1
|
Li J, Qi Y, Yang R, Chen X, Chen Z, Zhu JJ. Intellectualized Visualization of Single-Particle Raman Spectra for Sensitive Detection and Simultaneous Multianalysis of Heavy Metal Ions. Anal Chem 2023; 95:14736-14745. [PMID: 37737121 DOI: 10.1021/acs.analchem.3c02851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Easy-to-use, reliable, and real-time methods for detecting heavy metal ion contamination are urgently required, which is a primary concern for water pollution control and human health. However, present methods for this aim are still unable to achieve simultaneous multianalysis for complex real sample detection. Herein, an intellectualized vision-based single-nanoparticle Raman imaging strategy combined with ion-responsive functional nucleic acids (FNAs) was proposed to address these issues. We reported a correspondence between the concentration of the analytes and the density of particles (DOP) of specifically captured nanoparticles to achieve sensitive detection and simultaneous multianalysis of heavy metal ions. The specific detection of Pb2+ (Hg2+) was obtained with a detection linear range from 100 pM to 100 nM (from 500 fM to 100 nM) and limit of detections low to 1 pM (100 fM), with the advantages of good specificity, excellent homogeneity, and reproducibility. Furthermore, the differentiation of different heavy metal ions (Pb2+/Hg2+) was achieved, i.e., the simultaneous multianalysis, based on Raman imaging of the single particle and intelligent machine vision method. Finally, the Raman imaging assay was utilized for real sample analysis, and it provided a powerful and reliable tool for detecting trace Pb2+/Hg2+ in real water samples and facilitated the portable on-site monitoring of heavy metal ions.
Collapse
Affiliation(s)
- Jinxiang Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yongbing Qi
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ruixin Yang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, People's Republic of China
| |
Collapse
|
2
|
Zhou Z, Lan X, Zhu L, Zhang Y, Chen K, Zhang W, Xu W. Portable dual-aptamer microfluidic chip biosensor for Bacillus cereus based on aptamer tailoring and dumbbell-shaped probes. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130545. [PMID: 36493638 DOI: 10.1016/j.jhazmat.2022.130545] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
As food-borne pathogens, Bacillus cereus not only produce toxins that contaminate food and threaten human health, but also rely on spores to resist extreme environments. At present, the detection of B. cereus is still at the genome level and it is not easily distinguished from other Bacilli of the same group. Herein, we obtained the aptamers of B. cereus in different phases through Cell-SELEX technology. Then, through step-by-step tailoring and molecular docking, the two best performing aptamers were ascertained and the interaction revealed between the repeated G bases in the aptamer and the polar amino acids in the α-helix of the epiprotein. Based on these aptamers, a multifunctional dumbbell-shaped probe and an ultrasensitive microfluidic chip biosensor were designed. Tests showed that the novel sensor is able to complete detection within 1 h with a limit of detection (LOD) of 9.27 CFU/mL. Moreover, the sensor can be used in complex food environments, such as milk and rice, is able to detect both vegetative cells and spores, and it can also distinguish B. thuringiensis from the same flora. This study can provide a reference for the future development of food-borne pathogenic bacteria aptamer selecting, target interaction analysis, detection methods and equipment.
Collapse
Affiliation(s)
- Ziqi Zhou
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kehan Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
3
|
Dai X, Chen Y. Computational Biomaterials: Computational Simulations for Biomedicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2204798. [PMID: 35916024 DOI: 10.1002/adma.202204798] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/23/2022] [Indexed: 05/14/2023]
Abstract
With the flourishing development of material simulation methods (quantum chemistry methods, molecular dynamics, Monte Carlo, phase field, etc.), extensive adoption of computing technologies (high-throughput, artificial intelligence, machine learning, etc.), and the invention of high-performance computing equipment, computational simulation tools have sparked the fundamental mechanism-level explorations to predict the diverse physicochemical properties and biological effects of biomaterials and investigate their enormous application potential for disease prevention, diagnostics, and therapeutics. Herein, the term "computational biomaterials" is proposed and the computational methods currently used to explore the inherent properties of biomaterials, such as optical, magnetic, electronic, and acoustic properties, and the elucidation of corresponding biological behaviors/effects in the biomedical field are summarized/discussed. The theoretical calculation of the physiochemical properties/biological performance of biomaterials applied in disease diagnosis, drug delivery, disease therapeutics, and specific paradigms such as biomimetic biomaterials is discussed. Additionally, the biosafety evaluation applications of theoretical simulations of biomaterials are presented. Finally, the challenges and future prospects of such computational simulations for biomaterials development are clarified. It is anticipated that these simulations would offer various methodologies for facilitating the development and future clinical translations/utilization of versatile biomaterials.
Collapse
Affiliation(s)
- Xinyue Dai
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
- School of Medicine, Shanghai University, Shanghai, 200444, P. R. China
| |
Collapse
|
4
|
|
5
|
An electrophoresis approach with online thermal lens detection to monitoring DNA surface coatings on gold nanoparticles. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
6
|
Liu M, Wang L, Lo Y, Shiu SCC, Kinghorn AB, Tanner JA. Aptamer-Enabled Nanomaterials for Therapeutics, Drug Targeting and Imaging. Cells 2022; 11:159. [PMID: 35011722 PMCID: PMC8750369 DOI: 10.3390/cells11010159] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/06/2023] Open
Abstract
A wide variety of nanomaterials have emerged in recent years with advantageous properties for a plethora of therapeutic and diagnostic applications. Such applications include drug delivery, imaging, anti-cancer therapy and radiotherapy. There is a critical need for further components which can facilitate therapeutic targeting, augment their physicochemical properties, or broaden their theranostic applications. Aptamers are single-stranded nucleic acids which have been selected or evolved to bind specifically to molecules, surfaces, or cells. Aptamers can also act as direct biologic therapeutics, or in imaging and diagnostics. There is a rich field of discovery at the interdisciplinary interface between nanomaterials and aptamer science that has significant potential across biomedicine. Herein, we review recent progress in aptamer-enabled materials and discuss pending challenges for their future biomedical application.
Collapse
Affiliation(s)
- Mengping Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Lin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Young Lo
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Andrew B. Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Julian A. Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
| |
Collapse
|
7
|
|
8
|
Wang J, Wen J, Yan H. Recent Applications of Carbon Nanomaterials for microRNA Electrochemical Sensing. Chem Asian J 2020; 16:114-128. [DOI: 10.1002/asia.202001260] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Jiameng Wang
- College of Pharmaceutical Science Hebei University Institute of Life Science and Green Development, Key Laboratory of Pharmaceutical Quality Control of Hebei Province Baoding 071002 P. R. China
| | - Jia Wen
- College of Pharmaceutical Science Hebei University Institute of Life Science and Green Development, Key Laboratory of Pharmaceutical Quality Control of Hebei Province Baoding 071002 P. R. China
| | - Hongyuan Yan
- College of Pharmaceutical Science Hebei University Institute of Life Science and Green Development, Key Laboratory of Pharmaceutical Quality Control of Hebei Province Baoding 071002 P. R. China
- College of Public Health Hebei University Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education Baoding 071002 P. R. China
| |
Collapse
|
9
|
Beyond native deoxyribonucleic acid, templating fluorescent nanomaterials for bioanalytical applications: A review. Anal Chim Acta 2020; 1105:11-27. [DOI: 10.1016/j.aca.2020.01.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 12/16/2022]
|
10
|
Wang G, Chu LT, Hartanto H, Utomo WB, Pravasta RA, Chen TH. Microfluidic Particle Dam for Visual and Quantitative Detection of Lead Ions. ACS Sens 2020; 5:19-23. [PMID: 31808335 DOI: 10.1021/acssensors.9b01945] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lead contamination in drinking water is a primary concern in public health, but it is difficult to monitor by end-users. Here, we provide a rapid and power-free microfluidic particle dam which enables visual quantification of lead ions (Pb2+) by the naked eye. GR-5 DNAzyme with extended termini can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) by DNA hybridization, forming "MMPs-GR-5-PMPs". When Pb2+ is present, GR-5 is cleaved, resulting in an increasing number of free PMPs. To visually count the free PMPs, the solution is loaded to a capillary-driven microfluidic device that consists of a magnetic separator to remove the MMPs-GR-5-PMPs, followed by a particle dam that traps and accumulates the free PMPs into a visual bar with growing length proportional to the concentration of lead. The device achieved a limit of detection at 2.12 nM (0.44 ppb), high selectivity (>20,000-fold) against other metal ions, high tolerance to different pH and water hardness, and is compatible with tap water with a high recovery rate, enabling visual quantification and user-friendly interface for rapid screening of water safety.
Collapse
|
11
|
Yang Y, Mao G, Ji X, He Z. DNA-templated quantum dots and their applications in biosensors, bioimaging, and therapy. J Mater Chem B 2019; 8:9-17. [PMID: 31750850 DOI: 10.1039/c9tb01870k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the past 10 years, DNA functionalized quantum dots (QDs) have attracted considerable attention in sensing and imaging of disease-relevant biological targets, as well as cancer therapy. Considerable efforts have been devoted to obtaining DNA functionalized QDs with enhanced stability and quantum yield. Here, we focus on a one-pot method, in which phosphorothioate-modified DNA is used as the co-ligand on the basis of the strong binding of sulfur and Cd2+. After a short summary of the preparation of DNA-templated QDs, versatile bioapplications based on the constructed ratiometric fluorescent probes, nanobeacons and multiple bottom-up assemblies will be discussed. A substantial part of the review will focus on these applications, ranging from small molecule, biological macromolecule, cancer cell and pathogen sensing to in vitro and in vivo imaging. Besides, drug or siRNA delivery based on DNA-templated QD assemblies will also be briefly discussed here.
Collapse
Affiliation(s)
- Yeling Yang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Guobin Mao
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| |
Collapse
|
12
|
De la Cruz Morales K, Alarcón‐Angeles G, Merkoçi A. Nanomaterial‐based Sensors for the Study of DNA Interaction with Drugs. ELECTROANAL 2019. [DOI: 10.1002/elan.201900286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- K. De la Cruz Morales
- Universidad Autónoma Metropolitana-XochimilcoDepartamento de Sistemas Biológicos C.P. 04960 México City
| | - G. Alarcón‐Angeles
- Universidad Autónoma Metropolitana-XochimilcoDepartamento de Sistemas Biológicos C.P. 04960 México City
| | - A. Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST Campus UAB, Bellaterra 08193 Barcelona Spain
- ICREA – Catalan Institution for Research and Advanced Studies Barcelona 08010 Spain
| |
Collapse
|
13
|
Zhou M, Zou J, Gu Y, Yi R, Tu H. Preparation of magnetic polymer nanosphere and its profile control. J DISPER SCI TECHNOL 2019. [DOI: 10.1080/01932691.2019.1593860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ming Zhou
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation School of Materials Science and Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Jiaxi Zou
- School of Materials Science and Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Yinhua Gu
- School of Materials Science and Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - RongJun Yi
- School of Materials Science and Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Hongjun Tu
- School of Materials Science and Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| |
Collapse
|
14
|
Jiao M, Zhang P, Meng J, Li Y, Liu C, Luo X, Gao M. Recent advancements in biocompatible inorganic nanoparticles towards biomedical applications. Biomater Sci 2018; 6:726-745. [PMID: 29308496 DOI: 10.1039/c7bm01020f] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Due to their intrinsic physical properties potentially useful for imaging and therapy as well as their highly engineerable surface, biocompatible inorganic nanoparticles offer novel platforms to develop advanced diagnostic and therapeutic agents for improved detection and more efficacious treatment of major diseases. The in vivo application of inorganic nanoparticles was demonstrated more than two decades ago, however it turns out to be very complicated as nanomaterials exhibit much more sophisticated pharmacokinetic properties than conventional drugs. In this review, we first discuss the in vivo behavior of inorganic nanoparticles after systematic administration, including the basic requirements for nanoparticles to be used in vivo, the impact of the particles' physicochemical properties on their pharmacokinetics, and the effects of the protein corona formed across the nano-bio interface. Next, we summarize the state-of-the-art of the preparation of biocompatible inorganic nanoparticles and bioconjugation strategies for obtaining target-specific nanoprobes. Then, the advancements in sensitive tumor imaging towards diagnosis and visualization of the abnormal signatures in the tumor microenvironment, together with recent studies on atherosclerosis imaging are highlighted. Finally, the future challenges and the potential for inorganic nanoparticles to be translated into clinical applications are discussed.
Collapse
Affiliation(s)
- Mingxia Jiao
- Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Bei Yi Jie 2, Zhong Guan Cun, Beijing 100190, China.
| | | | | | | | | | | | | |
Collapse
|
15
|
Ocsoy I, Tasdemir D, Mazicioglu S, Tan W. Nanotechnology in Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:263-275. [DOI: 10.1007/10_2017_53] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
16
|
Ocsoy I, Isiklan N, Cansiz S, Özdemir N, Tan W. ICG-conjugated Magnetic Graphene Oxide for Dual Photothermal and Photodynamic Therapy. RSC Adv 2016; 6:30285-30292. [PMID: 27774142 PMCID: PMC5070673 DOI: 10.1039/c6ra06798k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aptamer-functionalized magnetic graphene oxide conjugates loaded with indocyanine green (ICG) dye, or Apt@ICG@mGO, have been successfully developed for dual-targeted photothermal and photodynamic therapy. In general, a drug or its carrier or their dosage can be imprtant important issues in terms of toxicity. However, in this system, each component used is quite safe, biocompatibe and clean. For instance, ICG, a Food and Drug Administration (FDA) approved near-infrared (NIR) dye, serves as both a photothermal and photodynamic agent. It is immobilized on the surface of mGO via a physical interaction called "π-π stacking". The mGO, as a most biocomptible member of the carbo family, is selected for use as a platform for aptamer and ICG dye conjugation, as well as as a photothermal agent. The light in the near-infrared region (NIR) was chosen as a harmless light source for activating the agents for photothermal therapy (PTT) and photodynamic therapy (PDT). The magnetic properties of mGO are also used for separation of Apt@ICG@mGO conjugates from the reaction medium. Aptamer sgc8 acts as a targeting ligand to selectively and specifically bind to a protein on the membrane of cancer cell line CCRF-CEM. After the aptamer- functionalized ICG@mGO conjugates are incubated with target CEM cells at 37 °C for 2 hours, they are bound to cells or they may be internalized into the cell via endocytosis. More significantly, we demonstrated that the Apt@ICG@mGO conjugates produce heat for photothermal therapy (PTT) and singlet oxygen for photodynamic therapy (PDT) upon NIR laser irradiation at 808 nm. Thus, remarkably efficient cancer cell destructions with ~41% and ~60% and ~82% cell killing using 10, 50 and 100 ppm Apt@ICG@mGO, respectively are achieved in 5 min light exposure.
Collapse
Affiliation(s)
- Ismail Ocsoy
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611; Department of Analytical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039 Turkey; Nanotechnology Research Center (ERNAM), Erciyes University, Kayseri, 38039 Turkey
| | - Nuran Isiklan
- Department of Chemistry, Science and Arts Faculty, Kırıkkale University, Kırıkkale, 7100 Turkey
| | - Sena Cansiz
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611
| | - Nalan Özdemir
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, 38039 Turkey
| | - Weihong Tan
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611
| |
Collapse
|
17
|
Xu W, Deng R, Wang L, Li J. Multiresponsive Rolling Circle Amplification for DNA Logic Gates Mediated by Endonuclease. Anal Chem 2014; 86:7813-8. [DOI: 10.1021/ac501726s] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Weidong Xu
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Ruijie Deng
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Lida Wang
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| |
Collapse
|
18
|
Pérez-Rentero S, Grijalvo S, Peñuelas G, Fàbrega C, Eritja R. Thioctic acid derivatives as building blocks to incorporate DNA oligonucleotides onto gold nanoparticles. Molecules 2014; 19:10495-523. [PMID: 25045890 PMCID: PMC6271687 DOI: 10.3390/molecules190710495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 01/26/2023] Open
Abstract
Oligonucleotide gold nanoparticle conjugates are being used as diagnostic tools and gene silencing experiments. Thiol-chemistry is mostly used to functionalize gold nanoparticles with oligonucleotides and to incorporate DNA or RNA molecules onto gold surfaces. However, the stability of such nucleic acid–gold nanoparticle conjugates in certain conditions may be a limitation due to premature break of the thiol-gold bonds followed by aggregation processes. Here, we describe a straightforward synthesis of oligonucleotides carrying thioctic acid moiety based on the use of several thioctic acid-l-threoninol derivatives containing different spacers, including triglycine, short polyethyleneglycol, or aliphatic spacers. The novel thioctic-oligonucleotides were used for the functionalization of gold nanoparticles and the surface coverage and stability of the resulting thioctic-oligonucleotide gold nanoparticles were assessed. In all cases gold nanoparticles functionalized with thioctic-oligonucleotides had higher loadings and higher stability in the presence of thiols than gold nanoparticles prepared with commercially available thiol-oligonucleotides. Furthermore, the thioctic derivative carrying the triglycine linker is sensitive to cathepsin B present in endosomes. In this way this derivative may be interesting for the cellular delivery of therapeutic oligonucleotides as these results provides the basis for a potential endosomal escape.
Collapse
Affiliation(s)
- Sónia Pérez-Rentero
- Institute for Advanced Chemistry of Catalonia (IQAC), Consejo Superior de Investigaciones Científicas (CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC), Consejo Superior de Investigaciones Científicas (CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Guillem Peñuelas
- Institute for Advanced Chemistry of Catalonia (IQAC), Consejo Superior de Investigaciones Científicas (CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC), Consejo Superior de Investigaciones Científicas (CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Consejo Superior de Investigaciones Científicas (CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| |
Collapse
|
19
|
Wang K, Huang J, Yang X, He X, Liu J. Recent advances in fluorescent nucleic acid probes for living cell studies. Analyst 2014; 138:62-71. [PMID: 23154215 DOI: 10.1039/c2an35254k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Living cell studies can offer tremendous opportunities for biological and disease studies. Due to their high sensitivity and selectivity, minimum interference with living biological systems, ease of design and synthesis, fluorescent nucleic acid probes (FNAPs) have been widely used in living cell studies, such as for intracellular detection, cell detection, and cell-to-cell communication. Here, we review the general requirements and the recent developments in FNAPs for living cell studies. We broadly classify these designs as hybridization probes and aptamer probes. For hybridization probes, we describe recently developed designs, such as nanomaterial-based and amplification-based hybridization probes. For aptamer probes, we discuss four general paradigms that have appeared most frequently in the literature: nanomaterial-based, nanomachine-based, cell surface-anchored and activatable aptamer probe designs in vivo. FNAPs promise to open up new and exciting opportunities in biological marks detection for a wide range of biological and medical applications.
Collapse
Affiliation(s)
- Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Changsha 410082, China.
| | | | | | | | | |
Collapse
|
20
|
|
21
|
Gao Y, Longenbach T, Vitol EA, Orynbayeva Z, Friedman G, Gogotsi Y. One-dimensional nanoprobes for single-cell studies. Nanomedicine (Lond) 2014; 9:153-68. [DOI: 10.2217/nnm.13.196] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Owing to variation of individual cells within a population, single-cell studies are of great interest to researchers. Recent developments in nanofabrication technology have made this area increasingly attractive as one-dimensional (1D) nanoscale probes can be manufactured with increasing accuracy. Here, we provide an overview and description of the major designs that have been reported to date. For more details of what applications could be realized and how, based on the probe shapes and designs, we summarize the most recently reported performances of 1D single-cell probes with their advantages and limitations. Minimally invasive probes are required for long-term experiments on single cells. Carbon nanotubes with their unique properties and structure are excellent candidates for multitask robotic intracellular probes. Carbon nanotube-tipped cellular endoscopes are less invasive compared with pipettes or cantilever tips. Advances in nanofabrication techniques have made it possible to produce more consistent nanoscale cellular probes that can capture a variety of information from optical, electrical and chemical signals. In addition, these tools can transfer tiny amounts of fluids and molecular materials in a highly localized fashion for the purpose of analyzing or stimulating a variety of responses at the level of individual cells and even cellular organelles. We conclude with a critical analysis of the current state of the field as well as the major obstacles for further probe development of minimally invasive probes and their widespread use in cell biology.
Collapse
Affiliation(s)
- Yang Gao
- Department of Electrical & Computer Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Travis Longenbach
- Department of Materials Science & Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Elina A Vitol
- Department of Materials Science & Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Zulfiya Orynbayeva
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- AJ Drexel Nanotechnology Institute, Drexel University, Philadelphia, PA 19104, USA
| | - Gary Friedman
- Department of Electrical & Computer Engineering, Drexel University, Philadelphia, PA 19104, USA
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- AJ Drexel Nanotechnology Institute, Drexel University, Philadelphia, PA 19104, USA
| | - Yury Gogotsi
- Department of Materials Science & Engineering, Drexel University, Philadelphia, PA 19104, USA
| |
Collapse
|
22
|
Sobrova P, Blazkova I, Chomoucka J, Drbohlavova J, Vaculovicova M, Kopel P, Hubalek J, Kizek R, Adam V. Quantum dots and prion proteins: is this a new challenge for neurodegenerative diseases imaging? Prion 2013; 7:349-58. [PMID: 24055838 PMCID: PMC4134339 DOI: 10.4161/pri.26524] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 08/19/2013] [Accepted: 09/17/2013] [Indexed: 12/27/2022] Open
Abstract
A diagnostics of infectious diseases can be done by the immunologic methods or by the amplification of nucleic acid specific to contagious agent using polymerase chain reaction. However, in transmissible spongiform encephalopathies, the infectious agent, prion protein (PrP(Sc)), has the same sequence of nucleic acids as a naturally occurring protein. The other issue with the diagnosing based on the PrP(Sc) detection is that the pathological form of prion protein is abundant only at late stages of the disease in a brain. Therefore, the diagnostics of prion protein caused diseases represent a sort of challenges as that hosts can incubate infectious prion proteins for many months or even years. Therefore, new in vivo assays for detection of prion proteins and for diagnosis of their relation to neurodegenerative diseases are summarized. Their applicability and future prospects in this field are discussed with particular aim at using quantum dots as fluorescent labels.
Collapse
Affiliation(s)
- Pavlina Sobrova
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno, Czech Republic EU
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Iva Blazkova
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno, Czech Republic EU
| | - Jana Chomoucka
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Jana Drbohlavova
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno, Czech Republic EU
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Pavel Kopel
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno, Czech Republic EU
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Jaromir Hubalek
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Rene Kizek
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno, Czech Republic EU
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| | - Vojtech Adam
- Department of Chemistry and Biochemistry; Faculty of Agronomy; Mendel University in Brno; Brno, Czech Republic EU
- Central European Institute of Technology; Brno University of Technology; Brno, Czech Republic EU
| |
Collapse
|
23
|
OCSOY ISMAIL, OCSOY MUSERREFARSLAN, YASUN EMIR, TAN WEIHONG. NUCLEIC ACID-FUNCTIONALIZED NANOMATERIALS. ACTA ACUST UNITED AC 2013. [DOI: 10.1142/s1793984413400047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nucleic acid (NA)-functionalized nanomaterials (NMs) have received considerable attention in recent years. The use of nucleic acid (DNA/RNA) for surface functionalization of NMs offers the ability to directly address desired targets and coat NMs with biocompatible polymers, such as poly [(ethylene)] glycol (PEG) and polyacrylamide (PA), enhancing the utility of these complexes in biomedicine. In particular, the target-specific recognition capacity of surface-functionalized NMs has opened up new avenues for disease diagnosis and therapy. This review focuses on the biological applications of a special type of nucleic acid, termed aptamer, conjugated with a variety of NMs for a wide spectrum of applications in nanobiomedicine.
Collapse
Affiliation(s)
- ISMAIL OCSOY
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida Gainesville, Forida 32611/7200, United States of America
| | - MUSERREF ARSLAN OCSOY
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida Gainesville, Forida 32611/7200, United States of America
| | - EMIR YASUN
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida Gainesville, Forida 32611/7200, United States of America
| | - WEIHONG TAN
- Center for Research at the Bio/Nano Interface, Department of Chemistry and Shands Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida Gainesville, Forida 32611/7200, United States of America
| |
Collapse
|
24
|
Singh K, Sareen D, Kaur P, Miyake H, Tsukube H. Materials-Based Receptors: Design Principle and Applications. Chemistry 2013; 19:6914-36. [DOI: 10.1002/chem.201300249] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Indexed: 12/12/2022]
|
25
|
Single-stranded DNA loops as fiducial markers for exploring DNA-protein interactions in single molecule imaging. Methods 2013; 60:122-30. [PMID: 23500656 DOI: 10.1016/j.ymeth.2013.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/20/2013] [Accepted: 03/01/2013] [Indexed: 11/21/2022] Open
Abstract
A polymerase chain reaction (PCR) based method of adding a single-stranded DNA (ssDNA) hairpin loop to one end of linear double-stranded (ds) DNA templates was developed. The loop structure serves as a fiducial marker in single molecule imaging by atomic force microscopy (AFM) and can be applied to study DNA-protein interactions. The nucleic acid end-labels allow discrimination of the polarity of the DNA template in the AFM while limiting non-specific interactions which might occur from non-nucleic acid labels. Homo-polynucleotide ssDNA loops made up of 20 base-pairs (bp) for each of the four bases (A, T, G, C) were investigated to determine the effects of sequence on template labelling. The products were produced with high efficiency and high yield with the loop readily distinguished from the dsDNA template by height and diameter in the AFM. The application of the method to study DNA transcription was investigated by firing Escherichia Coli RNA polymerase (RNAP) from a λPR promoter in the direction of the loop-labelled end. The ssDNA loops captured elongating complexes of RNAP, arresting transcription and preventing dissociation. The dual role of the loop as a polarity marker and retainer of previously active RNAP will allow mechanisms of gene expression to be studied with single molecule sensitivity by AFM. This will enable insight into molecular interactions of RNAP on single DNA templates in convergent or tandem transcription configurations.
Collapse
|
26
|
YANG XH, KONG WJ, YANG MH, ZHAO M, OUYANG Z. Application of Aptamer Identification Technology in Rapid Analysis of Mycotoxins. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60630-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
27
|
Ocsoy I, Gulbakan B, Shukoor MI, Xiong X, Chen T, Powell DH, Tan W. Aptamer-conjugated multifunctional nanoflowers as a platform for targeting, capture, and detection in laser desorption ionization mass spectrometry. ACS NANO 2013; 7:417-27. [PMID: 23211039 PMCID: PMC3568519 DOI: 10.1021/nn304458m] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Although many different nanomaterials have been tested as substrates for laser desorption and ionization mass spectrometry (LDI-MS), this emerging field still requires more efficient multifuncional nanomaterials for targeting, enrichment, and detection. Here, we report the use of gold manganese oxide (Au@MnO) hybrid nanoflowers as an efficient matrix for LDI-MS. The nanoflowers were also functionalized with two different aptamers to target cancer cells and capture adenosine triphosphate (ATP). These nanoflowers were successfully used for metabolite extraction from cancer cell lysates. Thus, in one system, our multifunctional nanoflowers can (1) act as an ionization substrate for mass spectrometry, (2) target cancer cells, and (3) detect and analyze metabolites from cancer cells.
Collapse
|
28
|
Huang J, Yang X, He X, Wang K, He Y, Quan K. A new strategy for designing a graphene oxide-based DNA hairpin probe: fluorescence upon switching the orientation of the sticky end. Chem Commun (Camb) 2013; 49:9827-9. [DOI: 10.1039/c3cc45307c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
29
|
Lee JH, Hwang JH, Nam JM. DNA-tailored plasmonic nanoparticles for biosensing applications. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 5:96-109. [DOI: 10.1002/wnan.1196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
30
|
|