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Abdolahzadeh A, Ang QR, Caine JR, Panchapakesan SSS, Thio S, Cojocaru R, Unrau PJ. Turn-on RNA Mango Beacons for trans-acting fluorogenic nucleic acid detection. RNA 2024; 30:392-403. [PMID: 38282417 PMCID: PMC10946430 DOI: 10.1261/rna.079833.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/03/2024] [Indexed: 01/30/2024]
Abstract
The Mango I and II RNA aptamers have been widely used in vivo and in vitro as genetically encodable fluorogenic markers that undergo large increases in fluorescence upon binding to their ligand, TO1-Biotin. However, while studying nucleic acid sequences, it is often desirable to have trans-acting probes that induce fluorescence upon binding to a target sequence. Here, we rationally design three types of light-up RNA Mango Beacons based on a minimized Mango core that induces fluorescence upon binding to a target RNA strand. Our first design is bimolecular in nature and uses a DNA inhibition strand to prevent folding of the Mango aptamer core until binding to a target RNA. Our second design is unimolecular in nature, and features hybridization arms flanking the core that inhibit G-quadruplex folding until refolding is triggered by binding to a target RNA strand. Our third design builds upon this structure, and incorporates a self-inhibiting domain into one of the flanking arms that deliberately binds to, and precludes folding of, the aptamer core until a target is bound. This design separates G-quadruplex folding inhibition and RNA target hybridization into separate modules, enabling a more universal unimolecular beacon design. All three Mango Beacons feature high contrasts and low costs when compared to conventional molecular beacons, with excellent potential for in vitro and in vivo applications.
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Affiliation(s)
- Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Quiana R Ang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Jana R Caine
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
| | | | - Shinta Thio
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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2
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Weigert N, Schweiger AL, Gross J, Matthes M, Corbacioglu S, Sommer G, Heise T. Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells. Biol Chem 2023; 404:1123-1136. [PMID: 37632732 DOI: 10.1515/hsz-2023-0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.
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Affiliation(s)
- Nina Weigert
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Anna-Lena Schweiger
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Jonas Gross
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Marie Matthes
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Selim Corbacioglu
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
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3
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Yang W, Jo JI, Tabata Y. A Reverse Transfection System with Cationized Gelatin Nanospheres Incorporating Molecular Beacon as a Tool to Visualize Cell Function. ACS Appl Bio Mater 2023; 6:3363-3375. [PMID: 36640270 DOI: 10.1021/acsabm.2c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The objective of this research is to design a reverse transfection system with cationized gelatin nanospheres (cGNS) incorporating a molecular beacon (MB) to visualize a cell function. The cGNS were prepared by the conventional coacervation method. The MB as an imaging probe was incorporated into the cGNS to prepare imaging complexes (cGNSMB). The conventional transfection of 2D culture was performed by incubating MC3T3 cells in the medium containing cGNSMB. The reverse transfection was done by incubating cells on the substrate which had been precoated with both gelatin and cGNSMB. Significantly higher internalization efficiency and fluorescence intensity of cGNSMB were observed in the reverse transfection system than in the conventional one. To apply this system for visualization of 3D cell aggregate, gelatin microspheres (GMS) were prepared, while cGNSMB were bound on the GMS to prepare the GMS-cGNSMB of a cell scaffold. Then the cells were incubated with GMS-cGNSMB to form 3D cell aggregates. On the other hand, as a control, the conventional transfection of 3D culture was performed by incubating the cell aggregates formed with the medium containing cGNSMB. Homogeneous fluorescence of MB from the inside to the outside of aggregates was observed for the reverse transfection group. However, for the conventional transfection, the fluorescence was observed only around the surface of cell aggregates. It is concluded that the reverse transfection system with cGNS incorporating MB is promising to visualize the cell function of a higher transfection efficiency for the 2D culture and in a homogeneous manner for the 3D culture.
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Affiliation(s)
- Wenxuan Yang
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto606-8507, Japan
| | - Jun-Ichiro Jo
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto606-8507, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto606-8507, Japan
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4
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Feng X, Li L, Zhao Y, Li M. Enzyme and MicroRNA Dual-Regulated Photodynamic Molecular Beacons for Cell-Selective Amplification of Antitumor Efficacy. Nano Lett 2023; 23:7743-7749. [PMID: 37406355 DOI: 10.1021/acs.nanolett.3c01814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Photodynamic molecular beacons (PMBs) are highly appealing for activatable photodynamic therapy (PDT), but their applications are hindered by limited therapeutic efficacy. Here, by molecular engineering of enzyme-responsive units in the loop region of DNA-based PMBs, we present for the first time the modular design of an enzyme/microRNA dual-regulated PMB (D-PMB) to achieve cancer-cell-selective amplification of PDT efficacy. In the design, the "inert" photosensitizers in D-PMB could be repeatedly activated in the presence of both tumor-specific enzyme and miRNA, leading to amplified generation of cytotoxic singlet oxygen species and therefore enhanced PDT efficacy in vitro and in vivo. By contrast, low photodynamic activity could be observed in healthy cells, as D-PMB activation has been largely avoided by the dual-regulatable design. This work presents a cooperatively activated PDT strategy, which enables enhanced therapeutic efficacy with improved tumor-specificity and thus conceptualizes an approach to expand the repertoire of designing smart tumor treatment modality.
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Affiliation(s)
- Xueyan Feng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, Beijing Key Laboratory for Bioengineering and Sensing Technology, University of Science and Technology Beijing, Beijing 100083, China
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5
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Murata Y, Jo JI, Tabata Y. Molecular Beacon Imaging System to Discriminate the Differentiation State of Cells from Energy Metabolic Pathways. ACS Sens 2023; 8:2207-2218. [PMID: 37253227 DOI: 10.1021/acssensors.3c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Metabolic pathways of energy production play an essential role as a function of cells. It is well recognized that the differentiation state of stem cells is highly associated with their metabolic profile. Therefore, visualization of the energy metabolic pathway makes it possible to discriminate the differentiation state of cells and predict the cell potential for reprogramming and differentiation. However, at present, it is technically difficult to directly assess the metabolic profile of individual living cells. In this study, we developed an imaging system of cationized gelatin nanospheres (cGNS) incorporating molecular beacons (MB) (cGNSMB) to detect intracellular pyruvate dehydrogenase kinase 1 (PDK1) and peroxisome proliferator-activated receptor γ, coactivator-1α (PGC-1α) mRNA of key regulators in the energy metabolism. The prepared cGNSMB was readily internalized into mouse embryonic stem cells, while their pluripotency was maintained. The high level of glycolysis in the undifferentiated state, the increased oxidative phosphorylation over the spontaneous early differentiation, and the lineage-specific neural differentiation were visualized based on the MB fluorescence. The fluorescence intensity corresponded well to the change of extracellular acidification rate and the oxygen consumption rate of representative metabolic indicators. These findings indicate that the cGNSMB imaging system is a promising tool to visually discriminate the differentiation state of cells from energy metabolic pathways.
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Affiliation(s)
- Yuki Murata
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jun-Ichiro Jo
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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6
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Han D, Ren XH, Liao XR, He XY, Guo T, Chen XS, Pang X, Cheng SX. A Multiple Targeting Nanoprobe for Identifying Cancer Metastatic Sites Based on Detection of Various mRNAs in Circulating Tumor Cells. Nano Lett 2023; 23:3678-3686. [PMID: 37052638 DOI: 10.1021/acs.nanolett.2c04643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Identification of cancer metastatic sites is of importance for adjusting therapeutic interventions and treatment choice. However, identifying the location of metastatic lesions with easy accessibility and high safety is challenging. Here we demonstrate that cancer metastatic sites can be accurately detected by a triple targeting nanoprobe. Through coencapsulating molecular beacons probing a cancer biomarker (CXCR4 mRNA), a lung metastatic biomarker (CTSC mRNA), and a bone metastatic biomarker (JAG1 mRNA), the nanoprobe decorated by SYL3C conjugated hyaluronic acid and ICAM-1 specific aptamer conjugated hyaluronic acid can target diverse phenotyped circulating tumor cells (CTCs) during epithelial-mesenchymal and mesenchymal-epithelial transitions in whole blood for sensitive probing. The detection of CTCs from cancer patients shows that the nanoprobe can provide accurate information to distinguish different cancer metastasis statuses including nonmetastasis, lung metastasis, and bone metastasis. This study proposes an efficient screening tool for identifying the location of distant metastatic lesions via facile blood biopsy.
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Affiliation(s)
- Di Han
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiao-He Ren
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, China
| | - Xin-Ru Liao
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiao-Yan He
- School of Life Sciences, Anhui Medical University, Hefei, Anhui 230011, China
| | - Tao Guo
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Anhui Medical University, Anhui Public Health Clinical Center, Hefei, Anhui 230011, China
| | - Xue-Si Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xuan Pang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, China
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7
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Xu J, Zheng M, Thng DKH, Toh TB, Zhou L, Bonney GK, Dan YY, Chow PKH, Xu C, Chow EKH. NanoBeacon.AI: AI-Enhanced Nanodiamond Biosensor for Automated Sensitivity Prediction to Oxidative Phosphorylation Inhibitors. ACS Sens 2023; 8:1989-1999. [PMID: 37129234 DOI: 10.1021/acssensors.3c00126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Spalt-like transcription factor 4 (SALL4) is an oncofetal protein that has been identified to drive cancer progression in hepatocellular carcinoma (HCC) and hematological malignancies. Furthermore, a high SALL4 expression level is correlated to poor prognosis in these cancers. However, SALL4 lacks well-structured small-molecule binding pockets, making it difficult to design targeted inhibitors. SALL4-induced expression of oxidative phosphorylation (OXPHOS) genes may serve as a therapeutically targetable vulnerability in HCC through OXPHOS inhibition. Because OXPHOS functions through a set of genes with intertumoral heterogeneous expression, identifying therapeutic sensitivity to OXPHOS inhibitors may not rely on a single clear biomarker. Here, we developed a workflow that utilized molecular beacons, nucleic-acid-based, activatable sensors with high specificity to the target mRNA, delivered by nanodiamonds, to establish an artificial intelligence (AI)-assisted platform for rapid evaluation of patient-specific drug sensitivity. Specifically, when the HCC cells were treated with the nanodiamond-medicated OXPHOS biosensor, high sensitivity and specificity of the sensor allowed for improved identification of OXPHOS expression in cells. Assisted by a trained convolutional neural network, drug sensitivity of cells toward an OXPHOS inhibitor, IACS-010759, could be accurately predicted. AI-assisted OXPHOS drug sensitivity assessment could be accomplished within 1 day, enabling rapid and efficient clinical decision support for HCC treatment. The work proposed here serves as a foundation for the patient-based subtype-specific therapeutic research platform and is well suited for precision medicine.
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Affiliation(s)
- Jingru Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Mengjia Zheng
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR 999077, People's Republic of China
| | - Dexter Kai Hao Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Tan Boon Toh
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Lei Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Glenn Kunnath Bonney
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore 119074, Singapore
| | - Yock Young Dan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Pierce Kah Hoe Chow
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore, Singapore 169856, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Chenjie Xu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR 999077, People's Republic of China
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University Singapore, Singapore 117599, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore 117456, Singapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
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8
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Walsh C, Rajora MA, Ding L, Nakamura S, Endisha H, Rockel J, Chen J, Kapoor M, Zheng G. Protease-Activatable Porphyrin Molecular Beacon for Osteoarthritis Management. Chem Biomed Eng 2023; 1:66-80. [PMID: 37122828 PMCID: PMC10131263 DOI: 10.1021/cbmi.3c00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/06/2023] [Accepted: 02/12/2023] [Indexed: 05/02/2023]
Abstract
Despite the substantial burden posed by osteoarthritis (OA) globally, difficult challenges remain in achieving early OA diagnosis and adopting effective disease-modifying treatments. In this study, we use a biomolecular approach to address these limitations by creating an inherently theranostic molecular beacon whose imaging and therapeutic capabilities are activated by early pathological changes in OA. This platform comprised (1) a peptide linker substrate for metalloproteinase-13 (MMP-13), a pathological protease upregulated in OA, which was conjugated to (2) a porphyrin moiety with inherent multimodal imaging, photodynamic therapy, and drug delivery capabilities, and (3) a quencher that silences the porphyrin's endogenous fluorescence and photoreactivity when the beacon is intact. In diseased OA tissue with upregulated MMP-13 expression, this porphyrin molecular beacon (PPMMP13B) was expected to undergo sequence-specific cleavage, yielding porphyrin fragments with restored fluorescence and photoreactivity that could, respectively, be used as a readout of MMP-13 activity within the joint for early OA imaging and disease-targeted photodynamic therapy. This study focused on the synthesis and characterization of PPMMP13B, followed by a proof-of-concept evaluation of its OA imaging and drug delivery potential. In solution, PPMMP13B demonstrated 90% photoactivity quenching in its intact form and robust MMP-13 activation, yielding a 13-fold increase in fluorescence post-cleavage. In vitro, PPMMP13B was readily uptaken and activated in an MMP-13 cell expression-dependent manner in primary OA synoviocytes without exuding significant cytotoxicity. This translated into effective intra-articular cartilage (to a 50 μm depth) and synovial uptake and activation of PPMMP13B in a destabilization of the medial meniscus OA mouse model, yielding strong fluorescence contrast (7-fold higher signal than background) at the diseased joint site. These results provide the foundation for further exploration of porphyrin molecular beacons for image-guided OA disease stratification, effective articular delivery of disease-modify agents, and OA photodynamic therapy.
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Affiliation(s)
- Connor Walsh
- Princess
Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, ON M5S 3G9, Canada
| | - Maneesha A. Rajora
- Princess
Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, ON M5S 3G9, Canada
| | - Lili Ding
- Princess
Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sayaka Nakamura
- Schroeder
Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Krembil
Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Helal Endisha
- Schroeder
Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Krembil
Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Jason Rockel
- Schroeder
Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Krembil
Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Juan Chen
- Princess
Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Mohit Kapoor
- Schroeder
Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Krembil
Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Gang Zheng
- Princess
Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto, ON M5S 3G9, Canada
- Department
of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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9
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Washisaka T, Tabata Y. Live Imaging of Monocyte/Macrophage Differentiation with Cationized Gelatin Nanospheres Incorporating a Molecular Beacon. ACS Biomater Sci Eng 2023; 9:2672-2682. [PMID: 37014020 DOI: 10.1021/acsbiomaterials.2c01420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
As one imaging method to evaluate monocyte-macrophage differentiation, cationized gelatin nanospheres incorporating a molecular beacon (MB) (cGNSMB) were designed. Cationized gelatin nanospheres (cGNS) of different apparent sizes were prepared by the conventional coacervation method, and then the MB of CD204 was incorporated into cGNS to prepare cGNSMB. When three types of cGNSMB were cultured with human monocytoma (THP-1) cells, the cGNSMB with a 110 nm diameter showed the highest MB delivery efficiency. In addition, no influence on the monocyte-macrophage differentiation was observed in terms of CD204 gene expression and cell viability. After incubation with cGNS incorporating CD204 MB (cGNSCD204), THP-1 cells were stimulated by phorbol 12-myristate 13-acetate (PMA) for monocyte differentiation into macrophages. The fluorescence intensity of macrophages increased with the incubation time. In contrast, the fluorescence intensity of macrophages incubated with MB alone was not changed. On the other hand, there was no change in the fluorescence intensity of original THP-1 cells cultured with cGNSCD204. It is concluded that the cGNSCD204 are promising to trace the differentiation of THP-1 cells into macrophages in their live condition.
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Affiliation(s)
- Taichi Washisaka
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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10
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Wang C, Zhu K, Yu J, Shi P. Complementary DNA Significantly Enhancing Signal Response and Sensitivity of a Molecular Beacon Probe to Aflatoxin B1. Biosensors (Basel) 2023; 13:195. [PMID: 36831960 PMCID: PMC9953557 DOI: 10.3390/bios13020195] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
This paper reported an improved molecular beacon method for the rapid detection of aflatoxin B1 (AFB1), a natural mycotoxin with severe carcinogenicity. With the assistance of a complementary DNA (cDNA) chain, the molecular beacon which consists of a DNA aptamer flanked by FAM and BHQ1 displayed a larger fluorescent response to AFB1, contributing to the sensitive detection of AFB1. Upon optimization of some key experimental factors, rapid detection of AFB1 ranging from 1 nM to 3 μM, within 20 min, was realized by using this method. A limit of detection (LoD) of 1 nM was obtained, which was lower than the LoD (8 nM) obtained without cDNA assistance. This aptamer-based molecular beacon detection method showed advantages in easy operation, rapid analysis and larger signal response. Good specificity and anti-interference ability were demonstrated. This method showed potential in real-sample analysis.
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Affiliation(s)
- Chao Wang
- College of Medicine, Linyi University, Linyi 276005, China
| | - Kexiao Zhu
- College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
| | - Jie Yu
- College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
| | - Pengfei Shi
- College of Medicine, Linyi University, Linyi 276005, China
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11
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Yu H, Zhao Q. Aptamer Molecular Beacon Sensor for Rapid and Sensitive Detection of Ochratoxin A. Molecules 2022; 27:molecules27238267. [PMID: 36500359 PMCID: PMC9737911 DOI: 10.3390/molecules27238267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Ochratoxin A (OTA) is a carcinogenic fungal secondary metabolite which causes wide contamination in a variety of food stuffs and environments and has a high risk to human health. Developing a rapid and sensitive method for OTA detection is highly demanded in food safety, environment monitoring, and quality control. Here, we report a simple molecular aptamer beacon (MAB) sensor for rapid OTA detection. The anti-OTA aptamer has a fluorescein (FAM) labeled at the 5' end and a black hole quencher (BHQ1) labeled at the 3' end. The specific binding of OTA induced a conformational transition of the aptamer from a random coil to a duplex-quadruplex structure, which brought FAM and BHQ1 into spatial proximity causing fluorescence quenching. Under the optimized conditions, this aptamer sensor enabled OTA detection in a wide dynamic concentration range from 3.9 nM to 500 nM, and the detection limit was about 3.9 nM OTA. This method was selective for OTA detection and allowed to detect OTA spiked in diluted liquor and corn flour extraction samples, showing the capability for OTA analysis in practical applications.
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Affiliation(s)
- Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- Correspondence:
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12
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Takehana S, Yang W, Tabata Y. Potential Method of Autophagy Imaging with Cationized Gelatin Nanospheres Incorporating Molecular Beacon. ACS Appl Bio Mater 2022; 5:2965-2975. [PMID: 35609115 DOI: 10.1021/acsabm.2c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The objective of this research is to develop an imaging method with cationized gelatin nanospheres incorporating molecular beacon (cGNSMB) to visualize an autophagy activity in living cells. Cationized gelatin nanospheres (cGNS) were prepared by the conventional coacervation method, and then molecular beacon (MB) was incorporated into them. The cGNSMB prepared were internalized into cells at a high efficiency. In this study, a starvation medium of serum and amino acids-free was used to induce autophagy. The autophagy activity was confirmed by an immunofluorescence staining for microtubule-associated proteins light chain 3B (LC3B) of an autophagy specific protein. With the autophagy induction time, the number of LC3 fluorescent dots increased, which indicated an increased autophagy activity. As the autophagy-related genes, sequestosome 1 (SQSTM1) and cathepsin F (CTSF), which up-regulate after autophagy induction, were chosen as the targets of cGNSMB. The fluorescence intensity of cGNSMB targeting to SQSTM1 and CTSF increased with the starvation treatment time, which well corresponded with the gene expression results. When applied to cells in different autophagy conditions, the cGNSMB visualized the autophagy activity corresponding with the autophagy condition of cells. From the results obtained, it was concluded that the cGNSMB provide a promising method to visualize the autophagy of cells. The advantage of cGNSMB visualization is to obtain the temporal and spatial information without destroying sample cells.
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Affiliation(s)
- Sho Takehana
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Wenxuan Yang
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Institute for Life and Medical Sciences, Kyoto University, Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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13
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Chen X, Feng Y, Chen H, Zhang Y, Wang X, Zhou N. Fluorescent Aptasensor for Highly Specific Detection of ATP Using a Newly Screened Aptamer. Sensors (Basel) 2022; 22:2425. [PMID: 35408040 DOI: 10.3390/s22072425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/16/2022]
Abstract
Owing to the significant roles of adenosine triphosphate (ATP) in diverse biological processes, ATP level is used to research and evaluate the physiological processes of organisms. Aptamer-based biosensors have been widely reported to achieve this purpose, which are superior in their flexible biosensing mechanism, with a high sensitivity and good biocompatibility; however, the aptamers currently used for ATP detection have a poor ability to discriminate ATP from adenosine diphosphate (ADP) and adenosine monophosphate (AMP). Herein, an ATP-specific aptamer was screened and applied to construct a fluorescent aptasensor for ATP by using graphene oxide (GO) and strand displacement amplification (SDA). The fluorescence intensity of the sensor is linearly related to the concentration of ATP within 0.1 μM to 25 μM under optimal experimental conditions, and the detection limit is 33.85 nM. The biosensor exhibits a satisfactory specificity for ATP. Moreover, the experimental results indicate that the biosensor can be applied to determine the ATP in human serum. In conclusion, the screened aptamer and the biosensor have promising applications in the determination of the real energy charge level and ATP content in a complex biological system.
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14
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Paramasivam P, Stöter M, Corradi E, Dalla Costa I, Höijer A, Bartesaghi S, Sabirsh A, Lindfors L, Yanez Arteta M, Nordberg P, Andersson S, Baudet ML, Bickle M, Zerial M. Quantitative intracellular retention of delivered RNAs through optimized cell fixation and immunostaining. RNA 2022; 28:433-446. [PMID: 34949721 PMCID: PMC8848937 DOI: 10.1261/rna.078895.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Detection of nucleic acids within subcellular compartments is key to understanding their function. Determining the intracellular distribution of nucleic acids requires quantitative retention and estimation of their association with different organelles by immunofluorescence microscopy. This is particularly important for the delivery of nucleic acid therapeutics, which depends on endocytic uptake and endosomal escape. However, the current protocols fail to preserve the majority of exogenously delivered nucleic acids in the cytoplasm. To solve this problem, by monitoring Cy5-labeled mRNA delivered to primary human adipocytes via lipid nanoparticles (LNP), we optimized cell fixation, permeabilization, and immunostaining of a number of organelle markers, achieving quantitative retention of mRNA and allowing visualization of levels that escape detection using conventional procedures. The optimized protocol proved effective on exogenously delivered siRNA, miRNA, as well as endogenous miRNA. Our protocol is compatible with RNA probes of single molecule fluorescence in situ hybridization (smFISH) and molecular beacon, thus demonstrating that it is broadly applicable to study a variety of nucleic acids in cultured cells.
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Affiliation(s)
- Prasath Paramasivam
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Martin Stöter
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Eloina Corradi
- Department CIBIO, University of Trento, Trento 38123, Italy
| | | | - Andreas Höijer
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Stefano Bartesaghi
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Alan Sabirsh
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Lennart Lindfors
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Marianna Yanez Arteta
- Advanced Drug Delivery, Pharmaceutical Science R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Peter Nordberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | - Shalini Andersson
- Oligonucleotide Discovery, Discovery Sciences R&D, AstraZeneca, 43150 Gothenburg, Sweden
| | | | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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15
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Marras SAE, Chen L, Shashkina E, Davidson RM, Strong M, Daley CL, Kreiswirth BN. A Molecular-Beacon-Based Multiplex Real-Time PCR Assay To Distinguish Mycobacterium abscessus Subspecies and Determine Macrolide Susceptibility. J Clin Microbiol 2021; 59:e0045521. [PMID: 33980653 PMCID: PMC8373218 DOI: 10.1128/jcm.00455-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/07/2021] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus is a rapidly growing nontuberculous mycobacterial species that comprises three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. These predominantly environmental microorganisms have emerged as life-threatening chronic pulmonary pathogens in both immunocompetent and immunocompromised patients, and their acquisition of macrolide resistance due to the erm(41) gene and mutations in the 23S rrl gene has dramatically impacted patient outcome. However, standard microbiology laboratories typically have limited diagnostic tools to distinguish M. abscessus subspecies, and the testing for macrolide resistance is often not done. Here, we describe the development of a real-time multiplex assay using molecular beacons to establish a robust, rapid, and highly accurate method to both distinguish M. abscessus subspecies and to determine which strains are susceptible to macrolides. We report a bioinformatic approach to identify robust subspecies sequence targets, the design and optimization of six molecular beacons to identify all genotypes, and the development and application of a 2-tube 3-color multiplex assay that can provide clinically significant treatment information in less than 3 h.
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Affiliation(s)
- Salvatore A. E. Marras
- Public Health Research Institute Center, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Elena Shashkina
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Rebecca M. Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, USA
| | - Charles L. Daley
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
- The University of Colorado, Aurora, Colorado, USA
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
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16
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Kim J, Ahn SY, Um SH. Bead-Immobilized Multimodal Molecular Beacon-Equipped DNA Machinery for Specific RNA Target Detection: A Prototypical Molecular Nanobiosensor. Nanomaterials (Basel) 2021; 11:nano11061617. [PMID: 34203018 PMCID: PMC8235652 DOI: 10.3390/nano11061617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/28/2022]
Abstract
A variety of nanostructured diagnostic tools have been developed for the precise detection of known genetic variants. Molecular beacon systems are very promising tools due to their specific selectivity coupled with relatively lower cost and time requirements than existing molecular detection tools such as next generation sequencing or real-time PCR (polymerase chain reaction). However, they are prone to errors induced by secondary structure responses to environmental fluctuations, such as temperature and pH. Herein, we report a temperature-insensitive, bead-immobilized, molecular beacon-equipped novel DNA nanostructure for detection of cancer miRNA variants with the consideration of thermodynamics. This system consists of three parts: a molecular beacon for cancer-specific RNA capture, a stem body as a core template, and a single bead for solid-support. This DNA system was selectively bound to nanosized beads using avidin-biotin chemistry. Synthetic DNA nanostructures, designed based on the principle of fluorescence-resonance enhanced transfer, were effectively applied for in vitro cancer-specific RNA detection. Several parameters were optimized for higher performance, with a focus on thermodynamic stability. Theoretical issues regarding the secondary structure of a single molecular beacon and its combinatory forms were also studied. This study provides design guidelines for new sensing systems of miRNA variation for next-generation biotechnological applications.
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Affiliation(s)
- Jeonghun Kim
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
| | - So Yeon Ahn
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
| | - Soong Ho Um
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea
- Correspondence:
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17
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Mukaida A, Adachi R, Akiyama Y, Kamimura M. Facile Preparation of a Hairpin DNA-Gold Nanoparticle Monoconjugate with a Single-Dye Molecule and Lactobionic Acid as Targeting Ligand. ANAL SCI 2021; 37:785-788. [PMID: 33678725 DOI: 10.2116/analsci.20scn07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We established a new design for a single molecular beacon-conjugated gold nanoparticle, named monoMB-GNP, which showed enhanced fluorescence emission only in the presence of the complementary DNA sequence. MonoMB-GNP also showed no apparent toxicity to NIH/3T3 cells at 1 nM, as determined by the water-soluble tetrazolium assay. Importantly, the lactobionic acid was successfully modified on the surface of monoMB-GNP. The proposed nanoparticle has prospects for use in several applications for targetable molecular beacon strategies.
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Affiliation(s)
- Akane Mukaida
- Department of Materials Science and Technology, Graduate School of Industrial Science and Technology, Tokyo University of Science
| | - Rihito Adachi
- Department of Materials Science and Technology, Graduate School of Industrial Science and Technology, Tokyo University of Science
| | - Yoshitsugu Akiyama
- Faculty of Industrial Science and Technology, Tokyo University of Science
| | - Masao Kamimura
- Department of Materials Science and Technology, Graduate School of Industrial Science and Technology, Tokyo University of Science
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18
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Murata Y, Jo JI, Tabata Y. Visualization of Apoptosis in Three-Dimensional Cell Aggregates Based on Molecular Beacon Imaging. Tissue Eng Part C Methods 2021; 27:264-275. [PMID: 33619986 DOI: 10.1089/ten.tec.2020.0338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The objective of this study is to visualize cell apoptosis in three-dimensional (3D) cell aggregates based on molecular beacons (MB). Two types of MB for messenger RNA were used: caspase-3 MB as a target for apoptosis and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) MB as a control of stable fluorescence in cells. To enhance the MB internalization into cells, caspase-3 and GAPDH MB were incorporated in cationized gelatin nanospheres (cGNS), respectively (cGNScasp3 MB and cGNSGAP MB). In addition, cGNS co-incorporating caspase-3 and GAPDH MB (cGNSdual MB) were prepared to perform the dual-color imaging for the same cell aggregate. The cGNSMB were incubated with mouse mesenchymal stem cells to label with MB in the two-dimensional culture. The cell apoptosis mediated by the addition of antibody for a death receptor Fas was ratiometrically detected by the cGNSdual MB to the same extent as single MB. The cell aggregates were prepared from MB-labeled cells, and the MB fluorescence was detected from almost all the cells even in the 3D aggregates to show the homogenous distribution. In addition to the Fas-mediated apoptosis, the aggregates were treated with camptothecin of a low-molecular weight apoptosis inducer. The fluorescence of caspase-3 MB was mainly distributed at the surface surrounding site of Fas-mediated apoptotic aggregates rather than the center site, while that of GAPDH MB was detected even in the interior site. On the other hand, in the camptothecin-induced apoptotic aggregates, both caspae-3 and GAPDH MB fluorescence were detected from the interior site of aggregates as well as the surrounding site. It is likely that the MB fluorescence reflected the localization of apoptotic position caused by the different molecular sizes of apoptosis inducer and the consequent penetration into the aggregates. It is concluded that the cGMSMB are a promising system to visualize cell apoptosis in 3D cell aggregates without the destruction of aggregates.
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Affiliation(s)
- Yuki Murata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jun-Ichiro Jo
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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Yang HC, Rhee WJ. Single Step In Situ Detection of Surface Protein and MicroRNA in Clustered Extracellular Vesicles Using Flow Cytometry. J Clin Med 2021; 10:jcm10020319. [PMID: 33477255 PMCID: PMC7831033 DOI: 10.3390/jcm10020319] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/21/2022] Open
Abstract
Because cancers are heterogeneous, it is evident that multiplexed detection is required to achieve disease diagnosis with high accuracy and specificity. Extracellular vesicles (EVs) have been a subject of great interest as sources of novel biomarkers for cancer liquid biopsy. However, EVs are nano-sized particles that are difficult to handle; thus, it is necessary to develop a method that enables efficient and straightforward EV biomarker detection. In the present study, we developed a method for single step in situ detection of EV surface proteins and inner miRNAs simultaneously using a flow cytometer. CD63 antibody and molecular beacon-21 were investigated for multiplexed biomarker detection in normal and cancer EVs. A phospholipid-polymer-phospholipid conjugate was introduced to induce clustering of the EVs analyzed using nanoparticle tracking analysis, which enhanced the detection signals. As a result, the method could detect and distinguish cancer cell-derived EVs using a flow cytometer. Thus, single step in situ detection of multiple EV biomarkers using a flow cytometer can be applied as a simple, labor- and time-saving, non-invasive liquid biopsy for the diagnosis of various diseases, including cancer.
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Affiliation(s)
- Hee Cheol Yang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon 22012, Korea;
| | - Won Jong Rhee
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, Incheon 22012, Korea;
- Division of Bioengineering, Incheon National University, Incheon 22012, Korea
- Correspondence: ; Tel.: +82-32-835-8299
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20
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Sun S, Yang S, Hu X, Zheng C, Song H, Wang L, Shen Z, Wu ZS. Combination of Immunomagnetic Separation with Aptamer-Mediated Double Rolling Circle Amplification for Highly Sensitive Circulating Tumor Cell Detection. ACS Sens 2020; 5:3870-3878. [PMID: 33205648 DOI: 10.1021/acssensors.0c01082] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most frequently diagnosed cancer among women, and the circulating tumor cell (CTC)-meditated distant metastasis is the leading cause of death. Thus, the detection of CTCs is of great importance for the early diagnosis of breast cancer and the prevention of metastasis. In this study, using human breast carcinoma BT474 cells as the model CTCs, a powerful assay platform is demonstrated by fluorescence spectrometry for the highly sensitive CTC detection by combining the dual-recognizing elements receptor-binding antibody and aptamer-mediated separation with double rolling circle amplification reactions (d-RCA, including RCA1 and RCA2). The aptamer-inserted RCA1 product (RCA1-p) exhibits the considerably improved affinity towards target cells originating from the multivalent binding effect. The immunomagnetic separation removes nontarget cells coexisting in complex biological milieu, while the centrifugal separation of cells/DNAs mixture eliminates the excess probes, thereby circumventing the unwanted interferences. The fluorescence spectrometric results show that a 34-fold enhanced fluorescence signal is achieved upon BT474 cells, and the target cells can be quantitatively detected down to 9 cells/200 μL with the linear range of five orders of magnitude, indicating a significantly enhanced detection performance. Even if BT474 cells are spiked in the fresh whole blood, no obvious fluctuation in the fluorescence signal is detected, demonstrating that the newly developed d-RCA assay system is suitable for screening CTCs in complex environments and is expected to be a promising tool for estimating distant metastasis and predicting the recurrence of tumors.
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Affiliation(s)
- Shujuan Sun
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Shulin Yang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xuemei Hu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Cheng Zheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Heart and Lung, Zhejiang 325000, P.R. China
| | - Huanxia Song
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Lisha Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zhifa Shen
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
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21
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Abstract
This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.
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Affiliation(s)
- Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Alexander A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
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Abstract
The objective of this study is to visualize the ability of cell proliferation based on molecular beacons (MB). Two types of MB to detect messenger RNA (mRNA) were used. One is a Ki67 MB of a target for cell proliferation ability. The other one is a glyceraldehyde-3-phosphate dehydrogenase (GAPDH) MB as a control of stable fluorescence in cells. To enhance the MB internalization into cells, the MB were incorporated into cationized gelatin nanospheres (cGNS). There was no difference in the physicochemical properties and the cell internalization between the cGNSKi67 MB and cGNSGAP MB. When basic fibroblast growth factor (bFGF) was added to KUM6 cells of a mouse bone marrow-derived mesenchymal stem cell line, the expression of Ki67 and the cell proliferation increased with the bFGF concentration. After the incubation for the cell internalization of cGNS incorporating MB (cGNSMB), the cells were further incubated for 24 h with or without different concentrations of bFGF. The fluorescence of cGNSKi67 MB significantly increased with the increase of bFGF concentration, whereas that of cGNSGAP MB was constant, irrespective of the bFGF concentration. A time-lapse imaging assay revealed a fast enhancement of cGNSKi67 MB fluorescence after the bFGF addition compared with no bFGF addition. On the other hand, for cGNSGAP MB, a constant fluorescence was observed even at any time point after the bFGF addition. It is concluded that the cGNSMB system is promising for the chronological visualization of proliferation ability in living cells.
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Affiliation(s)
- Yuki Murata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jun-Ichiro Jo
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasuhiko Tabata
- Laboratory of Biomaterials, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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23
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Li C, Luo M, Wang J, Niu H, Shen Z, Wu ZS. Rigidified DNA Triangle-Protected Molecular Beacon from Endogenous Nuclease Digestion for Monitoring microRNA Expression in Living Cells. ACS Sens 2020; 5:2378-2387. [PMID: 32786386 DOI: 10.1021/acssensors.0c00212] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Utilizing the nucleic acid-based self-assembly technology, Y-shaped backbone-rigidified DNA triangles with substantially enhanced nuclease resistance are built by designing a Y-shaped backbone in the center of a planar DNA triangle. Along this line, we developed aptamer-targeted DNA triangle-based molecular beacon (Apt-Tri-MB) probes for monitoring the microRNA expression in living cells with high sensitivity and specificity. For the Apt-Tri-MB probe, the MB is protected by the DNA triangle from unwanted enzymatic digestion, and a targeting ligand aptamer is introduced to endow the MB with active tumor cell-targeting capability. Thus, the digestion-induced false-positive signal is avoided, and the background fluorescence, which originates from the passive cell uptake (e.g., transfection) of reporting probes, is substantially suppressed. The imaging capability of the Apt-Tri-MB is superior to the commercial transfection agent-based counterpart and exhibits good universality suitable for imaging different miRNAs by changing the recognition fragment of the MB. Meanwhile, the disadvantages are efficiently circumvented, including the susceptibility of nucleic acids to nuclease-mediated degradation, inability of MB probes to enter cells, lipofectamine-determined cellular cytotoxicity, and nontargeting cell uptake. Inspired by the Y-shaped backbone-rigidified Apt-Tri-MB, we also constructed X-shaped backbone-rigidified quadrangle-based probes (Apt-Qua-MB). The experimental results show that cell imaging and antidegradation capability of Apt-Qua-MB are comparable with Apt-Tri-MB. As a proof-of-concept study, the Apt-Tri-MB is expected to open an exciting avenue for the further application of nucleic acid probes in the cellular level research and clinical disease diagnosis.
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Affiliation(s)
- Congcong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Mengxue Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Jue Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Zhifa Shen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
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Kitamura Y, Mishio K, Arslan P, Ikeda B, Imoto C, Katsuda Y, Ihara T. Electrochemical Molecular Beacon for Nucleic Acid Sensing in a Homogeneous Solution. ANAL SCI 2020; 36:959-964. [PMID: 32062630 DOI: 10.2116/analsci.19p456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/31/2020] [Indexed: 08/09/2023]
Abstract
Ferrocene (Fc) and β-cyclodextrin (βCyD) were modified at each end of stem-loop structured DNA as an electrochemical signal generator and its quencher, respectively, to give an electrochemical molecular beacon (eMB). A relatively high efficiency of signal quenching was achieved by an inclusion complex (βCyD ⊃ Fc) formation that was induced on the stem structure of the closed form (= stem-loop structure) of eMB. With the addition of target DNA, the structure of eMB opened to form a linear duplex, where the Fc dissociated from the βCyD to restore its intrinsic electrochemical signal. The signal contrast of the electric current for this off/on-type sensor was high, ca. 95. This technique did not require any modification of the electrode surface, and it realized the detection of the target nucleic acids in a homogeneous solution with a high sensitivity using high-performance liquid chromatography (HPLC) equipped with electrochemical detector.
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Affiliation(s)
- Yusuke Kitamura
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan.
| | - Kotaro Mishio
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan
| | - Pelin Arslan
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan
| | - Boui Ikeda
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan
| | - Chiharu Imoto
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan
| | - Yousuke Katsuda
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan
| | - Toshihiro Ihara
- Division of Materials Science, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, 860-8555, Japan.
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Zhang Z, Wang S, Ma J, Zhou T, Wang F, Wang X, Zhang G. Rolling Circle Amplification-Based Polyvalent Molecular Beacon Probe-Assisted Signal Amplification Strategies for Sensitive Detection of B16 Cells. ACS Biomater Sci Eng 2020; 6:3114-3121. [PMID: 33463255 DOI: 10.1021/acsbiomaterials.0c00288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We developed a simple and sensitive signal amplification method for the detection of B16 cells based on the combination of rolling circle amplification (RCA) and molecular beacons (MBs). A long-chain structure of DNA synthesized by RCA was used to turn on aptamer-based MBs. Because of the multiple complementary repeat units, the RCA scaffold hybridized tens or hundreds of MBs to form polyvalent aptamer probes. The unfold ability and the fluorescence intensity of MBs were both improved by RCA, as compared to short single chains. The cell experiment results demonstrated that RCA-based polyvalent MBs were significantly more effective than monovalent MBs in targeting B16 cells and signal sensitivity because of their multivalent effects. The establishment of this strategy would provide a powerful platform for early clinical diagnostics of cancer cells.
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Affiliation(s)
- Zhiqing Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Shanshan Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jie Ma
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ting Zhou
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiufeng Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Guodong Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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Chen Z, Peng Y, Xie X, Feng Y, Li T, Li S, Qin X, Yang H, Wu C, Zheng C, Zhu J, You F, Liu Y. Dendrimer-Functionalized Superparamagnetic Nanobeacons for Real-Time Detection and Depletion of HSP90α mRNA and MR Imaging. Am J Cancer Res 2019; 9:5784-5796. [PMID: 31534519 PMCID: PMC6735378 DOI: 10.7150/thno.36545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
Background & Aims: The use of antisense oligonucleotide-based nanosystems for the detection and regulation of tumor-related gene expression is thought to be a promising approach for cancer diagnostics and therapies. Herein, we report that a cubic-shaped iron oxide nanoparticle (IONC) core nanobeacon is capable of delivering an HSP90α mRNA-specific molecular beacon (HSP90-MB) into living cells and enhancing T2-weighted MR imaging in a tumor model. Methods: The nanobeacons were built with IONC, generation 4 poly(amidoamine) dendrimer (G4 PAMAM), Pluronic P123 (P123) and HSP90-MB labeled with a quencher (BHQ1) and a fluorophore (Alexa Fluor 488). Results: After internalization by malignant cells overexpressing HSP90α, the fluorescence of the nanobeacon was recovered, thus distinguishing cancer cells from normal cells. Meanwhile, MB-mRNA hybridization led to enzyme activity that degraded DNA/RNA hybrids and resulted in downregulation of HSP90α at both the mRNA and protein levels. Furthermore, the T2-weighted MR imaging ability of the nanobeacons was increased after PAMAM and P123 modification, which exhibited good biocompatibility and hemocompatibility. Conclusions: The nanobeacons show promise for applicability to tumor-related mRNA detection, regulation and multiscale imaging in the fields of cancer diagnostics and therapeutics.
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Bayer LV, Omar OS, Bratu DP, Catrina IE. PinMol: Python application for designing molecular beacons for live cell imaging of endogenous mRNAs. RNA 2019; 25:305-318. [PMID: 30573696 PMCID: PMC6380279 DOI: 10.1261/rna.069542.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Molecular beacons are nucleic acid oligomers labeled with a fluorophore and a quencher that fold in a hairpin-shaped structure, which fluoresce only when bound to their target RNA. They are used for the visualization of endogenous mRNAs in live cells. Here, we report a Python program (PinMol) that designs molecular beacons best suited for live cell imaging by using structural information from secondary structures of the target RNA, predicted via energy minimization approaches. PinMol takes into account the accessibility of the targeted regions, as well as the inter- and intramolecular interactions of each selected probe. To demonstrate its applicability, we synthesized an oskar mRNA-specific molecular beacon (osk1236), which is selected by PinMol to target a more accessible region than a manually designed oskar-specific molecular beacon (osk2216). We previously demonstrated osk2216 to be efficient in detecting oskar mRNA in in vivo experiments. Here, we show that osk1236 outperformed osk2216 in live cell imaging experiments.
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Affiliation(s)
- Livia V Bayer
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Omar S Omar
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Diana P Bratu
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Irina E Catrina
- Biological Sciences Department, Hunter College, City University of New York, New York, New York 10065, USA
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Widada H, Rohman A, Jenie RI. Optimization of Graphene Oxide-based Quencher-free Molecular Beacon for Meat Product Authentication. Pak J Biol Sci 2019; 22:220-225. [PMID: 31930865 DOI: 10.3923/pjbs.2019.220.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Sensitivity is very important in DNA detection. Various attempts have been made to increase detection sensitivity, including increasing the detection capabilities of devices and using DNA probes. This study was aimed to develop a DNA detection method using a quencher-free molecular beacon (QFMB) probe with the help of graphene oxide (GO) as a quencher. MATERIALS AND METHODS The GO has the specific ability to adsorb DNA in the form of a single strand but not in a double strand. The optimum interaction between the MB probe and the target DNA (pig DNA) could produce a double-stranded DNA (dsDNA) so that it is detached from the GO surface. The dsDNA that escapes from the surface of the GO can be detected using a spectrofluorometric technique at an excitation wavelength of 482 nm and an emission of 519 nm, with an intensity comparable to its concentration. RESULTS The optimum condition that can be used is a GO concentration of 5 μg mL-1, a reaction temperature of 65°C, an incubation time of 6 min, a reaction pH of 7.5 and cation levels of 40 nM. Analysis of the target pork meatball DNA carried out at a concentration interval of 0-500 pg mL-1. CONCLUSION So it was concluded that the DNA detection system uses a combination of a quencher-free molecular beacon and graphene oxide, providing a good prospect to be developed into a new method in the halal authentication of meat products using the spectrofluorometric method.
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Hwang JY, Kim ST, Kwon J, Lee J, Chun YO, Han JS, Han HS. Ultrasensitive Fluorescence Monitoring and in Vivo Live Imaging of Circulating Tumor Cell-Derived miRNAs Using Molecular Beacon System. ACS Sens 2018; 3:2651-2659. [PMID: 30426747 DOI: 10.1021/acssensors.8b01095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Circulating tumor cells (CTCs) have considerable clinical significance in cancer progression and prognosis. In this context, CTC-derived microRNAs (miRs) in blood and tissues have been proposed as the novel noninvasive biomarkers for monitoring tumor progression, especially at the early stages. To monitor circulating miRs, a tool should have high sensitivity, be a simple procedure, and allow detection in very small volumes. Thus, we designed a sensing tool for sensitive monitoring of blood or tissue miRs using a fluorophore-quencher probe-based molecular beacon (MB). This MB-based tool displayed an ultrasensitive limit of detection (LOD) level of 6.7 × 10-17 M and 8.7 × 10-17 for metastasis-derived miR-21a and miR-221, respectively. It also can discriminate miR-21a/221 from both guide strand miRs and its precursor forms (pre-miR). Furthermore, the tool discriminated between blood and tissue-related miR-21a/221-expression and detected metastasis and epithelial-mesenchymal transition and also describe a noninvasive miR fluorescence imaging of CTCs in a mouse model, showing the potential for clinical diagnosis and prognosis.
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Affiliation(s)
- Ji Yeon Hwang
- Preclinical Research Center, Biomedical Research Institute, Seoul National University Bundang Hospital, Gyeonggi-do 13620, Republic of Korea
- The Institute for the 3Rs, College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Tae Kim
- Department of Surgery, Seoul National University Bundang Hospital, Gyeonggi-do 13620, Republic of Korea
- Biomedical Research Institute, Seoul National University Bundang Hospital, Gyeonggi-do 13605, Republic of Korea
| | - Junyoung Kwon
- Department of Cogno-Mechatronics Engineering, Pusan National University, Busan 46240, Republic of Korea
| | - Jaebeom Lee
- Department of Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Young-Ok Chun
- Biomedical Research Institute, Seoul National University Bundang Hospital, Gyeonggi-do 13605, Republic of Korea
- Department of Molecular Biology, DanKook University, Gyeonggi-do 16890, Republic of Korea
| | - Jin Soo Han
- The Institute for the 3Rs, College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Ho-Seong Han
- Department of Surgery, Seoul National University Bundang Hospital, Gyeonggi-do 13620, Republic of Korea
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Yu Q, Zhai F, Zhou H, Wang Z. Aptamer Conformation Switching-Induced Two-Stage Amplification for Fluorescent Detection of Proteins. Sensors (Basel) 2018; 19:s19010077. [PMID: 30587808 PMCID: PMC6338969 DOI: 10.3390/s19010077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/14/2018] [Accepted: 12/22/2018] [Indexed: 02/07/2023]
Abstract
Basing on the conformation change of aptamer caused by proteins, a simple and sensitive protein fluorescent assay strategy is proposed, which is assisted by the isothermal amplification reaction of polymerase and nicking endonuclease. In the presence of platelet-derived growth factor (PDGF-BB), the natural conformation of a DNA aptamer would change into a Y-shaped complex, which could hybridize with a molecular beacon (MB) and form a DNA duplex, leading to the open state of the MB and generating a fluorescence signal. Subsequently, with further assistance of isothermal recycling amplification strategies, the designed aptamer sensing platform showed an increment of fluorescence. As a benefit of this amplified strategy, the limit of detection (LOD) was lowered to 0.74 ng/mL, which is much lower than previous reports. This strategy not only offers a new simple, specific, and efficient platform to quantify the target protein in low concentrations, but also shows a powerful approach without multiple washing steps, as well as a precious implementation that has the potential to be integrated into portable, low-cost, and simplified devices for diagnostic applications.
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Affiliation(s)
- Qiao Yu
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Fenfen Zhai
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
- Shandong Provincial Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China.
| | - Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China.
| | - Zonghua Wang
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
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Ruiz-Tórtola Á, Prats-Quílez F, González-Lucas D, Bañuls MJ, Maquieira Á, Wheeler G, Dalmay T, Griol A, Hurtado J, Bohlmann H, Götzen R, García-Rupérez J. Experimental study of the evanescent-wave photonic sensors response in presence of molecular beacon conformational changes. J Biophotonics 2018; 11:e201800030. [PMID: 29664230 DOI: 10.1002/jbio.201800030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/12/2018] [Indexed: 05/20/2023]
Abstract
An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes-upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors-is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them. The different photonic sensing responses obtained toward the target oligonucleotide detection, when the streptavidin molecule was bound to the MB probes or not, demonstrate the conformational change suffered by the MB upon hybridization, which promotes the displacement of the streptavidin molecule away from the surface of the photonic sensing structure.
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Affiliation(s)
- Ángela Ruiz-Tórtola
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
| | | | - Daniel González-Lucas
- Departamento de Química, IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Valencia, Spain
| | - María-José Bañuls
- Departamento de Química, IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Valencia, Spain
| | - Ángel Maquieira
- Departamento de Química, IDM, Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Valencia, Spain
| | - Guy Wheeler
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Amadeu Griol
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
| | - Juan Hurtado
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
| | - Helge Bohlmann
- microTEC Gesellschaft für Mikrotechnologie mbH, Duisburg, Germany
| | - Reiner Götzen
- microTEC Gesellschaft für Mikrotechnologie mbH, Duisburg, Germany
| | - Jaime García-Rupérez
- Nanophotonics Technology Center, Universitat Politècnica de València, Valencia, Spain
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Lio DCS, Liu C, Wiraja C, Qiu B, Fhu CW, Wang X, Xu C. Molecular Beacon Gold Nanosensors for Leucine-Rich Alpha-2-Glycoprotein-1 Detection in Pathological Angiogenesis. ACS Sens 2018; 3:1647-1655. [PMID: 30095245 DOI: 10.1021/acssensors.8b00321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leucine-rich alpha-2-glycoprotein-1 (Lrg1) is an emerging biomarker for angiogenesis. Its expression in ocular tissues is up-regulated in both human patients with proliferative diabetic retinopathy and rodent models of pathological angiogenesis. However, there is no existing sensor that allows visualization and monitoring of Lrg1 expression noninvasively and in real time. Herein, we report a nucleic acid-gold nanorod-based nanosensor for the noninvasive monitoring of cellular Lrg1 expression in angiogenesis. Specifically, this platform is constructed by covalently conjugating molecular beacons onto gold nanorods, which prequench the fluorophores on the molecular beacons. Upon intracellular entry and endosomal escape, the complexes interact with cellular Lrg1 mRNA through hybridization of the loop area of the molecular beacons. This complexation distances the fluorophores from nanorod and restores the prequenched fluorescence. The reliability of this platform is confirmed by examining the increased Lrg1 expression in migrating keratinocytes and the Lrg1 gene changes in different postnatal stages of mouse retinal vasculature growth in the mouse retina model.
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Affiliation(s)
- Daniel Chin Shiuan Lio
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
- NTU-Northwestern Institute for Nanomedicine, Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Chenghao Liu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Christian Wiraja
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Beiying Qiu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Dr, Singapore 138673, Singapore
| | - Chee Wai Fhu
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Xiaomeng Wang
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore 636921, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, 61 Biopolis Dr, Singapore 138673, Singapore
- Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower Level 6, Singapore 169856
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1 V 9EL, United Kingdom
| | - Chenjie Xu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
- NTU-Northwestern Institute for Nanomedicine, Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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Turner-Bridger B, Jakobs M, Muresan L, Wong HH, Franze K, Harris WA, Holt CE. Single-molecule analysis of endogenous β-actin mRNA trafficking reveals a mechanism for compartmentalized mRNA localization in axons. Proc Natl Acad Sci U S A 2018; 115:E9697-706. [PMID: 30254174 DOI: 10.1073/pnas.1806189115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
De novo protein synthesis in neuronal axons plays important roles in neural circuit formation, maintenance, and disease. Key to the selectivity of axonal protein synthesis is whether an mRNA is present at the right place to be translated, but the mechanisms behind axonal mRNA localization remain poorly understood. In this work, we quantitatively analyze the link between axonal β-actin mRNA trafficking and its localization patterns. By developing a single-molecule approach to live-image β-actin mRNAs in axons, we explore the biophysical drivers behind β-actin mRNA motion and uncover a mechanism for generating increased density at the axon tip by differences in motor protein-driven transport speeds. These results provide mechanistic insight into the control of local translation through mRNA trafficking. During embryonic nervous system assembly, mRNA localization is precisely regulated in growing axons, affording subcellular autonomy by allowing controlled protein expression in space and time. Different sets of mRNAs exhibit different localization patterns across the axon. However, little is known about how mRNAs move in axons or how these patterns are generated. Here, we couple molecular beacon technology with highly inclined and laminated optical sheet microscopy to image single molecules of identified endogenous mRNA in growing axons. By combining quantitative single-molecule imaging with biophysical motion models, we show that β-actin mRNA travels mainly as single copies and exhibits different motion-type frequencies in different axonal subcompartments. We find that β-actin mRNA density is fourfold enriched in the growth cone central domain compared with the axon shaft and that a modicum of directed transport is vital for delivery of mRNA to the axon tip. Through mathematical modeling we further demonstrate that directional differences in motor-driven mRNA transport speeds are sufficient to generate β-actin mRNA enrichment at the growth cone. Our results provide insight into how mRNAs are trafficked in axons and a mechanism for generating different mRNA densities across axonal subcompartments.
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Mohamad NA, Mustafa S, Khairil Mokhtar NF, El Sheikha AF. Molecular beacon-based real-time PCR method for detection of porcine DNA in gelatin and gelatin capsules. J Sci Food Agric 2018; 98:4570-4577. [PMID: 29505123 DOI: 10.1002/jsfa.8985] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The pharmaceutical industry has boosted gelatin consumption worldwide. This is supported by the availability of cost-effective gelatin production from porcine by-products. However, cross-contamination of gelatin materials, where porcine gelatin was unintentionally included in the other animal sources of gelatin, has caused significant concerns about halal authenticity. The real-time polymerase chain reaction (PCR) has enabled a highly specific and sensitive animal species detection method in various food products. Hence, such a technique was employed in the present study to detect and quantify porcine DNA in gelatin using a molecular beacon probe, with differences in performance between mitochondrial (cytochrome b gene) and chromosomal DNA-(MPRE42 repetitive element) based porcine-specific PCR assays being compared. RESULTS A higher sensitivity was observed in chromosomal DNA (MPRE-PCR assay), where this assay allows the detection of gelatin DNA at amounts as as low as 1 pg, whereas mitochondrial DNA (CBH-PCR assay) can only detect at levels down to 10 pg of gelatin DNA. When an analysis with commercial gelatin and gelatin capsule samples was conducted, the same result was observed, with a significantly more sensitive detection being provided by the repetitive element of chromosomal DNA. CONCLUSION The present study has established highly sensitive DNA-based porcine detection systems derived from chromosomal DNA that are feasible for highly processed products such as gelatin and gelatin capsules containing a minute amount of DNA. This sensitive detection method can also be implemented to assist the halal authentication process of various food products available on the market. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Nurhidayatul Asma Mohamad
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Putra Infoport, Selangor Darul Ehsan, Malaysia
| | - Shuhaimi Mustafa
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Putra Infoport, Selangor Darul Ehsan, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor Darul Ehsan, Malaysia
| | - Nur Fadhilah Khairil Mokhtar
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Putra Infoport, Selangor Darul Ehsan, Malaysia
| | - Aly Farag El Sheikha
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Food Science and Technology, Faculty of Agriculture, Minufiya University, Shibin El Kom, Minufiya Government, Egypt
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Sawamura K, Hashimoto M. A Fluorescence Quenching Assay Based on Molecular Beacon Formation through a Ligase Detection Reaction for Facile and Rapid Detection of Point Mutations. ANAL SCI 2018; 33:1457-1460. [PMID: 29225240 DOI: 10.2116/analsci.33.1457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A fluorescence quenching assay based on a ligase detection reaction was developed for facile and rapid detection of point mutations present in a mixed population of non-variant DNA. If the test DNA carried a targeted mutation, then the two allele-specific primers were ligated to form a molecular beacon resulting in the expected fluorescence quenching signatures. Using this method, we successfully detected as low as 5% mutant DNA in a mixture of wild-type DNA (t test at 99% confidence level).
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Affiliation(s)
- Kensuke Sawamura
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
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Sachdev D, Wasnik K, Patel AL, Sonkar SC, Desai P, Mania-Pramanik J, Kerkar S, Sethi S, Sharma N, Mittal P, Ghope P, Khandhari A, Saluja D. Multi-centric validation of an in-house-developed beacon-based PCR diagnostic assay kit for Chlamydia and Neisseria and portable fluorescence detector. J Med Microbiol 2018; 67:1287-1293. [PMID: 30051801 DOI: 10.1099/jmm.0.000803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE The development of an accurate, sensitive, specific, rapid, reproducible, stable-at-room-temperature and cost-effective diagnostic kit, and a low-cost portable fluorescence detector to fulfil the requirements of diagnostic facilities in developing countries. METHODS We developed the 'Chlamy and Ness CT/NG kit' based on molecular beacons for the detection of Chlamydia trachomatis (CT) and Neisseriagonorrhoeae (NG). Multi-centric evaluation of the CT/NG kit was performed using the commercially available nucleic acid amplification test (NAAT)-based FTD Urethritis basic kit for comparison from December 2014 to November 2016. The stability of the kit reagents at 4 and 37 ˚C and the inter-day reproducibility of results were also analysed. RESULTS The sensitivity and specificity of the kit were found to be 95.83 and 100.00 % for the detection of C. trachomatis and 93.24 and 99.75 % for N. gonorrhoeae, respectively, when tested against the commercial kit. The positive predictive value (PPV) was 100.00 and 98.57 %, whereas the negative predictive value (NPV) was 99.54 and 98.79 % for C. trachomatis and N. gonorrhoeae, respectively. Analysis of the kappa statistics enhanced the 'inter-rater' κ=0.976 for Chlamydia and κ=0.943 for Neisseria. CONCLUSION Our kit was found to be as sensitive and specific as commercially available kits. Its low cost and ease of use will make it suitable for the routine diagnosis of C. trachomatis and N. gonorrhoeae in the resource-limited settings of developing countries.
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Affiliation(s)
- Divya Sachdev
- 1Dr B. R. Ambedkar Center for Biomedical research (ACBR), University of Delhi, Delhi 110007, India
| | - Kirti Wasnik
- 2DSS Imagetech Pvt Ltd, A5-Mohan Co-Op Industrial Estate, New Delhi 110044, India
| | - Achchhe Lal Patel
- 1Dr B. R. Ambedkar Center for Biomedical research (ACBR), University of Delhi, Delhi 110007, India
| | - Subash C Sonkar
- 1Dr B. R. Ambedkar Center for Biomedical research (ACBR), University of Delhi, Delhi 110007, India
- 3Department of Obstetrics and Gynecology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India
| | - Parul Desai
- 2DSS Imagetech Pvt Ltd, A5-Mohan Co-Op Industrial Estate, New Delhi 110044, India
| | - Jayanti Mania-Pramanik
- 4Infectious Diseases Biology, ICMR National Institute for Research in Reproductive Health (NIRRH), Mumbai 400012, India
| | - Shilpa Kerkar
- 4Infectious Diseases Biology, ICMR National Institute for Research in Reproductive Health (NIRRH), Mumbai 400012, India
| | - Sunil Sethi
- 5Post Graduate Institute of Medical Education and Research (PGIMR), Chandigarh 160012, India
| | - Nandita Sharma
- 5Post Graduate Institute of Medical Education and Research (PGIMR), Chandigarh 160012, India
| | - Pratima Mittal
- 3Department of Obstetrics and Gynecology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India
| | - Priti Ghope
- 3Department of Obstetrics and Gynecology, Vardhman Mahavir Medical College and Safdarjung Hospital, Delhi 110029, India
| | - Ajay Khandhari
- 2DSS Imagetech Pvt Ltd, A5-Mohan Co-Op Industrial Estate, New Delhi 110044, India
| | - Daman Saluja
- 1Dr B. R. Ambedkar Center for Biomedical research (ACBR), University of Delhi, Delhi 110007, India
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Lee J, Kwon MH, Kim JA, Rhee WJ. Detection of exosome miRNAs using molecular beacons for diagnosing prostate cancer. Artif Cells Nanomed Biotechnol 2018; 46:S52-S63. [PMID: 30033809 DOI: 10.1080/21691401.2018.1489263] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Prostate cancer is the fifth leading cause of cancer-related deaths among males worldwide. However, the biomarker for diagnosing prostate cancer that is used currently has limitations that must be overcome. Recently, several studies have demonstrated that the cancer liquid biopsy can be implemented by using exosome miRNAs. However, the current methods for the detection of exosome miRNAs are time-consuming, expensive, and laborious. Thus, we investigated a novel method for diagnosing prostate cancer that involves the use of molecular beacons for the in situ detection of miRNAs in exosomes from prostate cancer cells. We chose miRNA-375 and miRNA-574-3p as the target miRNAs for prostate cancer, and these markers in exosomes produced by prostate cancer cells including DU145 and PC-3 were successfully detected using molecular beacons. High fluorescent signals were obtained from MB and miRNA hybridization in exosomes in a concentration-dependent manner. In addition, exosome miRNAs can be detected even in the presence of human urine, so this method can be applied directly using human urine to perform liquid biopsies for prostate cancer. Overall, the in situ detection of exosome miRNAs using molecular beacons can be developed as a simple, cost effective, and non-invasive liquid biopsy for diagnosing prostate cancer.
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Affiliation(s)
- Jinhee Lee
- a Division of Bioengineering , Incheon National University , Incheon , Republic of Korea
| | - Min Hee Kwon
- a Division of Bioengineering , Incheon National University , Incheon , Republic of Korea
| | - Jeong Ah Kim
- b Biomedical Omics Group , Korea Basic Science Institute , Cheongju , Republic of Korea
| | - Won Jong Rhee
- a Division of Bioengineering , Incheon National University , Incheon , Republic of Korea
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38
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Liu Y, Kannegulla A, Wu B, Cheng LJ. Quantum Dot Fullerene-Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection. ACS Appl Mater Interfaces 2018; 10:18524-18531. [PMID: 29763288 DOI: 10.1021/acsami.8b03552] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Spherical fullerene (C60) can quench the fluorescence of a quantum dot (QD) through energy-transfer and charge-transfer processes, with the quenching efficiency regulated by the number of proximate C60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C60-labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C60-based MBs carried by magnetic nanoparticles. The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance three-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (<10 min) with a small sample volume (1-10 μL). The high signal-to-noise ratio produced by the QD-C60 pairs and magnetic concentration yielded a detection limit of 100 fM (∼106 target DNA copies for a 10 μL analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.
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Affiliation(s)
- Ye Liu
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Akash Kannegulla
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Bo Wu
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Li-Jing Cheng
- Electrical Engineering and Computer Science , Oregon State University , Corvallis , Oregon 97331 , United States
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39
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Li Y, Gao X, Yu Z, Liu B, Pan W, Li N, Tang B. Reversing Multidrug Resistance by Multiplexed Gene Silencing for Enhanced Breast Cancer Chemotherapy. ACS Appl Mater Interfaces 2018; 10:15461-15466. [PMID: 29663807 DOI: 10.1021/acsami.8b02800] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multidrug resistance (MDR), as one of the main problems in clinical breast cancer chemotherapy, is closely related with the over expression of drug efflux transporter P-glycoprotein (P-gp). In this study, a novel drug-loaded nanosystem was developed for inhibiting the P-gp expression and reversing MDR by multiplexed gene silencing, which composes of graphene oxide (GO) modified with two molecular beacons (MBs) and Doxorubicin (Dox). When the nanosystem was uptaken by the MDR breast cancer cells, Dox was released in the acidic endosomes and MBs were hybridized with target sequences. The intracellular multidrug resistance 1 (MDR1) mRNA and upstream erythroblastosis virus E26 oncogene homolog 1 (ETS1) mRNA can be silenced by MBs, which can effectively inhibit the expression of P-gp and further prevent the efflux of Dox and reverse MDR. In vitro and in vivo studies indicated that the strategy of reversing MDR by multiplexed gene silencing could obviously increase MCF-7/Adr cells' Dox accumulation and enormously enhance the therapeutic efficacy of MDR breast cancer chemotherapy.
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Affiliation(s)
- Yanli Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
| | - Xiaonan Gao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
| | - Zhengze Yu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
| | - Bo Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Molecular and Nano Science , Shandong Normal University , Jinan 250014 , P. R. China
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Guo B, Sheng Y, Zhou K, Liu Q, Liu L, Wu HC. Analyte-Triggered DNA-Probe Release from a Triplex Molecular Beacon for Nanopore Sensing. Angew Chem Int Ed Engl 2018; 57:3602-3606. [PMID: 29488675 DOI: 10.1002/anie.201711690] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/14/2018] [Indexed: 12/26/2022]
Abstract
A new nanopore sensing strategy based on triplex molecular beacon was developed for the detection of specific DNA or multivalent proteins. The sensor is composed of a triplex-forming molecular beacon and a stem-forming DNA component that is modified with a host-guest complex. Upon target DNA hybridizing with the molecular beacon loop or multivalent proteins binding to the recognition elements on the stem, the DNA probe is released and produces highly characteristic current signals when translocated through α-hemolysin. The frequency of current signatures can be used to quantify the concentrations of the target molecules. This sensing approach provides a simple, quick, and modular tool for the detection of specific macromolecules with high sensitivity and excellent selectivity. It may find useful applications in point-of-care diagnostics with a portable nanopore kit in the future.
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Affiliation(s)
- Bingyuan Guo
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingying Sheng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Ke Zhou
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Quansheng Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Multidisciplinary Center, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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41
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Shi YJ, Wang LJ, Lee YC, Huang CH, Hu WP, Chang LS. A Turn-on Fluorescence Sensor for Heparin Detection Based on a Release of Taiwan Cobra Cardiotoxin from a DNA Aptamer or Adenosine-Based Molecular Beacon. Molecules 2018; 23:E460. [PMID: 29463054 DOI: 10.3390/molecules23020460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 11/17/2022] Open
Abstract
This study presents two sensitive fluorescent assays for sensing heparin on the basis of the electrostatic interaction between heparin and Naja naja atra cardiotoxin 3 (CTX3). Owing to CTX3-induced folded structure of an adenosine-based molecular beacon (MB) or a DNA aptamer against CTX3, a reduction in the fluorescent signal of the aptamer or MB 5'-end labeled with carboxyfluorescein (FAM) and 3'-end labeled with 4-([4-(dimethylamino)phenyl]azo)-benzoic acid (DABCYL) was observed upon the addition of CTX3. The presence of heparin and formation of the CTX3-heparin complex caused CTX3 detachment from the MB or aptamer, and restoration of FAM fluorescence of the 5'-FAM-and-3'-DABCYL-labeled MB and aptamer was subsequently noted. Moreover, the detection of heparin with these CTX3-aptamer and CTX3-MB sensors showed high sensitivity and selectivity toward heparin over chondroitin sulfate and hyaluronic acid regardless of the presence of plasma. The limit of detection for heparin in plasma was determined to be 16 ng/mL and 15 ng/mL, respectively, at a signal-to-noise ratio of 3. This study validates the practical utility of the CTX3-aptamer and CTX3-MB systems for determining the concentration of heparin in a biological matrix.
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42
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Ma C, Lv X, Wang K, Jin S, Liu H, Wu K, Zeng W. Simple fluorescence-based detection of protein kinase A activity using a molecular beacon probe. Bioengineered 2017; 8:716-722. [PMID: 28594266 DOI: 10.1080/21655979.2017.1338219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Protein kinase A was detected by quantifying the amount of ATP used after a protein kinase reaction. The ATP assay was performed using the T4 DNA ligase and a molecular beacon (MB). In the presence of ATP, DNA ligase catalyzed the ligation of short DNA. The ligation product then hybridized to MB, resulting in a fluorescence enhancement of the MB. This assay was capable of determining protein kinase A in the range of 12.5∼150 nM, with a detection limit of 1.25 nM. Furthermore, this assay could also be used to investigate the effect of genistein on protein kinase A. It was a universal, non-radioisotopic, and homogeneous method for assaying protein kinase A.
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Affiliation(s)
- Changbei Ma
- a State Key Laboratory of Medical Genetics & School of Life Sciences , Central South University , Changsha , China.,b State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha , China
| | - Xiaoyuan Lv
- b State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha , China
| | - Kemin Wang
- b State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha , China
| | - Shunxin Jin
- a State Key Laboratory of Medical Genetics & School of Life Sciences , Central South University , Changsha , China
| | - Haisheng Liu
- a State Key Laboratory of Medical Genetics & School of Life Sciences , Central South University , Changsha , China
| | - Kefeng Wu
- a State Key Laboratory of Medical Genetics & School of Life Sciences , Central South University , Changsha , China
| | - Weimin Zeng
- a State Key Laboratory of Medical Genetics & School of Life Sciences , Central South University , Changsha , China
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43
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Young ST, Moore JR, Bishop CP. A Rapid, Confirmatory Test for Body Fluid Identification. J Forensic Sci 2017; 63:511-516. [PMID: 28718918 DOI: 10.1111/1556-4029.13544] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 11/30/2022]
Abstract
We have developed a technique that allows investigators to confirm the presence of blood, semen, and/or saliva in a crime scene sample. It is a confirmatory test where multiple samples can be processed in less than an hour, and it is potentially portable, permitting samples to be processed at the crime scene. Samples at a scene giving a positive result can be further processed while those failing to do so may be ignored. There is a large and growing backlog of DNA evidence in the USA, slowing down the criminal justice system. This backlog has continued to grow despite an increase in the ability to process evidence faster. This technique uses quantum dot molecular beacons to test for tissue-specific RNA species, identifying particular body fluids. We have demonstrated the tissue specificity of molecular beacons for blood, semen, and saliva.
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Affiliation(s)
- Stephanie T Young
- Department of Biology, West Virginia University, PO Box 6057, Morgantown, WV, 26506-6057
| | - Joshua R Moore
- Department of Biology, West Virginia University, PO Box 6057, Morgantown, WV, 26506-6057
| | - Clifton P Bishop
- Department of Biology, West Virginia University, PO Box 6057, Morgantown, WV, 26506-6057
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Ki J, Jang E, Han S, Shin MK, Kang B, Huh YM, Haam S. Instantaneous pH-Boosted Functionalization of Stellate Gold Nanoparticles for Intracellular Imaging of miRNA. ACS Appl Mater Interfaces 2017; 9:17702-17709. [PMID: 28524648 DOI: 10.1021/acsami.6b16452] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Various types of nanoprobes have recently been utilized to monitor living organisms by detecting and imaging intracellular biomarkers, such as microRNAs (miRs). We here present a simple one-pot method to prepare stellate gold nanoparticles functionalized with miR-detecting molecular beacons (SGNP-MBs); low pH conditions permitted the rapid-high loading of MBs on the surface of SGNPs. Compared to the conventional gold nanoparticle-based MBs, SGNPs carried a 4.5-fold higher load of MBs and exhibited a 6.4-fold higher cellular uptake. We demonstrated that SGNP-MBs were successfully internalized in human gastric cancer cell lines and could be used to accurately detect and image intracellular miRs in an miR-specific manner. Furthermore, the relative levels of intracellular miRs in three different cell lines expressing miR-10b (high, moderate, and low levels) could be monitored using SGNP-MBs. Consequently, these results indicated that SGNP-MBs could have applications as highly potent, efficient nanoprobes to assess intracellular miR levels in living cells.
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Affiliation(s)
- Jisun Ki
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Eunji Jang
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Seungmin Han
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Moo-Kwang Shin
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Byunghoon Kang
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University , Seoul 120-752, South Korea
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, Yonsei University , Yonsei-ro 50, Seoul 120-749, South Korea
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Li WM, Chan CM, Miller AL, Lee CH. Dual Functional Roles of Molecular Beacon as a MicroRNA Detector and Inhibitor. J Biol Chem 2017; 292:3568-3580. [PMID: 28100783 PMCID: PMC5339743 DOI: 10.1074/jbc.m116.765776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/04/2017] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs are essential in many cellular processes. The ability to detect microRNAs is important for understanding its function and biogenesis. This study is aimed at using a molecular beacon to detect miR-430 in developing zebrafish embryos as a proof of principle. miR-430 is crucial for the clearance of maternal mRNA during maternal zygotic transition in embryonic development. Despite its known function, the temporal and spatial expression of miR-430 remains unclear. We used various imaging techniques, including laser scanning confocal microscopy, spinning disk, and lightsheet microscopy, to study the localization of miR-430 and any developmental defects possibly caused by the molecular beacon. Our results show that miR-430 is expressed early in development and is localized in distinct cytoplasmic granules where its target mRNA can be detected. We also show that the designed molecular beacon can inhibit the function of miR-430 and cause developmental defect in the brain, notochord, heart, and kidney, depending on the delivery site within the embryo, suggesting that miR-430 plays a diverse role in embryonic morphogenesis. When compared with morpholino, molecular beacon is 2 orders of magnitude more potent in inhibiting miR-430. Thus, our results reveal that in addition to being used as a valuable tool for the detection of microRNAs in vivo, molecular beacons can also be employed to inhibit microRNAs in a specific manner.
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Affiliation(s)
- Wai Ming Li
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada and
| | - Ching-Man Chan
- the Division of Life Science and Key State Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Andrew L Miller
- the Division of Life Science and Key State Laboratory for Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Chow H Lee
- From the Chemistry Program, University of Northern British Columbia, Prince George, British Columbia V2N 4Z9, Canada and
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Shi YJ, Chen YJ, Hu WP, Chang LS. Detection of Naja atra Cardiotoxin Using Adenosine-Based Molecular Beacon. Toxins (Basel) 2017; 9:toxins9010024. [PMID: 28067855 PMCID: PMC5308256 DOI: 10.3390/toxins9010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 01/02/2017] [Accepted: 01/04/2017] [Indexed: 02/07/2023] Open
Abstract
This study presents an adenosine (A)-based molecular beacon (MB) for selective detection of Naja atra cardiotoxin (CTX) that functions by utilizing the competitive binding between CTX and the poly(A) stem of MB to coralyne. The 5′- and 3′-end of MB were labeled with a reporter fluorophore and a non-fluorescent quencher, respectively. Coralyne induced formation of the stem-loop MB structure through A2-coralyne-A2 coordination, causing fluorescence signal turn-off due to fluorescence resonance energy transfer between the fluorophore and quencher. CTX3 could bind to coralyne. Moreover, CTX3 alone induced the folding of MB structure and quenching of MB fluorescence. Unlike that of snake venom α-neurotoxins, the fluorescence signal of coralyne-MB complexes produced a bell-shaped concentration-dependent curve in the presence of CTX3 and CTX isotoxins; a turn-on fluorescence signal was noted when CTX concentration was ≤80 nM, while a turn-off fluorescence signal was noted with a further increase in toxin concentrations. The fluorescence signal of coralyne-MB complexes yielded a bell-shaped curve in response to varying concentrations of N. atra crude venom but not those of Bungarus multicinctus and Protobothrops mucrosquamatus venoms. Moreover, N. nigricollis venom also functioned as N. atra venom to yield a bell-shaped concentration-dependent curve of MB fluorescence signal, again supporting that the hairpin-shaped MB could detect crude venoms containing CTXs. Taken together, our data validate that a platform composed of coralyne-induced stem-loop MB structure selectively detects CTXs.
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Affiliation(s)
- Yi-Jun Shi
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Ying-Jung Chen
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Wan-Ping Hu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Long-Sen Chang
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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Hwang JY, Kim ST, Han HS, Kim K, Han JS. Optical Aptamer Probes of Fluorescent Imaging to Rapid Monitoring of Circulating Tumor Cell. Sensors (Basel) 2016; 16:E1909. [PMID: 27886058 DOI: 10.3390/s16111909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/02/2016] [Accepted: 11/02/2016] [Indexed: 02/08/2023]
Abstract
Fluorescence detecting of exogenous EpCAM (epithelial cell adhesion molecule) or muc1 (mucin1) expression correlated to cancer metastasis using nanoparticles provides pivotal information on CTC (circulating tumor cell) occurrence in a noninvasive tool. In this study, we study a new skill to detect extracellular EpCAM/muc1 using quantum dot-based aptamer beacon (QD-EpCAM/muc1 ALB (aptamer linker beacon). The QD-EpCAM/muc1 ALB was designed using QDs (quantum dots) and probe. The EpCAM/muc1-targeting aptamer contains a Ep-CAM/muc1 binding sequence and BHQ1 (black hole quencher 1) or BHQ2 (black hole quencher2). In the absence of target EpCAM/muc1, the QD-EpCAM/muc1 ALB forms a partial duplex loop-like aptamer beacon and remained in quenched state because the BHQ1/2 quenches the fluorescence signal-on of the QD-EpCAM/muc1 ALB. The binding of EpCAM/muc1 of CTC to the EpCAM/muc1 binding aptamer sequence of the EpCAM/muc1-targeting oligonucleotide triggered the dissociation of the BHQ1/2 quencher and subsequent signal-on of a green/red fluorescence signal. Furthermore, acute inflammation was stimulated by trigger such as caerulein in vivo, which resulted in increased fluorescent signal of the cy5.5-EpCAM/muc1 ALB during cancer metastasis due to exogenous expression of EpCAM/muc1 in Panc02-implanted mouse model.
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48
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Ding Q, Zhan Q, Zhou X, Zhang T, Xing D. Theranostic Upconversion Nanobeacons for Tumor mRNA Ratiometric Fluorescence Detection and Imaging-Monitored Drug Delivery. Small 2016; 12:5944-5953. [PMID: 27647762 DOI: 10.1002/smll.201601724] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/18/2016] [Indexed: 06/06/2023]
Abstract
Remote optical detection and imaging of specific tumor-related biomarkers and simultaneous activation of therapy according to the expression level of the biomarkers in tumor site with theranostic probes should be an effective modality for treatment of cancers. Herein, an upconversion nanobeacon (UCNPs-MB/Dox) is proposed as a new theranostic nanoprobe to ratiometrically detect and visualize the thymidine kinase 1 (TK1) mRNA that can simultaneously trigger the Dox release to activate the chemotherapy accordingly. UCNPs-MB/Dox is constructed with the conjugation of a TK1 mRNA-specific molecular beacon (MB) bearing a quencher (BHQ-1) and an alkene handle modified upconversion nanoparticle (UCNP) through click reaction and subsequently loading with a chemotherapy drug (Dox). With this nanobeacon, quantitative ratiometric upconversion detection of the target with high sensitivity and selectivity as well as the target triggered Dox release in vitro is demonstrated. The sensitive and selective ratiometric detection and imaging of TK1 mRNA under the irradiation of near infrared light (980 nm) and the mRNA-dependent release of Dox for chemotherapy in the tumor MCF-7 cells and A549 cells are also shown. This work provides a smart and robust platform for gene-related tumor theranostics.
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Affiliation(s)
- Qianwen Ding
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, P. R. China
| | - Qiuqiang Zhan
- Centre for Optical and Electromagnetic Research, South China Academy of Advanced Optoelectronics, South China Normal University, Guangzhou, 510006, P. R. China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, P. R. China
| | - Tao Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, P. R. China
| | - Da Xing
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, P. R. China
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Junager NPL, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. Sensors (Basel) 2016; 16:s16081173. [PMID: 27472344 PMCID: PMC5017339 DOI: 10.3390/s16081173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023]
Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
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Affiliation(s)
- Nina P L Junager
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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50
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Vaidyanathan S, Chen J, Orr BG, Banaszak Holl MM. Cationic Polymer Intercalation into the Lipid Membrane Enables Intact Polyplex DNA Escape from Endosomes for Gene Delivery. Mol Pharm 2016; 13:1967-78. [PMID: 27111496 DOI: 10.1021/acs.molpharmaceut.6b00139] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Developing improved cationic polymer-DNA polyplexes for gene delivery requires improved understanding of DNA transport from endosomes into the nucleus. Using a FRET-capable oligonucleotide molecular beacon (OMB), we monitored the transport of intact DNA to cell organelles. We observed that for effective (jetPEI) and ineffective (G5 PAMAM) vectors, the fraction of cells displaying intact OMB in the cytosol (jetPEI ≫ G5 PAMAM) quantitatively predicted the fraction expressing transgene (jetPEI ≫ G5 PAMAM). Intact OMB delivered with PAMAM and confined to endosomes could be released to the cytosol by the subsequent addition of L-PEI, with a corresponding 10-fold increase in transgene expression. These results suggest that future vector development should optimize vectors for intercalation into, and destabilization of, the endosomal membrane. Finally, the study highlights a two-step strategy in which the pDNA is loaded in cells using one vector and endosomal release is mediated by a second agent.
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Affiliation(s)
- Sriram Vaidyanathan
- Departments of †Biomedical Engineering and ‡Chemistry and Programs in §Applied Physics and ⊥Macromolecular Science and Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Junjie Chen
- Departments of †Biomedical Engineering and ‡Chemistry and Programs in §Applied Physics and ⊥Macromolecular Science and Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bradford G Orr
- Departments of †Biomedical Engineering and ‡Chemistry and Programs in §Applied Physics and ⊥Macromolecular Science and Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Mark M Banaszak Holl
- Departments of †Biomedical Engineering and ‡Chemistry and Programs in §Applied Physics and ⊥Macromolecular Science and Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
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