1
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Kolossov VL, Kanakaraju K, Sarkar S, Arogundade OH, Kuo CW, Mara NR, Smith AM. Quantum Dot-Fab' Conjugates as Compact Immunolabels for Microtubule Imaging and Cell Classification. ACS NANO 2024. [PMID: 38815170 DOI: 10.1021/acsnano.4c02215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Antibodies and their conjugates of fluorescent labels are widely applied in life sciences research and clinical pathology. Among diverse label types, compact quantum dots (QDs) provide advantages of multispectral multiplexing, bright signals in the deep red and infrared, and low steric hindrance. However, QD-antibody conjugates have random orientation of the antigen-binding domain which may interfere with labeling and are large (20-30 nm) and heterogeneous, which limits penetration into biospecimens. Here, we develop conjugates of compact QDs and Fab' antibody fragments as primary immunolabels. Fab' fragments are conjugated site-specifically through sulfhydryl groups distal to antigen-binding domains, and the multivalent conjugates have small and homogeneous sizes (∼12 nm) near those of full-sized antibodies. Their performance as immunolabels for intracellular antigens is evaluated quantitatively by metrics of microtubule labeling density and connectivity in fixed cells and for cytological identification in fixed brain specimens, comparing results with probes based on spectrally-matched dyes. QD-Fab' conjugates outperformed QD conjugates of full-sized antibodies and could be imaged with bright signals with 1-photon and 2-photon excitation. The results demonstrate a requirement for smaller bioaffinity agents and site-specific orientation for the success of nanomaterial-based labels to enhance penetration in biospecimens and minimize nonspecific staining.
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Affiliation(s)
- Vladimir L Kolossov
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kaviamuthan Kanakaraju
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, Indian Institute of Technology Jodhpur, Rajasthan 342037, India
| | - Opeyemi H Arogundade
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nihar R Mara
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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2
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Zhao Z, Jiang M, He C, Yin W, Feng Y, Wang P, Ying L, Fu T, Su D, Peng R, Tan W. Enhancing Specific Fluorescence In Situ Hybridization with Quantum Dots for Single-Molecule RNA Imaging in Formalin-Fixed Paraffin-Embedded Tumor Tissues. ACS NANO 2024; 18:9958-9968. [PMID: 38547522 DOI: 10.1021/acsnano.3c10216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Single-molecule fluorescence in situ hybridization (smFISH) represents a promising approach for the quantitative analysis of nucleic acid biomarkers in clinical tissue samples. However, low signal intensity and high background noise are complications that arise from diagnostic pathology when performed with smFISH-based RNA imaging in formalin-fixed paraffin-embedded (FFPE) tissue specimens. Moreover, the associated complex procedures can produce uncertain results and poor image quality. Herein, by combining the high specificity of split DNA probes with the high signal readout of ZnCdSe/ZnS quantum dot (QD) labeling, we introduce QD split-FISH, a high-brightness smFISH technology, to quantify the expression of mRNA in both cell lines and clinical FFPE tissue samples of breast cancer and lung squamous carcinoma. Owing to its high signal-to-noise ratio, QD split-FISH is a fast, inexpensive, and sensitive method for quantifying mRNA expression in FFPE tumor tissues, making it suitable for biomarker imaging and diagnostic pathology.
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Affiliation(s)
- Zeyin Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Mengyuan Jiang
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chen He
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Wenjuan Yin
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yawei Feng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Peng Wang
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lisha Ying
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Pathology, Zhejiang Cancer Hospital, Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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3
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Ciolli Mattioli C, Avraham R. Single-Molecule Fluorescent In Situ Hybridization (smFISH) for RNA Detection in Bacteria. Methods Mol Biol 2024; 2784:3-23. [PMID: 38502475 DOI: 10.1007/978-1-0716-3766-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In this chapter, we describe in detail how to perform a successful smFISH experiment and how to quantify mRNA transcripts in bacterial cells. The flexibility of the method allows for straightforward adaptation to different bacterial species and experimental conditions. Thanks to the feasibility of the approach, the method can easily be adapted by other laboratories. Finally, we believe that this method has a great potential to generate insights into the complicated life of bacteria.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Roi Avraham
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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4
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Kim S, Bae Y, Park SH, Chen N, Eom S, Kang S, Park J. Compact and modular bioprobe: Integrating SpyCatcher/SpyTag recombinant proteins with zwitterionic polymer-coated quantum dots. J Colloid Interface Sci 2023; 652:184-194. [PMID: 37595436 DOI: 10.1016/j.jcis.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/05/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
The development of quantum dot (QD)-based modular bioprobe that has a compact size and enable a facile conjugation of various biofunctional groups is in high demand. To address this, we surface engineered QDs with zwitterion polymer ligands to have an inherent compact size and derivatized them sequentially with the recombinant proteins SpyCatcher/SpyTag (SC/ST) to use their protein ligation system. SC/ST spontaneously form one complex through the isopeptide bond between them. SC-conjugated QDs (QD-SC) were used as base building blocks. Then, ST-biomolecules were added for modular biofunctionalization. We synthesized compact sized (∼15 nm) QD-SC-ST-affibody (antibody-mimicking small protein for tumor detection) conjugates, which showed successful cell-receptor targeting. The target cell-receptor could be easily tuned by changing the type of ST-affibody. We also demonstrated that anti-human-chorionic-gonadotropin mouse IgG1 antibodies can be labeled on the QD surface by mixing QD-SC with the ST-MG1Nb (mouse-IgG1-specific protein). The immunoassay performance of the antibody-labeled QDs was evaluated using a pregnancy test kit, displaying equivalent detection sensitivity to a commercially available kit. This study proposed an innovative strategy for QD biofunctionalization in a modular manner, which can be expanded to a diverse range of colloidal particle derivatization.
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Affiliation(s)
- Sunghwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yoonji Bae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sung Han Park
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ning Chen
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Soomin Eom
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sebyung Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
| | - Jongnam Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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5
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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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6
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Jin Z, Dridi N, Palui G, Palomo V, Jokerst JV, Dawson PE, Sang QXA, Mattoussi H. Quantum Dot-Peptide Conjugates as Energy Transfer Probes for Sensing the Proteolytic Activity of Matrix Metalloproteinase-14. Anal Chem 2023; 95:2713-2722. [PMID: 36705737 DOI: 10.1021/acs.analchem.2c03400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We detail the assembly and characterization of quantum dot (QD)-dye conjugates constructed using a peptide bridge specifically designed to recognize and interact with a breast cancer biomarker─matrix metalloproteinase-14 (MMP-14). The assembled QD conjugates are then used as optically addressable probes, relying on Förster resonance energy transfer (FRET) interactions as a transduction mechanism to detect the activity of MMP-14 in solution phase. The QDs were first coated with dithiolane poly(ethylene glycol) (PEG) bearing a carboxyl group that allows coupling via amide bond formation with different dye-labeled peptides. The analytical capability of the conjugates is enabled by correlating changes in the FRET efficiency with the conjugate valence and/or QD-to-dye separation distance, triggered and modulated by enzymatic proteolysis of surface-tethered peptides. The FRET probe exhibits great sensitivity to enzyme digestion with sub-nanomolar limit of detection. We further analyze the proteolysis data within the framework of the Michaelis-Menten model, which considers the fact that surface-attached peptides have a slower diffusion coefficient than free peptides. This results in reduced collision frequency and lower catalytic efficiency, kcat/KM. Our results suggest that our conjugate design is promising, effective, and potentially useful for in vivo analysis.
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Affiliation(s)
- Zhicheng Jin
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Narjes Dridi
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Goutam Palui
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Valle Palomo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jesse V Jokerst
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Phillip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Qing-Xiang Amy Sang
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Hedi Mattoussi
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Tingey M, Schnell SJ, Yu W, Saredy J, Junod S, Patel D, Alkurdi AA, Yang W. Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA. Cells 2022; 11:cells11193079. [PMID: 36231040 PMCID: PMC9564294 DOI: 10.3390/cells11193079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.
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Tang B, Liu BH, Liu ZY, Luo MY, Shi XH, Pang DW. Quantum Dots with a Compact Amphiphilic Zwitterionic Coating. ACS APPLIED MATERIALS & INTERFACES 2022; 14:28097-28104. [PMID: 35686447 DOI: 10.1021/acsami.2c04438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Generally speaking, it is difficult to keep nanomaterials encapsulated in amphiphilic polymers like octylamine-grafted poly(acrylic acid) (OPA) compact in coating-layer, with a small hydrodynamic size. Here, we prepared stable hydrophilic quantum dots (QDs) via encapsulation in ∼3 nm-long amphiphilic and zwitterionic (AZ) molecules. After encapsulation with AZ molecules, the coated QDs are only 2.1 nm thicker in coating, instead of 5.4 nm with OPA. Meanwhile, the hydrodynamic sizes of CdSe/CdS, ZnCdSeS, ZnCdSe/ZnS, and CdSe/ZnS QDs encapsulated in AZ molecules (AZ-QDs) are less than 15 nm, and 6-7 nm smaller than those of QDs in OPA (OPA-QDs). Notably, both extracellular and intracellular nonspecific binding of AZ-QDs is approximately 100-folds lower than that of OPA-QDs.
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Affiliation(s)
- Bo Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Bing-Hua Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhen-Ya Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Meng-Yao Luo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xue-Hui Shi
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, Frontiers Science Center for Cell Responses, Nankai University, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300071, P. R. China
| | - Dai-Wen Pang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, Research Center for Analytical Sciences, College of Chemistry, Frontiers Science Center for Cell Responses, Nankai University, Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300071, P. R. China
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10
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Han Z, Vaidya RM, Arogundade OH, Ma L, Zahid MU, Sarkar S, Kuo CW, Selvin PR, Smith AM. Structural Design of Multidentate Copolymers as Compact Quantum Dot Coatings for Live-Cell Single-Particle Imaging. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2022; 34:4621-4632. [PMID: 36968145 PMCID: PMC10038122 DOI: 10.1021/acs.chemmater.2c00498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Quantum dots (QDs) are a class of semiconductor nanocrystal used broadly as fluorescent emitters for analytical studies in the life sciences. These nanomaterials are particularly valuable for single-particle imaging and tracking applications in cells and tissues. An ongoing technological goal is to reduce the hydrodynamic size of QDs to enhance access to sterically hindered biological targets. Multidentate polymer coatings are a focus of these efforts and have resulted in compact and stable QDs with hydrodynamic diameters near 10 nm. New developments are needed to reach smaller sizes to further enhance transport through pores in cells and tissues. Here, we describe how structural characteristics of linear multidentate copolymers determine hydrodynamic size, colloidal stability, and biomolecular interactions of coated QDs. We tune copolymer composition, degree of polymerization, and hydrophilic group length, and coat polymers on CdSe and (core)shell (HgCdSe)CdZnS QDs. We find that a broad range of polymer structures and compositions yield stable colloidal dispersions; however, hydrodynamic size minimization and nonspecific binding resistance can only be simultaneously achieved within a narrow range of properties, requiring short polymers, balanced compositions, and small nanocrystals. In quantitative single-molecule imaging assays in synapses of live neurons, size reduction progressively increases labeling specificity of neurotransmitter receptors. Our findings provide a design roadmap to next-generation QDs with sizes approaching fluorescent protein labels that are the standard of many live-cell biomolecular studies.
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Affiliation(s)
- Zhiyuan Han
- Department of Materials Science and Engineering and Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rohit M Vaidya
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Opeyemi H Arogundade
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Liang Ma
- Department of Materials Science and Engineering and Holonyak Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mohammad U Zahid
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, Center for the Physics of Living Cells, and Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States-8163
| | - Andrew M Smith
- Department of Materials Science and Engineering, Holonyak Micro and Nanotechnology Laboratory, Department of Bioengineering, Cancer Center at Illinois, and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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11
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Wan Q, Zeng F, Sun Y, Chen T, Yu J, Wu H, Zhao Z, Cao J, Pan F. Memristive Behaviors Dominated by Reversible Nucleation Dynamics of Phase-Change Nanoclusters. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105070. [PMID: 35048484 DOI: 10.1002/smll.202105070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/14/2021] [Indexed: 06/14/2023]
Abstract
One of the important steps for realizing artificial intelligence is identifying elementary units that are beneficial for neural network construction. A type of memristive behavior in which phase-change nanoclusters nucleate adaptively in two adjacent dielectric layers with distinct distribution patterns is demonstrated. This memristive system responds in potentiation to increased stimulation strength and fire action potential after threshold stimulation. Reversible nucleation of phase-change nanoclusters is confirmed after both in situ and ex situ examinations using high-resolution transmission electron microscopy. The dynamics at the nanoscale level dominates the actions of the two dielectric layers. The oscillation response over a long period is due to the competition between crystalline and amorphous phases in the layer near the bottom electrode. Weight mutation, that is, action potential firing, is caused by the blockage of the filament in the layer near the top electrode. The memristive system is compact and able to execute complicated functions of a complete neuron and performs an important role in neuromorphic computing.
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Affiliation(s)
- Qin Wan
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Fei Zeng
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
- Center for Brain Inspired Computing Research (CBICR), Tsinghua University, Beijing, 100084, P. R. China
| | - Yiming Sun
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Tongjin Chen
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Junwei Yu
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Huaqiang Wu
- Center for Brain Inspired Computing Research (CBICR), Tsinghua University, Beijing, 100084, P. R. China
- Microelectronics Institute, Tsinghua University, Beijing, 100084, P. R. China
| | - Zhen Zhao
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100082, P. R. China
| | - Jiangli Cao
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100082, P. R. China
| | - Feng Pan
- Key Laboratory of Advanced Materials (MOE), School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
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12
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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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13
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Egloff S, Melnychuk N, Cruz Da Silva E, Reisch A, Martin S, Klymchenko AS. Amplified Fluorescence in Situ Hybridization by Small and Bright Dye-Loaded Polymeric Nanoparticles. ACS NANO 2022; 16:1381-1394. [PMID: 34928570 DOI: 10.1021/acsnano.1c09409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Detection and imaging of RNA at the single-cell level is of utmost importance for fundamental research and clinical diagnostics. Current techniques of RNA analysis, including fluorescence in situ hybridization (FISH), are long, complex, and expensive. Here, we report a methodology of amplified FISH (AmpliFISH) that enables simpler and faster RNA imaging using small and ultrabright dye-loaded polymeric nanoparticles (NPs) functionalized with DNA. We found that the small size of NPs (below 20 nm) was essential for their access to the intracellular mRNA targets in fixed permeabilized cells. Moreover, proper selection of the polymer matrix of DNA-NPs minimized nonspecific intracellular interactions. Optimized DNA-NPs enabled sequence-specific imaging of different mRNA targets (survivin, actin, and polyA tails), using a simple 1 h staining protocol. Encapsulation of cyanine and rhodamine dyes with bulky counterions yielded green-, red-, and far-red-emitting NPs that were 2-100-fold brighter than corresponding quantum dots. These NPs enabled multiplexed detection of three mRNA targets simultaneously, showing distinctive mRNA expression profiles in three cancer cell lines. Image analysis confirmed the single-particle nature of the intracellular signal, suggesting single-molecule sensitivity of the method. AmpliFISH was found to be semiquantitative, correlating with RT-qPCR. In comparison with the commercial locked nucleic acid (LNA)-based FISH technique, AmpliFISH provides 8-200-fold stronger signal (dependent on the NP color) and requires only three steps vs ∼20 steps together with a much shorter time. Thus, combination of bright fluorescent polymeric NPs with FISH yields a fast and sensitive single-cell transcriptomic analysis method for RNA research and clinical diagnostics.
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Affiliation(s)
- Sylvie Egloff
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Nina Melnychuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Elisabete Cruz Da Silva
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Sophie Martin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
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14
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Pradhan D, Biswasroy P, Sahu A, Sahu DK, Ghosh G, Rath G. Recent Advances in Herbal Nanomedicines for Cancer Treatment. Curr Mol Pharmacol 2021; 14:292-305. [PMID: 32448111 DOI: 10.2174/1874467213666200525010624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
Abstract
Cancer continues to be one of the deadliest diseases that adversely impacts the large population of the world. A stack of scientific documents reflects a huge number of potent plant-based anticancer drugs such as curcumin (CUR), podophyllotoxin, camptothecin (CPT), vincristine, vinblastine, paclitaxel (PTX), etc. that have been integrated into the modern practice of cancer treatment. The demand for natural products raises exponentially as they are generally considered to be safe, and devoid of critical toxic effects at the therapeutic dose when compared to their synthetic counterparts. Despite rising interest towards the potent phytoconstituents, formulation developer faces various challenges in drug development processes such as poor water solubility, low bioavailability, marginal permeability, and nonspecific drug delivery at the target site, etc. Further, adverse drug reaction and multidrug resistance are other critical issues that need to be addressed. Nanomedicines owing to their unique structural and functional attributes help to fix the above challenges for improved translational outcomes. This review summarises the prospects and challenges of a nanotechnology-based drug delivery approach for the delivery of plant-based anticancer drugs.
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Affiliation(s)
- Deepak Pradhan
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Prativa Biswasroy
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Amita Sahu
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Dipak K Sahu
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Goutam Ghosh
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Goutam Rath
- Department of Pharmacognosy, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
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15
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Ma L, Geng J, Kolossov VL, Han Z, Pei Y, Lim SJ, Kilian KA, Smith AM. Antibody Self-Assembly Maximizes Cytoplasmic Immunostaining Accuracy of Compact Quantum Dots. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:4877-4889. [PMID: 35221487 PMCID: PMC8880911 DOI: 10.1021/acs.chemmater.1c00164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Antibody conjugates of quantum dots (QDs) are expected to transform immunofluorescence staining by expanding multiplexed analysis and improving target quantification. Recently, a new generation of small QDs coated with multidentate polymers has improved QD labeling density in diverse biospecimens, but new challenges prevent their routine use. In particular, these QDs exhibit nonspecific binding to fixed cell nuclei and their antibody conjugates have random attachment orientations. This report describes four high-efficiency chemical approaches to conjugate antibodies to compact QDs. Methods include click chemistry and self-assembly through polyhistidine coordination, both with and without adaptor proteins that directionally orient antibodies. Specific and nonspecific labeling are independently analyzed after application of diverse blocking agent classes, and a new assay is developed to quantitatively measure intracellular labeling density based on microtubule stain connectivity. Results show that protein conjugation to the QD surface is required to simultaneously eliminate nonspecific binding and maintain antigen specificity. Of the four conjugation schemes, polyhistidine-based coordination of adaptor proteins with antibody self-assembly yields the highest intracellular staining density and the simplest conjugation procedure. Therefore, antibody and adaptor protein orientation, in addition to blocking optimization, are important determinants of labeling outcomes, insights that can inform translational development of these more compact nanomaterials.
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Affiliation(s)
- Liang Ma
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junlong Geng
- Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vladimir L Kolossov
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhiyuan Han
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Pei
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sung Jun Lim
- Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Division of Nanotechnology, Dalseong-Gun 42988, Republic of Korea
| | - Kristopher A Kilian
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; School of Materials Science and Engineering and School of Chemistry, Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew M Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Holonyak Micro and Nanotechnology Laboratory, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, and Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States; Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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16
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Toufanian R, Chern M, Kong VH, Dennis AM. Engineering Brightness Matched Indium Phosphide Quantum Dots. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:1964-1975. [PMID: 34219920 PMCID: PMC8243842 DOI: 10.1021/acs.chemmater.0c03181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The size-dependent optoelectronic properties of semiconductor nanocrystals quantum dots (QDs) are hugely beneficial for color tunability but induce an inherent relative PL brightness mismatch in QDs emitting different colors, as larger emitters absorb more incident photons than smaller particles. Here, we examine the effect of core composition, shell composition, and shell thickness on optical properties including high energy absorption, quantum yield (QY), and the relative brightness of InP/ZnS and InP/ZnSe core/shell and InP/ZnSe/ZnS core/shell/shell QDs at different excitation wavelengths. Our analysis reveals that the presence of an intermediate ZnSe shell changes the wavelength of enhanced absorption onset and leads to highly excitation wavelength dependent QYs. Switching from commercial CdSe/ZnS to InP/ZnS reduces the brightness-mismatch between green and red emitters from 33- to 5-fold. Incorporating a 4-monolayer thick optically absorbing ZnSe shell into the QD heterostructure and heating the QDs in a solution of zinc oleate and trioctylphosphine produces InP/ZnSe/ZnS QDs that are ~10-fold brighter than their InP/ZnS counterparts. In contrast to CdSe/CdS/ZnS core/shell/shell QDs, which only photoluminesce at red wavelengths with thicker CdS shells due to their Quasi-Type II bandstructure, Type I InP/ZnSe/ZnS QDs are uniquely suited to creating a rainbow of visible-emitting, brightness matched emitters. By tailoring the thickness of the intermediate ZnSe shell, heavy metal-free, brightness-matched green and red emitters are produced. This study highlights the ability to overcome the inherent brightness mismatch seen in QDs through concerted materials design of heterostructured core/shell InP-based QDs.
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Affiliation(s)
- Reyhaneh Toufanian
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - Victoria H Kong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Allison M Dennis
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
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17
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Zhao Z, Chen C, Wei S, Xiong H, Hu F, Miao Y, Jin T, Min W. Ultra-bright Raman dots for multiplexed optical imaging. Nat Commun 2021; 12:1305. [PMID: 33637723 PMCID: PMC7910594 DOI: 10.1038/s41467-021-21570-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/29/2021] [Indexed: 02/06/2023] Open
Abstract
Imaging the spatial distribution of biomolecules is at the core of modern biology. The development of fluorescence techniques has enabled researchers to investigate subcellular structures with nanometer precision. However, multiplexed imaging, i.e. observing complex biological networks and interactions, is mainly limited by the fundamental ‘spectral crowding’ of fluorescent materials. Raman spectroscopy-based methods, on the other hand, have a much greater spectral resolution, but often lack the required sensitivity for practical imaging of biomarkers. Addressing the pressing need for new Raman probes, herein we present a series of Raman-active nanoparticles (Rdots) that exhibit the combined advantages of ultra-brightness and compact sizes (~20 nm). When coupled with the emerging stimulated Raman scattering (SRS) microscopy, these Rdots are brighter than previously reported Raman-active organic probes by two to three orders of magnitude. We further obtain evidence supporting for SRS imaging of Rdots at single particle level. The compact size and ultra-brightness of Rdots allows immunostaining of specific protein targets (including cytoskeleton and low-abundant surface proteins) in mammalian cells and tissue slices with high imaging contrast. These Rdots thus offer a promising tool for a large range of studies on complex biological networks. Raman-based imaging of biomarkers is often challenging due to low sensitivity. Here, the authors use a swelling-diffusion approach to develop a series of Raman probes that are both ultra-bright and compact in size, and demonstrate multiplexed imaging of specific protein targets in cells and tissue slices.
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Affiliation(s)
- Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Chen Chen
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Shixuan Wei
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Hanqing Xiong
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Fanghao Hu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Yupeng Miao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Tianwei Jin
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
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18
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Fluorescence In Situ Hybridization with Quantum Dot Labels in E. coli Cells. Methods Mol Biol 2021. [PMID: 33576988 DOI: 10.1007/978-1-0716-1115-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In this chapter we describe the use of fluorescent quantum dots (QDs) as labels for microbial mRNA transcripts using fluorescence in situ hybridization (FISH). Unlike organic dyes, which are the standard labels in modern FISH methods, QDs provide fluorescence signals that are much brighter and resistant to photobleaching, with an expanded spectral range for multiplexing. We describe the preparation of QDs with compact sizes necessary for accurate labeling, their application for analyzing lacZ transcripts in Escherichia coli cells using FISH, and an assessment of signal stability. We further discuss differences between methods for mammalian cells and bacteria, for which individual nucleic acids cannot be discretely counted due to the small cell size and the optical diffraction limit.
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19
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Klymchenko AS, Liu F, Collot M, Anton N. Dye-Loaded Nanoemulsions: Biomimetic Fluorescent Nanocarriers for Bioimaging and Nanomedicine. Adv Healthc Mater 2021; 10:e2001289. [PMID: 33052037 DOI: 10.1002/adhm.202001289] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Indexed: 12/16/2022]
Abstract
Lipid nanoemulsions (NEs), owing to their controllable size (20 to 500 nm), stability and biocompatibility, are now frequently used in various fields, such as food, cosmetics, pharmaceuticals, drug delivery, and even as nanoreactors for chemical synthesis. Moreover, being composed of components generally recognized as safe (GRAS), they can be considered as "green" nanoparticles that mimic closely lipoproteins and intracellular lipid droplets. Therefore, they attracted attention as carriers of drugs and fluorescent dyes for both bioimaging and studying the fate of nanoemulsions in cells and small animals. In this review, the composition of dye-loaded NEs, methods for their preparation, and emerging biological applications are described. The design of bright fluorescent NEs with high dye loading and minimal aggregation-caused quenching (ACQ) is focused on. Common issues including dye leakage and NEs stability are discussed, highlighting advanced techniques for their characterization, such as Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS). Attempts to functionalize NEs surface are also discussed. Thereafter, biological applications for bioimaging and single-particle tracking in cells and small animals as well as biomedical applications for photodynamic therapy are described. Finally, challenges and future perspectives of fluorescent NEs are discussed.
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Affiliation(s)
- Andrey S. Klymchenko
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Fei Liu
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
| | - Mayeul Collot
- Laboratory of Biophotonic and Pathologies CNRS UMR 7021 Université de Strasbourg Faculté de Pharmacie, 74, Route du Rhin Illkirch 67401 France
| | - Nicolas Anton
- Université de Strasbourg CNRS CAMB UMR 7199 Strasbourg F‐67000 France
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20
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Zhong GX, Ye CL, Wei HX, Yang LY, Wei QX, Liu ZJ, Fu LX, Lin XH, Chen JY. Ultrasensitive Detection of RNA with Single-Base Resolution by Coupling Electrochemical Sensing Strategy with Chimeric DNA Probe-Aided Ligase Chain Reaction. Anal Chem 2020; 93:911-919. [PMID: 33284015 DOI: 10.1021/acs.analchem.0c03563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate and sensitive detection of single-base mutations in RNAs is of great value in basic studies of life science and medical diagnostics. However, the current available RNA detection methods are challenged by heterogeneous clinical samples in which trace RNA mutants usually existed in a large pool of normal wild sequences. Thus, there is still great need for developing the highly sensitive and highly specific methods in detecting single-base mutations of RNAs in heterogeneous clinical samples. In the present study, a new chimeric DNA probe-aided ligase chain reaction-based electrochemical method (cmDNA-eLCR) was developed for RNA mutation detection through the BSA-based carrier platform and the horseradish peroxidase-hydrogen peroxide-tetramethylbenzidine (HRP-H2O2-TMB) system. The denaturing polyacrylamide gel electrophoresis and a fluorophore-labeled probe was ingeniously designed to demonstrate the advantage of cmDNA in ligation to normal DNA templated by RNA with the catalysis of T4 RNA ligase 2 as well as its higher selectivity than DNA ligase system. Finally, the proposed cmDNA-eLCR, compared with the traditional eLCR, showed excellent performance in discriminating single base-mismatched sequences, where the signal response for mismatched targets at a high concentration could overlap completely with that for the blank control. Besides, this cmDNA-eLCR assay had a wide linear range crossing six orders of magnitude from 1.0 × 10-15 to1.0 × 10-10 M with a limit of detection as low as 0.6 fM. Furthermore, this assay was applied to detect RNA in real sample with a satisfactory result, thereby demonstrating its great potential in diagnosis of RNA-related diseases.
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Affiliation(s)
- Guang-Xian Zhong
- Department of Orthopedics, Fujian Provincial Institute of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China
| | - Hong-Xiang Wei
- Department of Orthopedics, Fujian Provincial Institute of Orthopedics, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Liang-Yong Yang
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Xia Wei
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Zhou-Jie Liu
- Department of Pharmacy, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Leng-Xi Fu
- The Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou 350005, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, First Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou 350005, China
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21
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Collot M, Schild J, Fam KT, Bouchaala R, Klymchenko AS. Stealth and Bright Monomolecular Fluorescent Organic Nanoparticles Based on Folded Amphiphilic Polymer. ACS NANO 2020; 14:13924-13937. [PMID: 33022173 DOI: 10.1021/acsnano.0c06348] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fluorescent nanoparticles (NPs), owing to their superior brightness, are an attractive alternative to organic dyes. However, their cellular applications remain limited because of their large size, poor homogeneity, and nonspecific interactions in biological media. Herein, we propose a concept of monomolecular fluorescent organic nanoparticles of high brightness and very small size (10-14 nm) built of a single amphiphilic polymer bearing specially designed fluorescent dyes. We found that high PEGylation of poly(maleic anhydride-alt-1-octadecene (PMAO) favors a single-chain polymer folding into monomolecular stealth NPs with highly reduced nonspecific interactions with proteins and live cells. To ensure high stability of our NPs, the fluorophores (BODIPYs) are covalently linked to the polymer through an optimized linker. Among tested linkers of different lengths and polarity, a short medium-polar linker favoring location of the dyes at NPs interface ensures good fluorescence quantum yield and small particle size. The fluorescence brightness of these NPs has been dramatically enhanced by increasing the bulkiness of the BODIPY dyes that prevents their H-aggregation, reaching 2500000 M-1 cm-1 (extinction coefficient × quantum yield). Fluorescence microscopy revealed that the single-particle brightness of these NPs is ∼5-fold higher than that of QDot-585 using the same excitation wavelength (532 nm). Finally, when microinjected inside cells, these small and stealth NPs (10 nm diameter) distribute more evenly than 20 nm QDots inside the cytosol, showing similar spreading as a fluorescent protein. Thus, the developed monomolecular NPs, owing to their small size and stealth properties, are artificial analogues of fluorescent proteins, surpassing the latter >50-fold in terms of brightness.
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Affiliation(s)
- Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Jérémy Schild
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Kyong T Fam
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Redouane Bouchaala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route du Rhin, 67401 Illkirch, France
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22
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Perillo M, Paganos P, Spurrell M, Arnone MI, Wessel GM. Methodology for Whole Mount and Fluorescent RNA In Situ Hybridization in Echinoderms: Single, Double, and Beyond. Methods Mol Biol 2020; 2219:195-216. [PMID: 33074542 DOI: 10.1007/978-1-0716-0974-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Identifying the location of a specific RNA in a cell, tissue, or embryo is essential to understand its function. Here we use echinoderm embryos to demonstrate the power of fluorescence in situ RNA hybridizations to localize sites of specific RNA accumulation in whole mount embryo applications. We add to this technology the use of various probe-labeling technologies to colabel multiple RNAs in one application and we describe protocols for incorporating immunofluorescence approaches to maximize the information obtained in situ. We offer alternatives for these protocols and troubleshooting advice to identify steps in which the procedure may have failed. Overall, echinoderms are wonderfully suited for these technologies, and these protocols are applicable to a wide range of cells, tissues, and embryos.
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Affiliation(s)
- Margherita Perillo
- Department of Molecular and Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Periklis Paganos
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maxwell Spurrell
- Department of Molecular and Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Maria I Arnone
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Gary M Wessel
- Department of Molecular and Cellular Biology and Biochemistry, Brown University, Providence, RI, USA.
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23
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Le P, Vaidya R, Smith LD, Han Z, Zahid MU, Winter J, Sarkar S, Chung HJ, Perez-Pinera P, Selvin PR, Smith AM. Optimizing Quantum Dot Probe Size for Single-Receptor Imaging. ACS NANO 2020; 14:8343-8358. [PMID: 32525656 PMCID: PMC7872344 DOI: 10.1021/acsnano.0c02390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantum dots (QDs) are nanocrystals with bright fluorescence and long-term photostability, attributes particularly beneficial for single-molecule imaging and molecular counting in the life sciences. The size of a QD nanocrystal determines its physicochemical and photophysical properties, both of which dictate the success of imaging applications. Larger nanocrystals typically have better optical properties, with higher brightness, red-shifted emission, reduced blinking, and greater stability. However, larger nanocrystals introduce molecular-labeling biases due to steric hindrance and nonspecific binding. Here, we systematically analyze the impact of nanocrystal size on receptor labeling in live and fixed cells. We designed three (core)shell QDs with red emission (600-700 nm) and crystalline sizes of 3.2, 5.5, and 8.3 nm. After coating with the same multidentate polymer, hydrodynamic sizes were 9.2 nm (QD9.2), 13.3 nm (QD13.3), and 17.4 nm (QD17.4), respectively. The QDs were conjugated to streptavidin and applied as probes for biotinylated neurotransmitter receptors. QD9.2 exhibited the highest labeling specificity for receptors in the narrow synaptic cleft (∼20-30 nm) in living neurons. However, for dense receptor labeling for molecular counting in live and fixed HeLa cells, QD13.3 yielded the highest counts. Nonspecific binding rose sharply for hydrodynamic sizes larger than 13.3 nm, with QD17.4 exhibiting particularly diminished specificity. Our comparisons further highlight needs to continue engineering the smallest QDs to increase single-molecule intensity, suppress blinking frequency, and inhibit nonspecific labeling in fixed and permeabilized cells. These results lay a foundation for designing QD probes with further reduced sizes to achieve unbiased labeling for quantitative and single-molecule imaging.
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Affiliation(s)
- Phuong Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rohit Vaidya
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lucas D Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhiyuan Han
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mohammad U Zahid
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Urbana, Illinois 61801 United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Departments of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Urbana, Illinois 61801 United States
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24
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Lin C, Jiang M, Duan S, Qiu J, Hong Y, Wang X, Chen X, Ke R. Visualization of individual microRNA molecules in fixed cells and tissues using target-primed padlock probe assay. Biochem Biophys Res Commun 2020; 526:607-611. [PMID: 32247612 DOI: 10.1016/j.bbrc.2020.03.134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression at the posttranscriptional level. Precisely profiling of miRNA expression will help us to better understand their roles in normal and diseased cells and tissues. Here we describe in situ miRNA detection by padlock probing and miRNA target-primed rolling circle amplification. We optimized our protocol and showed it can be applied to both fixed cells and tissue sections. The method can be used in basic research and potentially in clinical diagnostics in the future.
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Affiliation(s)
- Chen Lin
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
| | - Meng Jiang
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
| | - Shanshan Duan
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
| | - Jianlong Qiu
- Department of Pathology, 910th Hospital of the Joint Logistics Support Force of PLA, Quanzhou, Fujian, China
| | - Yujuan Hong
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Xin Wang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, China
| | - Xiaoyuan Chen
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Quanzhou, Fujian, China.
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25
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Han Z, Sarkar S, Smith AM. Zwitterion and Oligo(ethylene glycol) Synergy Minimizes Nonspecific Binding of Compact Quantum Dots. ACS NANO 2020; 14:3227-3241. [PMID: 32105448 PMCID: PMC7321848 DOI: 10.1021/acsnano.9b08658] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantum dots (QDs) are a class of fluorescent nanocrystals in development as labels for molecular imaging in cells and tissues. Recently, coatings for quantum dots based on multidentate polymers have improved labeling performance in a range of bioanalytical applications, primarily due to reduced probe hydrodynamic size. Now, an ongoing challenge is to eliminate nonspecific binding between these small probes and cellular components that mask specifically labeled molecules. Here, we describe insights into controlling and minimizing intermolecular interactions governing nonspecific binding using multidentate polymers with tunable hydrophilic functional groups that are cationic, anionic, zwitterionic (ZW), or nonionic (oligoethylene glycol; OEG). By fixing surface-binding groups and polymer length, coated colloids have similar sizes but diverse physicochemical properties. We measure binding to globular proteins, fixed cells, and living cells and observe a substantial improvement in nonspecific binding resistance when surfaces are functionalized with a combination of ZW and OEG. The independent underlying effects of counterion adsorption and flexibility appear to synergistically resist adsorption when combined, particularly for fixed cells enriched in both charged and hydrophobic moieties. We further show that ZW-OEG QDs are stable under diverse conditions and can be self-assembled with antibodies to specifically label surface antigens on living cells and cytoplasmic proteins in fixed cells. This surface engineering strategy can be adopted across the diverse range of colloidal materials currently in use and in development for biomedical applications to optimize their molecular labeling specificity.
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Affiliation(s)
- Zhiyuan Han
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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26
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Nag OK, Muroski ME, Hastman DA, Almeida B, Medintz IL, Huston AL, Delehanty JB. Nanoparticle-Mediated Visualization and Control of Cellular Membrane Potential: Strategies, Progress, and Remaining Issues. ACS NANO 2020; 14:2659-2677. [PMID: 32078291 DOI: 10.1021/acsnano.9b10163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The interfacing of nanoparticle (NP) materials with cells, tissues, and organisms for a range of applications including imaging, sensing, and drug delivery continues at a rampant pace. An emerging theme in this area is the use of NPs and nanostructured surfaces for the imaging and/or control of cellular membrane potential (MP). Given the important role that MP plays in cellular biology, both in normal physiology and in disease, new materials and methods are continually being developed to probe the activity of electrically excitable cells such as neurons and muscle cells. In this Review, we highlight the current state of the art for both the visualization and control of MP using traditional materials and techniques, discuss the advantageous features of NPs for performing these functions, and present recent examples from the literature of how NP materials have been implemented for the visualization and control of the activity of electrically excitable cells. We conclude with a forward-looking perspective of how we expect to see this field progress in the near term and further into the future.
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Affiliation(s)
- Okhil K Nag
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
| | - Megan E Muroski
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- American Society for Engineering Education, Washington, D.C. 20036, United States
| | - David A Hastman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Bethany Almeida
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
- American Society for Engineering Education, Washington, D.C. 20036, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
| | - Alan L Huston
- Division of Optical Sciences, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, United States
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27
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Sarkar S, Le P, Geng J, Liu Y, Han Z, Zahid MU, Nall D, Youn Y, Selvin PR, Smith AM. Short-Wave Infrared Quantum Dots with Compact Sizes as Molecular Probes for Fluorescence Microscopy. J Am Chem Soc 2020; 142:3449-3462. [PMID: 31964143 PMCID: PMC7335634 DOI: 10.1021/jacs.9b11567] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Materials with short-wave infrared (SWIR) emission are promising contrast agents for in vivo animal imaging, providing high-contrast and high-resolution images of blood vessels in deep tissues. However, SWIR emitters have not been developed as molecular labels for microscopy applications in the life sciences, which require optimized probes that are bright, stable, and small. Here, we design and synthesize semiconductor quantum dots (QDs) with SWIR emission based on HgxCd1-xSe alloy cores red shifted to the SWIR by epitaxial deposition of thin HgxCd1-xS shells with a small band gap. By tuning alloy composition alone, the emission can be shifted across the visible-to-SWIR (VIR) spectra while maintaining a small and equal size, allowing direct comparisons of molecular labeling performance across a broad range of wavelength. After coating with click-functional multidentate polymers, the VIR-QD spectral series has high quantum yield in the SWIR (14-33%), compact size (13 nm hydrodynamic diameter), and long-term stability in aqueous media during continuous excitation. We show that these properties enable diverse applications of SWIR molecular probes for fluorescence microscopy using conjugates of antibodies, growth factors, and nucleic acids. A broadly useful outcome is a 10-55-fold enhancement of the signal-to-background ratio at both the single-molecule level and the ensemble level in the SWIR relative to visible wavelengths, primarily due to drastically reduced autofluorescence. We anticipate that VIR-QDs with SWIR emission will enable ultrasensitive molecular imaging of low-copy number analytes in biospecimens with high autofluorescence.
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Affiliation(s)
- Suresh Sarkar
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Phuong Le
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Junlong Geng
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yang Liu
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Zhiyuan Han
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Mohammad U Zahid
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Duncan Nall
- Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for the Physics of Living Cells , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yeoan Youn
- Center for the Physics of Living Cells , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Paul R Selvin
- Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for the Physics of Living Cells , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Andrew M Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carle Illinois College of Medicine , Urbana , Illinois 61801 , United States
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28
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Sensitive and selective fluorometric determination of DNA by using layered hexagonal nanosheets of a covalent organic framework prepared from p-phenylenediamine and benzene-1,3,5-tricarboxaldehyde. Mikrochim Acta 2019; 186:833. [DOI: 10.1007/s00604-019-3944-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
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29
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Jiang M, Liu L, Hong C, Chen D, Yao X, Chen X, Lin C, Ke R. Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues. RNA (NEW YORK, N.Y.) 2019; 25:1038-1046. [PMID: 31064786 PMCID: PMC6633204 DOI: 10.1261/rna.070599.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/06/2019] [Indexed: 06/09/2023]
Abstract
Visualization of gene expression at single RNA molecular level represents a great challenge to both imaging technologies and molecular engineering. Here we show a single molecule chromogenic in situ hybridization (smCISH) assay that enables counting and localizing individual RNA molecules in fixed cells and tissue under bright-field microscopy. Our method is based on in situ padlock probe assays directly using RNA as a ligation template and rolling circle amplification combined with enzyme catalyzed chromogenic reaction for amplification product visualization. We show potential applications of our method by detecting gene expression variations in single cells, subcellular localization information of expressed genes, and gene expression heterogeneity in formalin-fixed, paraffin-embedded tissue sections. This facile and straightforward method can in principle be applied to any type of RNA molecules in different samples.
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Affiliation(s)
- Meng Jiang
- Center for Precision Medicine, School of Biomedical Sciences and School of Medicine, Huaqiao University, Quanzhou, Fujian, 362021, China
| | - Ling Liu
- Center for Precision Medicine, School of Biomedical Sciences and School of Medicine, Huaqiao University, Quanzhou, Fujian, 362021, China
| | - Chengye Hong
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, 362000, China
| | - Debo Chen
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, 362000, China
| | - Xihu Yao
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian, 362000, China
| | - Xiaoyuan Chen
- Center for Precision Medicine, School of Biomedical Sciences and School of Medicine, Huaqiao University, Quanzhou, Fujian, 362021, China
| | - Chen Lin
- Center for Precision Medicine, School of Biomedical Sciences and School of Medicine, Huaqiao University, Quanzhou, Fujian, 362021, China
| | - Rongqin Ke
- Center for Precision Medicine, School of Biomedical Sciences and School of Medicine, Huaqiao University, Quanzhou, Fujian, 362021, China
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30
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Pratiwi FW, Kuo CW, Chen BC, Chen P. Recent advances in the use of fluorescent nanoparticles for bioimaging. Nanomedicine (Lond) 2019; 14:1759-1769. [DOI: 10.2217/nnm-2019-0105] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Rapid and recent progress in fluorescence microscopic techniques has allowed for routine discovery and viewing of biological structures and processes in unprecedented spatiotemporal resolution. In these imaging techniques, fluorescent nanoparticles (NPs) play important roles in the improvement of reporting systems. A short overview of recently developed fluorescent NPs used for advanced in vivo imaging will be discussed in this mini-review. The discussion begins with the contribution of fluorescence imaging in exploring the fate of NPs in biological systems. NP applications for in vivo imaging, including cell labeling, multimodal imaging and theranostic agents, are then discussed. Finally, despite all of the advancements in bioimaging, some unsolved challenges will be briefly discussed concerning future research directions.
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Affiliation(s)
| | - Chiung Wen Kuo
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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31
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Wang Z, Liu W, Fan C, Chen N. Visualizing mRNA in live mammalian cells. Methods 2019; 161:16-23. [DOI: 10.1016/j.ymeth.2019.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/06/2023] Open
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32
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Patel S, Kim J, Herrera M, Mukherjee A, Kabanov AV, Sahay G. Brief update on endocytosis of nanomedicines. Adv Drug Deliv Rev 2019; 144:90-111. [PMID: 31419450 PMCID: PMC6986687 DOI: 10.1016/j.addr.2019.08.004] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/06/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
The complexity of nanoscale interactions between biomaterials and cells has limited the realization of the ultimate vision of nanotechnology in diagnostics and therapeutics. As such, significant effort has been devoted to advancing our understanding of the biophysical interactions of the myriad nanoparticles. Endocytosis of nanomedicine has drawn tremendous interest in the last decade. Here, we highlight the ever-present barriers to efficient intracellular delivery of nanoparticles as well as the current advances and strategies deployed to breach these barriers. We also introduce new barriers that have been largely overlooked such as the glycocalyx and macromolecular crowding. Additionally, we draw attention to the potential complications arising from the disruption of the newly discovered functions of the lysosomes. Novel strategies of exploiting the inherent intracellular defects in disease states to enhance delivery and the use of exosomes for bioanalytics and drug delivery are explored. Furthermore, we discuss the advances in imaging techniques like electron microscopy, super resolution fluorescence microscopy, and single particle tracking which have been instrumental in our growing understanding of intracellular pathways and nanoparticle trafficking. Finally, we advocate for the push towards more intravital analysis of nanoparticle transport phenomena using the multitude of techniques available to us. Unraveling the underlying mechanisms governing the cellular barriers to delivery and biological interactions of nanoparticles will guide the innovations capable of breaching these barriers.
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Affiliation(s)
- Siddharth Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 SW Moody Avenue, Portland, OR 97201, USA
| | - Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 SW Moody Avenue, Portland, OR 97201, USA
| | - Marco Herrera
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 SW Moody Avenue, Portland, OR 97201, USA
| | - Anindit Mukherjee
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 SW Moody Avenue, Portland, OR 97201, USA
| | - Alexander V Kabanov
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599, USA; Laboratory of Chemical Design of Bionanomaterials, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Science Building, 2730 SW Moody Avenue, Portland, OR 97201, USA; Department of Biomedical Engineering, Oregon Health and Science University, Robertson Life Science Building, 2730 SW Moody Avenue, Portland, OR 97201, USA.
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33
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Zhou W, Li D, Yuan R, Xiang Y. Programmable DNA Ring/Hairpin-Constrained Structure Enables Ligation-Free Rolling Circle Amplification for Imaging mRNAs in Single Cells. Anal Chem 2019; 91:3628-3635. [DOI: 10.1021/acs.analchem.8b05613] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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