further understand the role of RNA dynamics in cellular functions. Molecular beacons (MBs) are stem-loop hairpin-structured oligonucleotides equipped with a fluorescence quencher at one end and a fluorescent dye (also called reporter or fluorophore) at the opposite end. This structure permits that MB in the absence of their target complementary sequence do not fluoresce. Upon binding to targets, MBs emit fluorescence, due to the spatial separation of the quencher and the reporter. Molecular beacons are promising probes for the development of RNA imaging techniques; nevertheless much work remains to be done in order to obtain a robust technology for imaging various RNA molecules together in real time and in living cells. The present work concentrates on the different requirements needed to use successfully MB for cellular studies, summarizing recent advances in this area.
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Affiliation(s)
- Ricardo Monroy-Contreras
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico, DF, Mexico
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25
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Le Goff A, Gorgy K, Holzinger M, Haddad R, Zimmerman M, Cosnier S. Tris(bispyrene-bipyridine)iron(II): A Supramolecular Bridge for the Biofunctionalization of Carbon Nanotubes via π-Stacking and Pyrene/β-Cyclodextrin Host-Guest Interactions. Chemistry 2011; 17:10216-21. [DOI: 10.1002/chem.201101283] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Indexed: 11/08/2022]
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26
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Yamada T, Yoshimura H, Inaguma A, Ozawa T. Visualization of Nonengineered Single mRNAs in Living Cells Using Genetically Encoded Fluorescent Probes. Anal Chem 2011; 83:5708-14. [DOI: 10.1021/ac2009405] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Toshimichi Yamada
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asumi Inaguma
- The Department of Structural Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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27
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Andou T, Endoh T, Mie M, Kobatake E. Direct detection of RNAs in living cells using peptide-inserted Renilla luciferase. Analyst 2011; 136:2446-9. [PMID: 21541389 DOI: 10.1039/c1an15130d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this study, non-engineered RNAs were detected in living cells using bioluminescence. Two types of probe were utilized: a peptide inserted RLuc (PI-RLuc) probe and a split-RNA probe. Incorporation of the PI-RLuc and split-RNA probes enabled the direct detection of RNA introduced into living cells.
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Affiliation(s)
- Takashi Andou
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
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28
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Murata A, Sato SI, Kawazoe Y, Uesugi M. Small-molecule fluorescent probes for specific RNA targets. Chem Commun (Camb) 2011; 47:4712-4. [PMID: 21412566 DOI: 10.1039/c1cc10393h] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A method was developed that uses small molecules as fluorescent probes to detect specific mRNAs. In this approach, the fluorescence of fluorophore-quencher conjugates is restored by the binding of an mRNA aptamer tag to the quencher segment of the molecules. The method allows real-time detection of mRNA transcripts in vitro.
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Affiliation(s)
- Asako Murata
- Institute for Integrated Cell-Material Sciences, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
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29
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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30
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Okabe K, Harada Y, Zhang J, Tadakuma H, Tani T, Funatsu T. Real time monitoring of endogenous cytoplasmic mRNA using linear antisense 2'-O-methyl RNA probes in living cells. Nucleic Acids Res 2011; 39:e20. [PMID: 21106497 PMCID: PMC3045578 DOI: 10.1093/nar/gkq1196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 10/27/2010] [Accepted: 11/05/2010] [Indexed: 12/21/2022] Open
Abstract
Visualization and monitoring of endogenous mRNA in the cytoplasm of living cells promises a significant comprehension of refined post-transcriptional regulation. Fluorescently labeled linear antisense oligonucleotides can bind to natural mRNA in a sequence-specific way and, therefore, provide a powerful tool in probing endogenous mRNA. Here, we investigated the feasibility of using linear antisense probes to monitor the variable and dynamic expression of endogenous cytoplasmic mRNAs. Two linear antisense 2'-O-methyl RNA probes, which have different interactive fluorophores at the 5'-end of one probe and at the 3'-end of the other, were used to allow fluorescence resonance energy transfer (FRET) upon hybridization to the target mRNA. By characterizing the formation of the probe-mRNA hybrids in living cells, we found that the probe composition and concentration are crucial parameters in the visualization of endogenous mRNA with high specificity. Furthermore, rapid hybridization (within 1 min) of the linear antisense probe enabled us to visualize dynamic processes of endogenous c-fos mRNA, such as fast elevation of levels after gene induction and the localization of c-fos mRNA in stress granules in response to cellular stress. Thus, our approach provides a basis for real time monitoring of endogenous cytoplasmic mRNA in living cells.
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Affiliation(s)
- Kohki Okabe
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoshie Harada
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Junwei Zhang
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hisashi Tadakuma
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tokio Tani
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
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31
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Oh YH, Kim Y, Kim YP, Seo SW, Mitsudomi T, Ahn MJ, Park K, Kim HS. Rapid detection of the epidermal growth factor receptor mutation in non-small-cell lung cancer for analysis of acquired resistance using molecular beacons. J Mol Diagn 2011; 12:644-52. [PMID: 20805561 DOI: 10.2353/jmoldx.2010.090208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A secondary mutation (T790M) in epidermal growth factor receptor (EGFR) is a hallmark of acquired resistance to EGFR inhibitors used to treat non-small-cell lung cancer (NSCLC). Therefore, identifying the T790M mutation is crucial to guide treatment decisions. Given that DNA sequencing methods are time-consuming and insensitive, we developed and investigated the feasibility of using molecular beacons for the detection of the T790M mutation in EGFR. A molecular beacon complementary to the region of the secondary EGFR mutation (T790M) was designed and used in NSCLC samples bearing drug-sensitive and -resistant EGFR mutations. For a rapid and simple assay, we attempted to use the molecular beacon with real-time PCR and in situ fluorescence imaging. The ability of the designed molecular beacon to specifically detect the T790M mutation of EGFR was tested for samples from two patients with drug resistance and compared with conventional DNA sequencing methods. The molecular beacon successfully detected the T790M mutation in patient samples with drug resistance. The sensitivity of the molecular beacon, which detected as little as 2% of genomic DNA from the drug-resistant cells (H1975), was much higher than direct sequencing. Furthermore, in situ fluorescence imaging with the molecular beacon gave rise to a distinguishable signal for the T790M mutation in drug-resistant cells. The molecular beacon-based approach enabled rapid and sensitive detection of the EGFR mutation (T790M) in NSCLC with in situ fluorescence imaging, which can be directed to determine various treatment options in patients with cancer.
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Affiliation(s)
- Young-Hee Oh
- Department of Biological Sciences, KAIST (Korea Advanced Institute of Science and Technology), Daejon, Korea
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32
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Campolongo MJ, Kahn JS, Cheng W, Yang D, Gupton-Campolongo T, Luo D. Adaptive DNA-based materials for switching, sensing, and logic devices. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm03854g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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33
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Kubota T, Ikeda S, Yanagisawa H, Yuki M, Okamoto A. Sets of RNA repeated tags and hybridization-sensitive fluorescent probes for distinct images of RNA in a living cell. PLoS One 2010; 5:e13003. [PMID: 20885944 PMCID: PMC2946342 DOI: 10.1371/journal.pone.0013003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 08/26/2010] [Indexed: 01/02/2023] Open
Abstract
Background Imaging the behavior of RNA in a living cell is a powerful means for understanding RNA functions and acquiring spatiotemporal information in a single cell. For more distinct RNA imaging in a living cell, a more effective chemical method to fluorescently label RNA is now required. In addition, development of the technology labeling with different colors for different RNA would make it easier to analyze plural RNA strands expressing in a cell. Methodology/Principal Findings Tag technology for RNA imaging in a living cell has been developed based on the unique chemical functions of exciton-controlled hybridization-sensitive oligonucleotide (ECHO) probes. Repetitions of selected 18-nucleotide RNA tags were incorporated into the mRNA 3′-UTR. Pairs with complementary ECHO probes exhibited hybridization-sensitive fluorescence emission for the mRNA expressed in a living cell. The mRNA in a nucleus was detected clearly as fluorescent puncta, and the images of the expression of two mRNAs were obtained independently and simultaneously with two orthogonal tag–probe pairs. Conclusions/Significance A compact and repeated label has been developed for RNA imaging in a living cell, based on the photochemistry of ECHO probes. The pairs of an 18-nt RNA tag and the complementary ECHO probes are highly thermostable, sequence-specifically emissive, and orthogonal to each other. The nucleotide length necessary for one tag sequence is much shorter compared with conventional tag technologies, resulting in easy preparation of the tag sequences with a larger number of repeats for more distinct RNA imaging.
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Affiliation(s)
| | - Shuji Ikeda
- RIKEN Advanced Science Institute, Saitama, Japan
| | | | - Mizue Yuki
- RIKEN Advanced Science Institute, Saitama, Japan
| | - Akimitsu Okamoto
- RIKEN Advanced Science Institute, Saitama, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Saitama, Japan
- * E-mail:
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34
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Tsuji A, Yoshikawa K. ON-OFF switching of transcriptional activity of large DNA through a conformational transition in cooperation with phospholipid membrane. J Am Chem Soc 2010; 132:12464-71. [PMID: 20704293 PMCID: PMC2931404 DOI: 10.1021/ja105154k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Indexed: 01/13/2023]
Abstract
We report that structural transitions of DNA cause the ON-OFF switching of transcriptional activity in cooperation with phospholipid membrane in a reconstituted artificial cell. It has been shown that long DNA of more than 20-30 kilo base-pairs exhibits a discrete conformational transition between a coiled state and highly folded states in aqueous solution, depending on the presence of various condensing agents such as polyamine. Recently, we reported a conformational transition of long DNA through interplay with phospholipid membrane, from a folded state in aqueous phase to an extended coil state on a membrane surface, in a cell-sized water-in-oil microdroplet covered by phosphatidylethanolamine monolayer (Kato, A.; Shindo, E.; Sakaue, T.; Tsuji, A.; Yoshikawa, K. Biophys. J. 2009, 97, 1678-1686). In this study, to elucidate the effects of these conformational changes on the biologically important function of DNA, transcription, we investigated the transcriptional activity of DNA in a microdroplet. Transcriptional activity was evaluated at individual DNA molecule level by a method we developed, in which mRNA molecules are labeled with fluorescent oligonucleotide probes. Transcription proceeded on almost all of the DNA molecules with a coiled conformation in the aqueous phase. In the presence of a tetravalent amine, spermine, the DNA had a folded conformation, and transcription was completely inhibited. When the Mg(2+) concentration was increased, DNA was adsorbed onto the inner surface of the membrane and exhibited an extended conformation. The transcription experiments showed that this conformational transition recovered transcriptional activity; transcription occurred on DNA molecules that were on the membrane.
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Li F, Huang Y, Yang Q, Zhong Z, Li D, Wang L, Song S, Fan C. A graphene-enhanced molecular beacon for homogeneous DNA detection. NANOSCALE 2010; 2:1021-6. [PMID: 20648302 DOI: 10.1039/b9nr00401g] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work, we report the design of a novel graphene-based molecular beacon (MB) that could sensitively and selectively detect specific DNA sequences. The ability of water-soluble graphene oxide (GO) to differentiated hairpin and dsDNA offered a new approach to detect DNA. We found that the background fluorescence of MB was significantly suppressed in the presence of GO, which increased the signal-to-background ratio, hence the sensitivity. Moreover, the single-mismatch differentiation ability of hairpin DNA was maintained, leading to high selectivity of this new method.
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Affiliation(s)
- Fan Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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Shi H, He X, Yang X, Wang K, Wang Q, Guo Q, Huo X. Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles. Sci China Chem 2010; 53:704-719. [PMID: 32214997 PMCID: PMC7088759 DOI: 10.1007/s11426-010-0110-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 02/07/2010] [Indexed: 01/10/2023]
Abstract
With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for real-time, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.
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Affiliation(s)
- Hui Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - XiaoXiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - XiaoHai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - KeMin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - QiuPing Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
| | - XiQin Huo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082 China
- College of Chemistry and Chemical Engineering, Biomedical Engineering Center, Hunan University, Changsha, 410082 China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Changsha, 410082 China
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Single-cell analysis and isolation for microbiology and biotechnology: methods and applications. Appl Microbiol Biotechnol 2010; 86:1281-92. [DOI: 10.1007/s00253-010-2524-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 01/14/2023]
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38
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Chen AK, Behlke MA, Tsourkas A. Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons. Nucleic Acids Res 2010; 37:e149. [PMID: 19820111 PMCID: PMC2794186 DOI: 10.1093/nar/gkp837] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Molecular beacons (MBs) have shown great potential for the imaging of RNAs within single living cells; however, the ability to perform accurate measurements of RNA expression can be hampered by false-positives resulting from nonspecific interactions and/or nuclease degradation. These false-positives could potentially be avoided by introducing chemically modified oligonucleotides into the MB design. In this study, fluorescence microscopy experiments were performed to elucidate the subcellular trafficking, false-positive signal generation, and functionality of 2′-O-methyl (2Me) and 2′-O-methyl-phosphorothioate (2MePS) MBs. The 2Me MBs exhibited rapid nuclear sequestration and a gradual increase in fluorescence over time, with nearly 50% of the MBs being opened nonspecifically within 24 h. In contrast, the 2MePS MBs elicited an instantaneous increase in false-positives, corresponding to ∼5–10% of the MBs being open, but little increase was observed over the next 24 h. Moreover, trafficking to the nucleus was slower. After 24 h, both MBs were localized in the nucleus and lysosomal compartments, but only the 2MePS MBs were still functional. When the MBs were retained in the cytoplasm, via conjugation to NeutrAvidin, a significant reduction in false-positives and improvement in functionality was observed. Overall, these results have significant implications for the design and applications of MBs for intracellular RNA measurement.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 and Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
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Santangelo PJ. Molecular beacons and related probes for intracellular RNA imaging. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2009; 2:11-9. [DOI: 10.1002/wnan.52] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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41
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Prigodich AE, Seferos DS, Massich MD, Giljohann DA, Lane BC, Mirkin CA. Nano-flares for mRNA regulation and detection. ACS NANO 2009; 3:2147-52. [PMID: 19702321 PMCID: PMC2742376 DOI: 10.1021/nn9003814] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
We build off the previously described concept of a nanoflare to develop an oligonucleotide gold nanoparticle conjugate that is capable of both detecting and regulating intracellular levels of mRNA. We characterize the binding rate and specificity of these materials using survivin, a gene associated with the diagnosis and treatment of cancer, as a target. The nanoconjugate enters cells and binds mRNA, thereby decreasing the relative abundance of mRNA in a dose- and sequence-dependent manner, resulting in a fluorescent response. This represents the first demonstration of a single material capable of both mRNA regulation and detection. Further, we investigate the intracellular biochemistry of the nanoconjugate, elucidating its mechanism of gene regulation. This work is important to the study of biologically active nanomaterials such as the nanoflare and is a first step toward the development of an mRNA responsive "theranostic".
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Affiliation(s)
- Andrew E Prigodich
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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42
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Nitin N, Rhee WJ, Bao G. Translation inhibition reveals interaction of 2'-deoxy and 2'-O-methyl molecular beacons with mRNA targets in living cells. Nucleic Acids Res 2009; 37:4977-86. [PMID: 19528073 PMCID: PMC2731902 DOI: 10.1093/nar/gkp517] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding the interaction between oligonucleotide probes and RNA targets in living cells is important for biological and clinical studies of gene expression in vivo. Here, we demonstrate that starvation of cells and translation inhibition by blocking the mTOR or PI-3 kinase pathway could significantly reduce the fluorescence signal from 2′-deoxy molecular beacons (MBs) targeting K-ras and GAPDH mRNAs in living cells. However, the intensity and localization of fluorescence signal from MBs targeting nontranslated 28S rRNA remained the same in normal and translation-inhibited cells. We also found that, in targeting K-ras and GAPDH mRNAs, the signal level from MBs with 2′-O-methyl backbone did not change when translation was repressed. Taken together, our findings suggest that MBs with DNA backbone hybridize preferentially with mRNAs in their translational state in living cells, whereas those with 2′-O-methyl chemistry tend to hybridize to mRNA targets in both translational and nontranslational states. This work may thus provide a significant insight into probe design for detection of RNA molecules in living cells and RNA biology.
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Affiliation(s)
- Nitin Nitin
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
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Wang H, Kim Y, Liu H, Zhu Z, Bamrungsap S, Tan W. Engineering a Unimolecular DNA-Catalytic Probe for Single Lead Ion Monitoring. J Am Chem Soc 2009; 131:8221-6. [DOI: 10.1021/ja901132y] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Haipeng Liu
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Zhi Zhu
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Suwussa Bamrungsap
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200
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Furukawa K, Abe H, Hibino K, Sako Y, Tsuneda S, Ito Y. Reduction-Triggered Fluorescent Amplification Probe for the Detection of Endogenous RNAs in Living Human Cells. Bioconjug Chem 2009; 20:1026-36. [DOI: 10.1021/bc900040t] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Abe
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kayo Hibino
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasushi Sako
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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45
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Wang K, Tang Z, Yang C, Kim Y, Fang X, Li W, Wu Y, Medley C, Cao Z, Li J, Colon P, Lin H, Tan W. Molekulartechnische DNA-Modifizierung: Molecular Beacons. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200800370] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Kubota T, Ikeda S, Okamoto A. Doubly Thiazole Orange-Labeled DNA for Live Cell RNA Imaging. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.110] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Wang K, Tang Z, Yang CJ, Kim Y, Fang X, Li W, Wu Y, Medley CD, Cao Z, Li J, Colon P, Lin H, Tan W. Molecular engineering of DNA: molecular beacons. Angew Chem Int Ed Engl 2009; 48:856-70. [PMID: 19065690 PMCID: PMC2772660 DOI: 10.1002/anie.200800370] [Citation(s) in RCA: 492] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem-loop structure holds the fluorescence-donor and fluorescence-acceptor moieties in close proximity to one another, which results in resonant energy transfer. A spontaneous conformation change occurs upon hybridization to separate the two moieties and restore the fluorescence of the donor. Recent research has focused on the improvement of probe composition, intracellular gene quantitation, protein-DNA interaction studies, and protein recognition.
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Affiliation(s)
- Kemin Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Zhiwen Tang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Chaoyong James Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (P.R. China)
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Xiaohong Fang
- Institute of Chemistry, Chinese Academy of Sciences 2 Zhongguancun Beiyijie, Beijing 100190 (P.R. China)
| | - Wei Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Yanrong Wu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Colin D. Medley
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Zehui Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Jun Li
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
| | - Patrick Colon
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Hui Lin
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Genetics Institute and Shands Cancer Center, University of Florida, Gainesville, FL 32611-7200 (USA), Fax: (+1) 352-846-2410
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082 (P.R. China)
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Nitin N, Bao G. NLS peptide conjugated molecular beacons for visualizing nuclear RNA in living cells. Bioconjug Chem 2008; 19:2205-11. [PMID: 18939859 PMCID: PMC3170665 DOI: 10.1021/bc800322a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Imaging the expression and localization of RNAs in live-cell nucleus can provide important information on RNA synthesis, processing, and transport. Here, we report the development of a bifunctional molecular beacon (NLS-MB) composed of a single nuclear localization sequence (NLS) peptide conjugated to a molecular beacon for efficient delivery and imaging of endogenous RNAs in the nuclei of living cells. We characterized the NLS-MBs by comparing their signal-to-noise ratios with unmodified molecular beacons and determined their efficiency of nuclear import. We demonstrated the specificity and sensitivity of the method by observing in living cells the localization and colocalization of small nuclear RNAs (snRNA) U1 and U2 at discrete foci in the nucleoplasm, and the localization of small nucleolar RNA U3 in the nucleolus. These snRNAs were chosen because of their essential roles in RNA biogenesis. The results were validated using in situ hybridization as positive control and random beacons as negative control. This novel approach may be applied to imaging other nuclear RNAs and pre-mRNAs in living cells.
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Affiliation(s)
- Nitin Nitin
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332
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Andou T, Endoh T, Mie M, Kobatake E. RNA detection using peptide-inserted Renilla luciferase. Anal Bioanal Chem 2008; 393:661-8. [PMID: 18979090 DOI: 10.1007/s00216-008-2473-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 10/06/2008] [Accepted: 10/09/2008] [Indexed: 11/26/2022]
Abstract
A novel complementation system with short peptide-inserted-Renilla luciferase (PI-Rluc) and split-RNA probes was constructed for noninvasive RNA detection. The RNA binding peptides HIV-1 Rev and BIV Tat were used as inserted peptides. They display induced fit conformational changes upon binding to specific RNAs and trigger complementation or discomplementation of Rluc. Split-RNA probes were designed to reform the peptide binding site upon hybridization with arbitrarily selected target RNA. This set of recombinant protein and split-RNA probes enabled a high degree of sensitivity in RNA detection. In this study, we show that the Rluc system is comparable to Fluc, but that its detection limit for arbitrarily selected RNA (at least 100 pM) exceeds that of Fluc by approximately two orders of magnitude.
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Affiliation(s)
- Takashi Andou
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259, Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
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50
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Li Y, Zhou X, Ye D. Molecular beacons: An optimal multifunctional biological probe. Biochem Biophys Res Commun 2008; 373:457-61. [DOI: 10.1016/j.bbrc.2008.05.038] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
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