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Sun D, Wu S, Martin JP, Tayutivutikul K, Du G, Combs C, Darland DC, Zhao JX. Streamlined synthesis of potential dual-emissive fluorescent silicon quantum dots (SiQDs) for cell imaging. RSC Adv 2023; 13:26392-26405. [PMID: 37671347 PMCID: PMC10476025 DOI: 10.1039/d3ra03669c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/27/2023] [Indexed: 09/07/2023] Open
Abstract
One of the current challenges of working with nanomaterials in bioapplications is having a tool that is biocompatible (non-toxic) and produces stable, intense fluorescence for bioimaging. To address these challenges, we have developed a streamlined and one-pot synthetic route for silicon-based quantum dots (SiQDs) using a hydrothermal method. Part of our unique approach for designing the SiQDs was to incorporate (3-aminopropyl) triethoxysilane (APTES), which is an amphipathic molecule with hydroxyl and amine functional groups available for modification. In order to reduce the toxicity of APTES, we chose glucose as a reducing agent for the reaction. The resulting SiQDs produced potent, stable, potential dual-emissive fluorescence emission peaks in the visible and near-infrared (NIR) ranges. Both peaks could be used as distinguishing fluorescence signals for bioimaging, separately or in combination. The physical and optical properties of the SiQDs were determined under a range of environmental conditions. The morphology, surface composition, and electronic structure of the SiQDs were characterized using high resolution-transmission electronic microscopy (HR-TEM), energy dispersive X-ray spectroscopy (EDS), Fourier-transform infrared spectroscopy (FT-IR), X-ray powder diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The stability of the SiQDs was evaluated under a wide range of pHs. The biocompatibility and imaging potential of the SiQDs were tested in microvascular endothelial cells (MVEC), neural stem cells (NSC), and RAW 264.7 macrophage cells. The images obtained revealed different subcellular localizations, particularly during cell division, with distinct fluorescence intensities. The results demonstrated that SiQDs are a promising, non-toxic labeling tool for a variety of cell types, with the added advantage of having dual emission peaks both in visible and NIR ranges for bioimaging.
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Affiliation(s)
- Di Sun
- Department of Chemistry, University of North Dakota Grand Forks ND 58202 USA
| | - Steven Wu
- Department of Chemistry, University of North Dakota Grand Forks ND 58202 USA
- Department of Chemistry, University of South Dakota Vermillion SD 57069 USA
| | - Jeremy P Martin
- Department of Biology, University of North Dakota Grand Forks ND 58202 USA
| | | | - Guodong Du
- Department of Chemistry, University of North Dakota Grand Forks ND 58202 USA
| | - Colin Combs
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota Grand Forks ND 58202 USA
| | - Diane C Darland
- Department of Biology, University of North Dakota Grand Forks ND 58202 USA
| | - Julia Xiaojun Zhao
- Department of Chemistry, University of North Dakota Grand Forks ND 58202 USA
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2
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Usharani N, Kanth SV, Saravanan N. Current nanotechnological strategies using lipids, carbohydrates, proteins and metal conjugates-based carrier systems for diagnosis and treatment of tuberculosis - A review. Int J Biol Macromol 2023; 227:262-272. [PMID: 36521715 DOI: 10.1016/j.ijbiomac.2022.12.087] [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: 08/23/2022] [Revised: 12/03/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Tuberculosis is a fatal disease caused by Mycobacterium tuberculosis with highest morbidity and mortality every year. The evolution of anti-TB drugs is promising in controlling and treating TB. Yet, the drug response varies depending on the bacterial load and host immunological profiles. The prolonged anti-TB treatment regimen and high pill burden leads to poor adherence to treatment and acquired drug resistance. In the clinical arena, sustainable nanotechnology improves the targeted strategies leading to enhance therapeutic recovery with minimum treatment duration and virtuous drug adherence. Determinants of nanosystems are the size, nature, formulation techniques, stable dosing patterns, bioavailability and toxicity. In the treatment of chronic illness, nanomedicines inclusive of biological macromolecules such as lipids, peptides, and nucleic acids occur to be a successive alternative to synthetic carriers. Most biological nanomaterials possess antimicrobial properties with other intrinsic characteristics. Recently, the pulmonary delivery of anti-TB drugs through polymeric nanocarrier systems is shown to be effective in achieving optimal drug levels in lungs for longer duration, enhanced tissue permeation and sustained systemic clearance. This thematic review provides a holistic insight into the nanodelivery systems pertinent to the therapeutic applications in pulmonary tuberculosis describing the choice of carriers, optimized process, metabolic action and excretion processes.
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Affiliation(s)
- Nagarajan Usharani
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Swarna Vinodh Kanth
- Centre for Human and Organizational Resources Development, CSIR-Central Leather Research Institute, Chennai, India
| | - Natarajan Saravanan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai, India.
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3
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Shin JS, Li S. DNA-Immobilized Fluorescent Polystyrene Nanoparticles as Probes with Tunable Detection Limits. ACS Omega 2022; 7:48310-48319. [PMID: 36591202 PMCID: PMC9798753 DOI: 10.1021/acsomega.2c06498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
DNA-immobilized nanoparticle probes show high target specificity; thus, they are employed in various bioengineering and biomedicine applications. When the nanoparticles employed are dye-loaded polymer particles, the resulting probes have the additional benefit of biocompatibility and versatile surface properties. In this study, we construct DNA-immobilized fluorescent polystyrene (PS) nanoparticles through controlled surface reactions. PS nanoparticles with surface carboxyl groups are utilized, and amine-functionalized dye molecules and capture DNAs are covalently immobilized via a one-pot reaction. We show that the surface chemistry employed allows for quantitative control over the number of fluorescent dyes and DNA strands immobilized on the PS nanoparticle surfaces. The nanoparticles thus prepared are then used for DNA detection. The off state of the nanoprobe is achieved by hybridizing quencher-functionalized DNAs (Q-DNAs) to the capture DNAs immobilized on nanoparticle surfaces. Target-DNAs (T-DNAs) are detected by the displacement of the prehybridized Q-DNAs. The nanoprobes show successful detection of T-DNAs with high sequence specificity and long-term stability. They also show excellent detection sensitivity, and the detection limit can be tuned by adjusting the capture DNA-to-dye ratio.
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4
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Li S, Zhu L, Lin S, Xu W. Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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5
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Brown JWP, Alford RG, Walsh JC, Spinney RE, Xu SY, Hertel S, Berengut JF, Spenkelink LM, van Oijen AM, Böcking T, Morris RG, Lee LK. Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor. ACS Nano 2022; 16:6455-6467. [PMID: 35316035 DOI: 10.1021/acsnano.2c00699] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.
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Affiliation(s)
- James W P Brown
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Rokiah G Alford
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - James C Walsh
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard E Spinney
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Stephanie Y Xu
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Sophie Hertel
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Chemistry, University of Sydney, Sydney 2006, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Till Böcking
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard G Morris
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney 2052, Australia
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6
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Abstract
Rapid diagnosis is one key pillar to end tuberculosis (TB). Point-of-care tests (POCTs) facilitate early detection, immediate treatment, and reduced transmission of TB disease. This Review evaluates current diagnostic assays endorsed by the World Health Organization and identifies the gaps between existing conventional tests and the ideal POCT. We discuss the commercial development of new rapid tests and research studies on nonsputum-based diagnostic biomarkers from both pathogen and host. Last, we highlight advances in integrated microfluidics technology that may aid the development of new POCTs.
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Affiliation(s)
- Jia Mei Hong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Hyeyoung Lee
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Nishanth V Menon
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore.,Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Luke P Lee
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Berkeley Sensor and Actuator Center, University of California, Berkeley, Berkeley, CA 94720-1764, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Biophysics Graduate Program, University of California, Berkeley, Berkeley, CA 94720, USA.,Harvard Medical School, Brigham and Women's Hospital, Harvard Institute of Medicine, Harvard University, Boston, MA 02115, USA.,Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon, Korea
| | - Catherine W M Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Institute for Health Innovation & Technology (iHealthtech), National University of Singapore, Singapore 117599, Singapore
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7
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Geng H, Vilms Pedersen S, Ma Y, Haghighi T, Dai H, Howes PD, Stevens MM. Noble Metal Nanoparticle Biosensors: From Fundamental Studies toward Point-of-Care Diagnostics. Acc Chem Res 2022; 55:593-604. [PMID: 35138817 PMCID: PMC7615491 DOI: 10.1021/acs.accounts.1c00598] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Noble metal nanoparticles (NMNPs) have become firmly established as effective agents to detect various biomolecules with extremely high sensitivity. This ability stems from the collective oscillation of free electrons and extremely large electric field enhancement under exposure to light, leading to various light-matter interactions such as localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering. A remarkable feature of NMNPs is their customizability by mechanisms such as particle etching, growth, and aggregation/dispersion, yielding distinct color changes and excellent opportunities for colorimetric biosensing in user-friendly assays and devices. They are readily functionalized with a large variety of capping agents and biomolecules, with resultant bioconjugates often possessing excellent biocompatibility, which can be used to quantitatively detect analytes from physiological fluids. Furthermore, they can possess excellent catalytic properties that can achieve significant signal amplification through mechanisms such as the catalytic transformation of colorless substrates to colored reporters. The various excellent attributes of NMNP biosensors have put them in the spotlight for developing high-performance in vitro diagnostic (IVD) devices that are particularly well-suited to mitigate the societal threat that infectious diseases pose. This threat continues to dominate the global health care landscape, claiming millions of lives annually. NMNP IVDs possess the potential to sensitively detect infections even at very early stages with affordable and field-deployable devices, which will be key to strengthening infectious disease management. This has been the major focal point of current research, with a view to new avenues for early multiplexed detection of infectious diseases with portable devices such as smartphones, especially in resource-limited settings.In this Account, we provide an overview of our original inspiration and efforts in NMNP-based assay development, together with some more sophisticated IVD assays by ourselves and many others. Our work in the area has led to our recent efforts in developing IVDs for high-profile infectious diseases, including Ebola and HIV. We emphasize that integration with digital platforms represents an opportunity to establish and efficiently manage widespread testing, tracking, epidemiological intelligence, and data sharing backed by community participation. We highlight how digital technologies can address the limitations of conventional diagnostic technologies at the point of care (POC) and how they may be used to abate and contain the spread of infectious diseases. Finally, we focus on more recent integrations of noble metal nanoparticles with Raman spectroscopy for accurate, noninvasive POC diagnostics with improved sensitivity and specificity.
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Affiliation(s)
- Hongya Geng
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 171 77, Sweden
| | - Simon Vilms Pedersen
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Yun Ma
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Tabasom Haghighi
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Hongliang Dai
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, China
| | - Philip D Howes
- Division of Mechanical Engineering and Design, School of Engineering, London South Bank University, London SE1 0AA, U.K
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, U.K
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 171 77, Sweden
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8
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Gliddon HD, Kaforou M, Alikian M, Habgood-Coote D, Zhou C, Oni T, Anderson ST, Brent AJ, Crampin AC, Eley B, Heyderman R, Kern F, Langford PR, Ottenhoff THM, Hibberd ML, French N, Wright VJ, Dockrell HM, Coin LJ, Wilkinson RJ, Levin M. Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification. Front Immunol 2021; 12:637164. [PMID: 33763081 PMCID: PMC7982854 DOI: 10.3389/fimmu.2021.637164] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 12/02/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantification of the concentrations of signature transcripts in blood have not been reported, but would facilitate diagnostic test development. To identify minimal transcript signatures, we applied a transcript selection procedure to microarray data from African adults comprising 536 patients with TB, other diseases (OD) and latent TB (LTBI), divided into training and test sets. Signatures were further investigated using reverse transcriptase (RT)-digital PCR (dPCR). A four-transcript signature (GBP6, TMCC1, PRDM1, and ARG1) measured using RT-dPCR distinguished TB patients from those with OD (area under the curve (AUC) 93.8% (CI95% 82.2-100%). A three-transcript signature (FCGR1A, ZNF296, and C1QB) differentiated TB from LTBI (AUC 97.3%, CI95%: 93.3-100%), regardless of HIV. These signatures have been validated across platforms and across samples offering strong, quantitative support for their use as diagnostic biomarkers for TB.
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Affiliation(s)
- Harriet D Gliddon
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom.,National Public Health Speciality Training Programme, South West, United Kingdom
| | - Myrsini Kaforou
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Mary Alikian
- Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom.,Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Dominic Habgood-Coote
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Tolu Oni
- School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Suzanne T Anderson
- Brighton and Sussex Medical School, Brighton, United Kingdom.,Brighton and Malawi Liverpool Wellcome Trust Unit, Blantyre, Malawi
| | - Andrew J Brent
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom
| | - Amelia C Crampin
- Malawi Epidemiology and Intervention Research Unit, Chilumba, Malawi.,London School of Hygiene & Tropical Medicine, London, United Kingdom.,Karonga Prevention Study, Chilumba, Malawi
| | - Brian Eley
- Paediatric Infectious Diseases Unit, Red Cross War Memorial Children's Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
| | - Robert Heyderman
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Florian Kern
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom.,Brighton and Sussex University Hospitals National Health Service (NHS) Trust, Brighton, United Kingdom
| | - Paul R Langford
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Neil French
- Tropical and Infectious Disease Unit, Royal Liverpool and Broadgreen University Hospitals National Health Service (NHS) Trust, Liverpool, United Kingdom.,Centre for Global Vaccine Research, Institute of Infection & Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Victoria J Wright
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Hazel M Dockrell
- Department of Immunology and Infection, and Tuberculosis (TB) Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert J Wilkinson
- The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Imperial College London, London, United Kingdom.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Michael Levin
- Section of Paediatrics, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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9
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Larkey NE, Phillips JL, Jang HS, Kolluri SK, Burrows SM. Small RNA Biosensor Design Strategy To Mitigate Off-Analyte Response. ACS Sens 2020; 5:377-384. [PMID: 31942801 DOI: 10.1021/acssensors.9b01968] [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: 10/25/2022]
Abstract
Several bottlenecks in the design of current sensor technologies for small noncoding RNA must be addressed. The small size of the sensors and the large number of other nucleotides that may have sequence similarity makes selectivity a real concern. Many of the current sensors have one strand with an exposed region called a toehold. The toehold serves as a place for the analyte nucleic acid strand to bind and initiate competitive displacement of sensors' secondary strands. Since the toehold region is not protected, any endogenous oligonucleotide sequences that are similar or only different by a few nucleic acids will interact with the toehold and cause false signals. To address sensor selectivity, we investigated how the toehold location in the sensor impacts the sensitivity and selectivity for the analyte of interest. We will discuss the differences in sensitivity and selectivity for a miR-146a-5p biosensor in the presence of different naturally occurring mismatch sequences. We found that altering the toehold location lowered the rate of the false signal from off-analyte microRNA by upward of 20 percentage points. Detection limits as low as 56 pM were observed when the sensor concentration was 5 nM. The findings herein are broadly applicable to other small and large RNAs as well as other types of sensing platforms.
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Affiliation(s)
- Nicholas E. Larkey
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Jessica L. Phillips
- Department of Environmental and Molecular Toxicology, Cancer Research Laboratory, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hyo Sang Jang
- Department of Environmental and Molecular Toxicology, Cancer Research Laboratory, Oregon State University, Corvallis, Oregon 97331, United States
| | - Siva K. Kolluri
- Department of Environmental and Molecular Toxicology, Cancer Research Laboratory, Oregon State University, Corvallis, Oregon 97331, United States
| | - Sean M. Burrows
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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Minakshi P, Ghosh M, Brar B, Kumar R, Lambe UP, Ranjan K, Manoj J, Prasad G. Nano-antimicrobials: A New Paradigm for Combating Mycobacterial Resistance. Curr Pharm Des 2020; 25:1554-1579. [PMID: 31218956 DOI: 10.2174/1381612825666190620094041] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Mycobacterium group contains several pathogenic bacteria including M. tuberculosis where the emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) is alarming for human and animal health around the world. The condition has further aggravated due to the speed of discovery of the newer drugs has been outpaced by the rate of resistance developed in microorganisms, thus requiring alternative combat strategies. For this purpose, nano-antimicrobials have emerged as a potential option. OBJECTIVE The current review is focused on providing a detailed account of nanocarriers like liposome, micelles, dendrimers, solid lipid NPs, niosomes, polymeric nanoparticles, nano-suspensions, nano-emulsion, mesoporous silica and alginate-based drug delivery systems along with the recent updates on developments regarding nanoparticle-based therapeutics, vaccines and diagnostic methods developed or under pipeline with their potential benefits and limitations to combat mycobacterial diseases for their successful eradication from the world in future. RESULTS Distinct morphology and the underlying mechanism of pathogenesis and resistance development in this group of organisms urge improved and novel methods for the early and efficient diagnosis, treatment and vaccination to eradicate the disease. Recent developments in nanotechnology have the potential to meet both the aspects: nano-materials are proven components of several efficient targeted drug delivery systems and the typical physicochemical properties of several nano-formulations have shown to possess distinct bacteriocidal properties. Along with the therapeutic aspects, nano-vaccines and theranostic applications of nano-formulations have grown in popularity in recent times as an effective alternative means to combat different microbial superbugs. CONCLUSION Nanomedicine holds a bright prospect to perform a key role in global tuberculosis elimination program.
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Affiliation(s)
- Prasad Minakshi
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125 004, Haryana, India
| | - Mayukh Ghosh
- Department of Veterinary Biochemistry, Ranchi Veterinary College, Birsa Agricultural University, Ranchi-834 006, Jharkhand, India
| | - Basanti Brar
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125 004, Haryana, India
| | - Rajesh Kumar
- Department of Veterinary Physiology, COVAS, KVASU, Pookode, Wayanad- 673576, Kerala, India
| | - Upendra P Lambe
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125 004, Haryana, India
| | | | - Jinu Manoj
- RVDEC Mahendergarh, LUVAS, Haryana, India
| | - Gaya Prasad
- SVP University of Agriculture and Technology, Meerut, India
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11
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12
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Li X, Yang J, Yuan R, Xiang Y. Programming cascaded recycling amplifications for highly sensitive and label-free electrochemical sensing of transcription factors in tumor cells. Biosens Bioelectron 2019; 142:111574. [DOI: 10.1016/j.bios.2019.111574] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/24/2019] [Accepted: 08/04/2019] [Indexed: 11/26/2022]
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13
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Park JC, Choi SY, Yang MY, Nan L, Na H, Lee HN, Chung HJ, Hong CA, Nam YS. Subnanomolar FRET-Based DNA Assay Using Thermally Stable Phosphorothioated DNA-Functionalized Quantum Dots. ACS Appl Mater Interfaces 2019; 11:33525-33534. [PMID: 31455080 DOI: 10.1021/acsami.9b07717] [Citation(s) in RCA: 11] [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: 06/10/2023]
Abstract
Quantum dots (QDs) can serve as an attractive Förster resonance energy transfer (FRET) donor for DNA assay due to their excellent optical properties. However, the specificity and sensitivity of QD-based FRET analysis are prominently reduced by nonspecific DNA adsorption and poor colloidal stability during DNA hybridization, which hinders the practical applications of QDs as a biosensing platform. Here, we report subnanomolar FRET assay of DNA through the stabilization of DNA/QD interface using DNA-functionalized QDs with phosphorothioated single-stranded DNA (pt-ssDNA) as a multivalent ligand in an aqueous solution. In situ DNA functionalization was achieved during the aqueous synthesis of CdTe/CdS QDs, resulting in the maximum photoluminescence quantum yields of 76.9% at an emission wavelength of 732 nm. Conventional monothiolated ssDNA-capped QDs exhibited particle aggregation and photoluminescence (PL) quenching during DNA hybridization at 70 °C due to the dissociation of surface ligands. Such colloidal instability induced the nonspecific adsorption of DNA, resulting in false-positive signal and decreased sensitivity with the limit of detection (LOD) of 16.1 nM. In contrast, the pt-ssDNA-functionalized QDs maintained their colloidal stability and PL properties at elevated temperatures. The LOD of the pt-ssDNA-functionalized QDs was >30 times lower (0.47 nM) while maintaining the high specificity to a target sequence because the strong multivalent binding of pt-ssDNA to the surface of QDs prevents the detachment of pt-ssDNA and nonspecific adsorption of DNA. The study suggests that the ligand design to stabilize the surface of QDs in an aqueous milieu is critically important for the high performance of QDs for specific DNA assay.
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Affiliation(s)
| | | | | | | | | | | | | | - Cheol Am Hong
- School of Chemistry and Biochemistry , Yeungnam University , 280 Daehak-Ro , Gyeongsan , Gyeongbuk 38541 , Republic of Korea
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Ali AA, Kang M, Kharbash R, Kim Y. Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomed Eng 2019; 1:6. [PMID: 32903305 DOI: 10.1186/s42490-019-0008-x] [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: 10/24/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response. Results In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.
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Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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Wang Y, Howes PD, Kim E, Spicer CD, Thomas MR, Lin Y, Crowder SW, Pence IJ, Stevens MM. Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using Compact Quantum Dot-DNA Conjugates. ACS Appl Mater Interfaces 2018; 10:28290-28300. [PMID: 30113161 PMCID: PMC6141140 DOI: 10.1021/acsami.8b07250] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/31/2018] [Indexed: 05/18/2023]
Abstract
Advances in nanotechnology have provided new opportunities for the design of next-generation nucleic acid biosensors and diagnostics. Indeed, combining advances in functional nanoparticles, DNA nanotechnology, and nuclease-enzyme-based amplification can give rise to new assays with advantageous properties. In this work, we developed a microRNA (miRNA) assay using bright fluorescent quantum dots (QDs), simple DNA probes, and the enzyme duplex-specific nuclease. We employed an isothermal target-recycling mechanism, where a single miRNA target triggers the cleavage of many DNA signal probes. The incorporation of DNA-functionalized QDs enabled a quantitative fluorescent readout, mediated by Förster resonance energy transfer (FRET)-based interaction with the DNA signal probes. Our approach splits the reaction in two, performing the enzyme-mediated amplification and QD-based detection steps separately such that each reaction could be optimized for performance of the active components. Target recycling gave ca. 3 orders of magnitude amplification, yielding highly sensitive detection with a limit of 42 fM (or 1.2 amol) of miR-148, with excellent selectivity versus mismatched sequences and other miRNAs. Furthermore, we used an alternative target (miR-21) and FRET pair for direct and absolute quantification of miR-21 in RNA extracts from human cancer and normal cell lines.
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Abstract
Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.
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Affiliation(s)
- William J. Peveler
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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Gladyshev PP, Tumanov YV, Ibragimova SA, Kouznetsov VV, Gribova ED. Quantum dots in proteomic studies and medical diagnostics. Russ Chem Bull 2018; 67:600-13. [DOI: 10.1007/s11172-018-2114-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Gliddon HD, Herberg JA, Levin M, Kaforou M. Genome-wide host RNA signatures of infectious diseases: discovery and clinical translation. Immunology 2017; 153:171-178. [PMID: 28921535 PMCID: PMC5765383 DOI: 10.1111/imm.12841] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [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: 05/15/2017] [Revised: 09/11/2017] [Accepted: 09/11/2017] [Indexed: 12/31/2022] Open
Abstract
The use of whole blood gene expression to derive diagnostic biomarkers capable of distinguishing between phenotypically similar diseases holds great promise but remains a challenge. Differential gene expression analysis is used to identify the key genes that undergo changes in expression relative to healthy individuals, as well as to patients with other diseases. These key genes can act as diagnostic, prognostic and predictive markers of disease. Gene expression ‘signatures’ in the blood hold the potential to be used for the diagnosis of infectious diseases, where current diagnostics are unreliable, ineffective or of limited potential. For diagnostic tests based on RNA signatures to be useful clinically, the first step is to identify the minimum set of gene transcripts that accurately identify the disease in question. The second requirement is rapid and cost‐effective detection of the gene expression levels. Signatures have been described for a number of infectious diseases, but ‘clinic‐ready’ technologies for RNA detection from clinical samples are limited, though existing methods such as RT‐PCR are likely to be superseded by a number of emerging technologies, which may form the basis of the translation of gene expression signatures into routine diagnostic tests for a range of disease states.
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Affiliation(s)
- Harriet D Gliddon
- London Centre for Nanotechnology, University College London, London, UK
| | | | - Michael Levin
- Department of Medicine, Imperial College London, London, UK
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Yao J, Li L, Li P, Yang M. Quantum dots: from fluorescence to chemiluminescence, bioluminescence, electrochemiluminescence, and electrochemistry. Nanoscale 2017; 9:13364-13383. [PMID: 28880034 DOI: 10.1039/c7nr05233b] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, nanotechnology has become one of the major forces driving basic and applied research. As a novel class of inorganic fluorochromes, research into quantum dots (QDs) has become one of the fastest growing fields of nanotechnology today. QDs are made of a semiconductor material with tunable physical dimensions as well as unique optoelectronic properties, and have attracted multidisciplinary research efforts to further their potential bioanalytical applications. Recently, numerous optical properties of QDs, such as narrow emission band peaks, broad absorption spectra, intense signals, and remarkable resistance to photobleaching, have made them biocompatible and sensitive for biological assays. In this review, we give an overview of these exciting materials and describe their potential, especially in biomolecules analysis, including fluorescence detection, chemiluminescence detection, bioluminescence detection, electrochemiluminescence detection, and electrochemical detection. Finally, conclusions are made, including highlighting some critical challenges remaining and a perspective of how this field can be expected to develop in the future.
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Affiliation(s)
- Jun Yao
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan 610500, People's Republic of China.
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Abstract
The interplay of photonics, nanotechnology, and biochemistry has significantly improved the identification and characterization of multiple types of biomarkers by optical biosensors. Great achievements in fluorescence-based technologies have been realized, for example, by the advancement of multiplexing techniques or the introduction of nanoparticles to biochemical and clinical research. This review presents a concise overview of recent advances in fluorescence sensing techniques for the detection of circulating disease biomarkers. Detection principles of representative approaches, including fluorescence detection using molecular fluorophores, quantum dots, and metallic and silica nanoparticles, are explained and illustrated by pertinent examples from the recent literature. Advanced detection technologies and material development play a major role in modern biosensing and consistently provide significant improvements toward robust, sensitive, and versatile platforms for early detection of circulating diagnostic biomarkers.
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Affiliation(s)
- Oya Tagit
- NanoBioPhotonics
(nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay, France
- Department
of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Niko Hildebrandt
- NanoBioPhotonics
(nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405 Orsay, France
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