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Mishra R, Kaur P, Soni R, Madan A, Agarwal P, Singh G. Decoding the photoprotection strategies and manipulating cyanobacterial photoprotective metabolites, mycosporine-like amino acids, for next-generation sunscreens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108744. [PMID: 38781638 DOI: 10.1016/j.plaphy.2024.108744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
The most recent evaluation of the impacts of UV-B radiation and depletion of stratospheric ozone points out the need for effective photoprotection strategies for both biological and nonbiological components. To mitigate the disruptive consequences of artificial sunscreens, photoprotective compounds synthesized from gram-negative, oxygenic, and photoautotrophic prokaryote, cyanobacteria have been studied. In a quest to counteract the harmful UV radiation, cyanobacterial species biosynthesize photoprotective metabolites named as mycosporine-like amino acids (MAAs). The investigation of MAAs as potential substitutes for commercial sunscreen compounds is motivated by their inherent characteristics, such as antioxidative properties, water solubility, low molecular weight, and high molar extinction coefficients. These attributes contribute to the stability of MAAs and make them promising candidates for natural alternatives in sunscreen formulations. They are effective at reducing direct damage caused by UV radiation and do not lead to the production of reactive oxygen radicals. In order to better understand the role, ecology, and its application at a commercial scale, tools like genome mining, heterologous expression, and synthetic biology have been explored in this review to develop next-generation sunscreens. Utilizing tactical concepts of bio-nanoconjugate formation for the development of an efficient MAA-nanoparticle conjugate structure would not only give the sunscreen complex stability but would also serve as a promising tool for the production of analogues. This review would provide insight on efforts to produce MAAs by diversifying the biosynthetic pathways, modulating the precursors and stress conditions, and comprehending the gene cluster arrangement for MAA biosynthesis and its application in developing effective sunscreen.
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Affiliation(s)
- Reema Mishra
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Pritam Kaur
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Renu Soni
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Akanksha Madan
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Preeti Agarwal
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Garvita Singh
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
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2
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Lin Y, Tao X, Gao S, Li N, Dai Z. Highly sensitive and stable fluorescent aptasensor based on an exonuclease III-assisted amplification strategy for ATP detection. Anal Biochem 2023:115210. [PMID: 37329966 DOI: 10.1016/j.ab.2023.115210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023]
Abstract
Fluctuations in intracellular adenosine triphosphate (ATP) concentration are closely associated with some cancer diseases. Thus, it is a worthwhile undertaking to predict sickness by monitoring changes in ATP levels. However, the detection limits of current fluorescent aptamer sensors for ATP detection are in the range of nmol L-1 to μmol L-1. It has become crucial to employ amplification strategies to increase the sensitivity of fluorescent aptamer sensors. In the current paper, a duplex hybrid aptamer probe was developed based on exonuclease III (Exo III)-catalyzed target recycling amplification for ATP detection. The target ATP forced the duplex probe configuration to change into a molecular beacon that can be hydrolyzed with Exo III to achieve the target ATP cycling to amplify the fluorescence signal. Significantly, many researchers ignore that FAM is a pH-sensitive fluorophore, leading to the fluorescence instability of FAM-modified probes in different pH buffers. The negatively charged ions on the surface of AuNPs were replaced by new ligands bis(p-sulfonatophenyl)phenylphosphine dihydrate dipotassium salt (BSPP) to improve the drawback of FAM instability in alkaline solutions in this work. The aptamer probe was designed to eliminate the interference of other similar small molecules, showing specific selectivity and providing ultra-sensitive detection of ATP with detection limits (3σ) as low as 3.35 nM. Such detection limit exhibited about 4-500-fold better than that of the other amplification strategies for ATP detection. Thus, a relatively general high sensitivity detection system can be established according to the wide target adaptability of aptamers, which can form specific binding with different types of targets.
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Affiliation(s)
- Yushuang Lin
- School of Textile Science and Engineering, Tiangong University, Tianjin, 300387, China
| | - Xuejiao Tao
- School of Textile Science and Engineering, Tiangong University, Tianjin, 300387, China
| | - Suhan Gao
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, China
| | - Nan Li
- School of Chemistry, Tiangong University, Tianjin, 300387, China.
| | - Zhao Dai
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, China.
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3
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Myres GJ, Harris JM. Stable Immobilization of DNA to Silica Surfaces by Sequential Michael Addition Reactions Developed with Insights from Confocal Raman Microscopy. Anal Chem 2023; 95:3499-3506. [PMID: 36718639 DOI: 10.1021/acs.analchem.2c05594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The immobilization of DNA to surfaces is required for numerous biosensing applications related to the capture of target DNA sequences, proteins, or small-molecule analytes from solution. For these applications to be successful, the chemistry of DNA immobilization should be efficient, reproducible, and stable and should allow the immobilized DNA to adopt a secondary structure required for association with its respective target molecule. To develop and characterize surface immobilization chemistry to meet this challenge, it is invaluable to have a quantitative, surface-sensitive method that can report the interfacial chemistry at each step, while also being capable of determining the structure, stability, and activity of the tethered DNA product. In this work, we develop a method to immobilize DNA to silica, glass, or other oxide surfaces by carrying out the reactions in porous silica particles. Due to the high specific surface area of porous silica, the local concentrations of surface-immobilized molecules within the particle are sufficiently high that interfacial chemistry can be monitored at each step of the process with confocal Raman microscopy, providing a unique capability to assess the molecular composition, structure, yield, and surface coverage of these reactions. We employ this methodology to investigate the steps for immobilizing thiolated-DNA to thiol-modified silica surfaces through sequential Michael addition reactions with the cross-linker 1,4-phenylene-bismaleimide. A key advantage of employing a phenyl-bismaleimide over a comparable alkyl coupling reagent is the efficient conversion of the initial phenyl-thiosuccinimide to a more stable succinamic acid thioether linkage. This transformation was confirmed by in situ Raman spectroscopy measurements, and the resulting succinamic acid thioether product exhibited greater than 95% retention of surface-immobilized DNA after 12 days at room temperature in aqueous buffer. Confocal Raman microscopy was also used to assess the conformational freedom of surface-immobilized DNA by comparing the structure of a 23-mer DNA hairpin sequence under duplex-forming and unfolding conditions. We find that the immobilized DNA hairpin can undergo reversible intramolecular duplex formation based on the changes in frequencies and intensities of the phosphate backbone and base-specific vibrational modes that are informative of the hybridization state of DNA.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850 United States
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4
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Stein F, Schielke A, Barcikowski S, Rehbock C. Influence of Gold/Silver Ratio in Ablative Nanoparticles on Their Interaction with Aptamers and Functionality of the Obtained Conjugates. Bioconjug Chem 2021; 32:2439-2446. [PMID: 34730343 DOI: 10.1021/acs.bioconjchem.1c00468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Nano-bio-conjugates, featuring noble metal gold-silver alloy nanoparticles, represent a versatile tool in diagnostics and therapeutics due to their plasmonic and antimicrobial properties tunable by the particle's gold molar fraction. However, little is known about how the binding of thiolated biomolecules to noble metal nanoparticles is influenced by the fraction of gold and silver atoms on the nanoparticle's surface and to which extend this would affect the functionality of the conjugated biomolecules. In this work, we generated gold-silver alloy nanoparticles with average diameters of 7-8 nm using the modern, surfactant-free laser ablation in liquids (LAL) synthesis approach. We conjugated them with thiolated miniStrep aptamer ligands at well-controlled aptamer-to-nanoparticle surface area ratios with maxima between 12 and 27 pmol aptamer/cm2 particle surface area. The results revealed a clear correlation between surface coverage and the nanoparticles' nominal gold/silver ratio, with maximum coverage reached for gold-rich alloys and a pronounced maximum for silver-rich alloys. However, the conjugates' functionality, evaluated by binding of streptavidin, was surprisingly robust and hardly affected by the nominal composition. However, 1.5 times higher surface coverage was needed to obtain maximum functionality in the silver-rich conjugates. Based on these results, it may be concluded that the nominal composition of gold-silver alloy nano-bioconjugates is freely tunable without a pronounced impact on the attached ligands' functionality, a finding highly relevant for the flexible design of nano-bio-conjugates for future biomedical applications. This study's results may facilitate the design of alloy nano-bio-conjugates for future applications in therapeutics and diagnostics.
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Affiliation(s)
- Frederic Stein
- Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitätsstr. 7, 45141 Essen, Germany
| | - Andreas Schielke
- Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitätsstr. 7, 45141 Essen, Germany
| | - Stephan Barcikowski
- Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitätsstr. 7, 45141 Essen, Germany
| | - Christoph Rehbock
- Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Universitätsstr. 7, 45141 Essen, Germany
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Lai Q, Chen W, Zhang Y, Liu Z. Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors. Analyst 2021; 146:5822-5835. [PMID: 34581324 DOI: 10.1039/d1an00765c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.
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Affiliation(s)
- Qingteng Lai
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Wei Chen
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China. .,Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Yanke Zhang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Zhengchun Liu
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
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6
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Li SJ, Shi X. Tailoring Antifouling Properties of Nanocarriers via Entropic Collision of Polymer Grafting. ACS NANO 2021; 15:5725-5734. [PMID: 33710849 DOI: 10.1021/acsnano.1c01173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymer graftings (PGs) are widely employed in antifouling surfaces and drug delivery systems to regulate the interaction with a foreign environment. Through molecular dynamics simulations and scaling theory analysis, we investigate the physical antifouling properties of PGs via their collision behaviors. Compared with mushroom-like PGs with low grafting density, we find brush-like PGs with high grafting density could generate large deformation-induced entropic repulsive force during a collision, revealing a microscopic mechanism for the hop motions of polymer-grafted nanoparticles for drug delivery observed in experiment. In addition, the collision elasticity of PGs is found to decay with the collision velocity by a power law, i.e., a concise dynamic scaling despite the complex process involved, which is beyond expectation. These results elucidate the dynamic interacting mechanism of PGs, which are of immediate interest for a fundamental understanding of the antifouling performance of PGs and the rational design of PG-coated nanoparticles in nanomedicine for drug delivery.
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Affiliation(s)
- Shu-Jia Li
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, No. 11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, No. 11 ZhongGuanCun BeiYiTiao, Beijing 100190, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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7
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Liu Y, Pan B, Li H, Lang D, Zhao Q, Zhang D, Wu M, Steinberg CEW, Xing B. Can the properties of engineered nanoparticles be indicative of their functions and effects in plants? ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111128. [PMID: 32827963 DOI: 10.1016/j.ecoenv.2020.111128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The extensive applicability of engineered nanoparticles (ENPs) in various fields such as environment, agriculture, medicine or biotechnology has mostly been attributed to their better physicochemical properties as compared with conventional bulk materials. However, functions and biological effects of ENPs change across different scenarios which impede the progress in their risk assessment and safety management. This review thus intends to figure out whether properties of ENPs can be indicators of their behavior through summarizing and analyzing the available literature and knowledge. The studies have indicated that size, shape, solubility, specific surface area, surface charge and surface reactivity constitute a more accurate measure of ENPs functions and toxic effects in addition to mass concentration. Effects of ENPs are also highly dependent on dose metrics, species and strains of organisms, environmental conditions, exposure route and duration. Searching correlations between properties and functions or biological effects may serve as an effective way in understanding positive and negative impacts of ENPs. This will ensure safe design and sustainable future use of ENPs.
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Affiliation(s)
- Yang Liu
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China
| | - Bo Pan
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China.
| | - Hao Li
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China
| | - Di Lang
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China
| | - Qing Zhao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Di Zhang
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China
| | - Min Wu
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China
| | - Christian E W Steinberg
- Yunnan Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science & Engineering, Kunming University of Science & Technology, Kunming, 650500, China; Institute of Biology, Freshwater & Stress Ecology, Humboldt University, Berlin, 12437, Germany
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States.
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8
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He Z, Yin H, Chang CC, Wang G, Liang X. Interfacing DNA with Gold Nanoparticles for Heavy Metal Detection. BIOSENSORS 2020; 10:E167. [PMID: 33172098 PMCID: PMC7694790 DOI: 10.3390/bios10110167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
The contamination of heavy metals (e.g., Hg, Pb, Cd and As) poses great risks to the environment and human health. Rapid and simple detection of heavy metals of considerable toxicity in low concentration levels is an important task in biological and environmental analysis. Among the many convenient detection methods for heavy metals, DNA-inspired gold nanoparticles (DNA-AuNPs) have become a well-established approach, in which assembly/disassembly of AuNPs is used for colorimetric signaling of the recognition event between DNA and target heavy metals at the AuNP interface. This review focuses on the recent efforts of employing DNA to manipulate the interfacial properties of AuNPs, as well as the major advances in the colorimetric detection of heavy metals. Beginning with the introduction of the fundamental aspects of DNA and AuNPs, three main strategies of constructing DNA-AuNPs with DNA binding-responsive interface are discussed, namely, crosslinking, electrostatic interaction and base pair stacking. Then, recent achievements in colorimetric biosensing of heavy metals based on manipulation of the interface of DNA-AuNPs are surveyed and compared. Finally, perspectives on challenges and opportunities for future research in this field are provided.
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Affiliation(s)
- Zhiyu He
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
| | - Huiling Yin
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
| | - Chia-Chen Chang
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
- Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan 33302, Taiwan
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; (Z.H.); (H.Y.); (X.L.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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9
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Cajigas S, Orozco J. Nanobioconjugates for Signal Amplification in Electrochemical Biosensing. Molecules 2020; 25:molecules25153542. [PMID: 32756410 PMCID: PMC7436128 DOI: 10.3390/molecules25153542] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023] Open
Abstract
Nanobioconjugates are hybrid materials that result from the coalescence of biomolecules and nanomaterials. They have emerged as a strategy to amplify the signal response in the biosensor field with the potential to enhance the sensitivity and detection limits of analytical assays. This critical review collects a myriad of strategies for the development of nanobioconjugates based on the conjugation of proteins, antibodies, carbohydrates, and DNA/RNA with noble metals, quantum dots, carbon- and magnetic-based nanomaterials, polymers, and complexes. It first discusses nanobioconjugates assembly and characterization to focus on the strategies to amplify a biorecognition event in biosensing, including molecular-, enzymatic-, and electroactive complex-based approaches. It provides some examples, current challenges, and future perspectives of nanobioconjugates for the amplification of signals in electrochemical biosensing.
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10
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Daly CA, Allen C, Rozanov N, Chong G, Melby ES, Kuech TR, Lohse SE, Murphy CJ, Pedersen JA, Hernandez R. Surface Coating Structure and Its Interaction with Cytochrome c in EG 6-Coated Nanoparticles Varies with Surface Curvature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5030-5039. [PMID: 32302137 DOI: 10.1021/acs.langmuir.0c00681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The composition, orientation, and conformation of proteins in biomolecular coronas acquired by nanoparticles in biological media contribute to how they are identified by a cell. While numerous studies have investigated protein composition in biomolecular coronas, relatively little detail is known about how the nanoparticle surface influences the orientation and conformation of the proteins associated with them. We previously showed that the peripheral membrane protein cytochrome c adopts preferred poses relative to negatively charged 3-mercaptopropionic acid (MPA)-gold nanoparticles (AuNPs). Here, we employ molecular dynamics simulations and complementary experiments to establish that cytochrome c also assumes preferred poses upon association with nanoparticles functionalized with an uncharged ligand, specifically ω-(1-mercaptounde-11-cyl)hexa(ethylene glycol) (EG6). We find that the display of the EG6 ligands is sensitive to the curvature of the surface-and, consequently, the effective diameter of the nearly spherical nanoparticle core-which in turn affects the preferred poses of cytochrome c.
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Affiliation(s)
- Clyde A Daly
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Caley Allen
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Nikita Rozanov
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Gene Chong
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric S Melby
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Thomas R Kuech
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel E Lohse
- Department of Chemistry, University of Illinois-Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois-Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Joel A Pedersen
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Departments of Soil Science, Chemistry, and Civil & Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Departments of Chemical & Biomolecular Engineering and Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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11
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An N, Fleming AM, Rosecrans NC, Liao Y, Burrows CJ. Synthesis of Site-Specific Crown Ether Adducts to DNA Abasic Sites: 8-Oxo-7,8-Dihydro-2'-Deoxyguanosine and 2'-Deoxycytidine. Methods Mol Biol 2019; 1973:15-25. [PMID: 31016693 DOI: 10.1007/978-1-4939-9216-4_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Formation of adducts to DNA is of great benefit to DNA sequencing and damage detection technology and to enzymology. Here we describe the synthesis and characterization procedures of 18-crown-6 adducts formed to abasic (AP) sites, 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG), and 2'-deoxycytidine (C) residues in DNA oligodeoxynucleotides. These crown ether adducts were used as site-specific modifications to facilitate nanopore technology. The methods described can be readily expanded to attach other suitable primary amines of interest.
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Affiliation(s)
- Na An
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | | | - Yi Liao
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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12
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Chenab KK, Eivazzadeh-Keihan R, Maleki A, Pashazadeh-Panahi P, Hamblin MR, Mokhtarzadeh A. Biomedical applications of nanoflares: Targeted intracellular fluorescence probes. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2019; 17:342-358. [PMID: 30826476 PMCID: PMC6520197 DOI: 10.1016/j.nano.2019.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/08/2019] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
Nanoflares are intracellular probes consisting of oligonucleotides immobilized on various nanoparticles that can recognize intracellular nucleic acids or other analytes, thus releasing a fluorescent reporter dye. Single-stranded DNA (ssDNA) complementary to mRNA for a target gene is constructed containing a 3'-thiol for binding to gold nanoparticles. The ssDNA "recognition sequence" is prehybridized to a shorter DNA complement containing a fluorescent dye that is quenched. The functionalized gold nanoparticles are easily taken up into cells. When the ssDNA recognizes its complementary target, the fluorescent dye is released inside the cells. Different intracellular targets can be detected by nanoflares, such as mRNAs coding for genes over-expressed in cancer (epithelial-mesenchymal transition, oncogenes, thymidine kinase, telomerase, etc.), intracellular levels of ATP, pH values and inorganic ions can also be measured. Advantages include high transfection efficiency, enzymatic stability, good optical properties, biocompatibility, high selectivity and specificity. Multiplexed assays and FRET-based systems have been designed.
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Affiliation(s)
- Karim Khanmohammadi Chenab
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Reza Eivazzadeh-Keihan
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
| | - Paria Pashazadeh-Panahi
- Department of Biochemistry and Biophysics, Metabolic Disorders Research Center, Gorgan Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Golestan Province, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA; Department of Dermatology, Harvard Medical School, Boston, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA.
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran.
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13
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Zdrali E, Baer MD, Okur HI, Mundy CJ, Roke S. The Diverse Nature of Ion Speciation at the Nanoscale Hydrophobic/Water Interface. J Phys Chem B 2019; 123:2414-2423. [DOI: 10.1021/acs.jpcb.8b10207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Evangelia Zdrali
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Marcel D. Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Halil I. Okur
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christopher J. Mundy
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Sylvie Roke
- Laboratory for fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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14
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Li MX, Zhao W, Wang H, Li XL, Xu CH, Chen HY, Xu JJ. Dynamic Single Molecular Rulers: Toward Quantitative Detection of MicroRNA-21 in Living Cells. Anal Chem 2018; 90:14255-14259. [PMID: 30474960 DOI: 10.1021/acs.analchem.8b03322] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Innovative techniques to measure microRNA (miRNA) in vivo could greatly improve the fundamental understanding of complex cellular processes. Herein, we report a novel method for real-time, quantitative miRNA detection inside living cells based on core-satellite plasmon rulers (PRs). This approach allows for the statistical analysis of single hybridization event caused by target miRNA. We investigated hundreds of satellite leaving events and found that the distribution of the time range for one strand displacement event is miRNA concentration-dependent, which obeyed Poisson statistics. Probing several such PRs under dark-field microscopy would provide precise determination of miRNA in vitro and in living cells, without photobleaching or blinking of the fluorophores. We believe the simple and practical approach on the basis of dynamic PRs with single-molecule sensitivity combined with statistical analysis hold promising potential to visualize native nucleic acids with short sequence and low-abundance.
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Affiliation(s)
- Mei-Xing Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Hui Wang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Xiang-Ling Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Cong-Hui Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
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15
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Rodriguez-Quijada C, Sánchez-Purrà M, de Puig H, Hamad-Schifferli K. Physical Properties of Biomolecules at the Nanomaterial Interface. J Phys Chem B 2018; 122:2827-2840. [DOI: 10.1021/acs.jpcb.8b00168] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | - Maria Sánchez-Purrà
- Department of Engineering, University of Massachusetts, Boston, Massachusetts 02125, United States
| | - Helena de Puig
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kimberly Hamad-Schifferli
- Department of Engineering, University of Massachusetts, Boston, Massachusetts 02125, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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16
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Nanostructure and Corresponding Quenching Efficiency of Fluorescent DNA Probes. MATERIALS 2018; 11:ma11020272. [PMID: 29425163 PMCID: PMC5848969 DOI: 10.3390/ma11020272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 12/25/2022]
Abstract
Based on the fluorescence resonance energy transfer (FRET) mechanism, fluorescent DNA probes were prepared with a novel DNA hairpin template method, with SiO2 coated CdTe (CdTe/SiO2) core/shell nanoparticles used as the fluorescence energy donors and gold (Au) nanoparticles (AuNPs) as the energy acceptors. The nanostructure and energy donor/acceptor ratio in a probe were controlled with this method. The relationship between the nanostructure of the probes and FRET efficiency (quenching efficiency) were investigated. The results indicated that when the donor/acceptor ratios were 2:1, 1:1, and 1:2; the corresponding FRET efficiencies were about 33.6%, 57.5%, and 74.2%, respectively. The detection results indicated that the fluorescent recovery efficiency of the detecting system was linear when the concentration of the target DNA was about 0.0446–2.230 nmol/L. Moreover, the probes showed good sensitivity and stability in different buffer conditions with a low detection limit of about 0.106 nmol/L.
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17
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Zdrali E, Chen Y, Okur HI, Wilkins DM, Roke S. The Molecular Mechanism of Nanodroplet Stability. ACS NANO 2017; 11:12111-12120. [PMID: 29224343 DOI: 10.1021/acsnano.7b05100] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mixtures of nano- and microscopic oil droplets in water have recently been rediscovered as miniature reaction vessels in microfluidic environments and are important constituents of many environmental systems, food, personal care, and medical products. The oil nanodroplet/water interface stabilized by surfactants determines the physicochemical properties of the droplets. Surfactants are thought to stabilize nanodroplets by forming densely packed monolayers that shield the oil phase from the water. This idea has been inferred from droplet stability measurements in combination with molecular structural data obtained from extended planar interfaces. Here, we present a molecular level investigation of the surface structure and stability of nanodroplets and show that the surface structure of nanodroplets is significantly different from that of extended planar interfaces. Charged surfactants form monolayers that are more than 1 order of magnitude more dilute than geometrically packed ones, and there is no experimental correlation between stability and surfactant surface density. Moreover, dilute negatively charged surfactant monolayers produce more stable nanodroplets than dilute positively charged and dense geometrically packed neutral surfactant monolayers. Droplet stability is found to depend on the relative cooperativity between charge-charge, charge-dipole, and hydrogen-bonding interactions. The difference between extended planar interfaces and nanoscale interfaces stems from a difference in the thermally averaged total charge-charge interactions in the two systems. Low dielectric oil droplets with a size smaller than the Debye length in oil permit repulsive interactions between like charges from opposing interfaces in small droplets. This behavior is generic and extends up to the micrometer length scale.
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Affiliation(s)
- Evangelia Zdrali
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Yixing Chen
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Halil I Okur
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - David M Wilkins
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics, Institutes of Bioengineering and Materials Science and Engineering, School of Engineering, and Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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18
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Guo J, Chen Y, Jiang Y, Ju H. Polyadenine-Modulated DNA Conformation Monitored by Surface-Enhanced Raman Scattering (SERS) on Multibranched Gold Nanoparticles and Its Sensing Application. Chemistry 2017; 23:9332-9337. [PMID: 28504862 DOI: 10.1002/chem.201700883] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 11/11/2022]
Abstract
This work proposes a facile way to modulate the conformation of DNA from the "Lie-Down" to the "Stand-Up" conformation on the surface of multibranched gold nanoparticles (AuNPs). This is realized by regulating the length of polyadenine (polyA) linked to the DNA sequence and/or the hybridization of this sequence with the target DNA, and can be monitored by the Raman signal owing to the excellent performance of multibranched AuNPs (AuNSs) as a surface-enhanced Raman scattering (SERS) substrate and the distance change between the Raman reporter and the substrate. The probable mechanism, which depends on the repulsion of polyA from the sequence and the tip assembly, has also been probed through theoretical simulation using the finite difference time domain method. By virtue of this strategy, a conformation-transformation-based DNA@AuNS sensor is constructed for the identification of a specific oligonucleotide, which has been used for the detection of DNA sequences associated with Severe Acute Respiratory Syndrome (SARS). This strategy leads to a novel sensing platform with good extendibility for DNA analysis, and provides a powerful protocol for facilitating the cognition of DNA conformation on metal surfaces.
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Affiliation(s)
- Jingxing Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yongjia Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
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19
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Laser-fabricated gold nanoparticles for lateral flow immunoassays. Colloids Surf B Biointerfaces 2017; 149:351-357. [DOI: 10.1016/j.colsurfb.2016.10.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/14/2016] [Accepted: 10/17/2016] [Indexed: 11/21/2022]
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20
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Paul T, Bera SC, Agnihotri N, Mishra PP. Single-Molecule FRET Studies of the Hybridization Mechanism during Noncovalent Adsorption and Desorption of DNA on Graphene Oxide. J Phys Chem B 2016; 120:11628-11636. [DOI: 10.1021/acs.jpcb.6b06017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tapas Paul
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF
Bidhannagar, Kolkata 700064, India
| | - Subhas Chandra Bera
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF
Bidhannagar, Kolkata 700064, India
| | - Nidhi Agnihotri
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF
Bidhannagar, Kolkata 700064, India
| | - Padmaja P. Mishra
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF
Bidhannagar, Kolkata 700064, India
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21
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Broda J, Setzler J, Leifert A, Steitz J, Benz R, Simon U, Wenzel W. Ligand-lipid and ligand-core affinity control the interaction of gold nanoparticles with artificial lipid bilayers and cell membranes. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:1409-19. [DOI: 10.1016/j.nano.2015.12.384] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/28/2015] [Accepted: 12/28/2015] [Indexed: 12/14/2022]
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22
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The fate of silica based Stöber particles soaked into growth media (RPMI and M254): A DLS and ζ-potential study. Colloids Surf B Biointerfaces 2015; 135:840-845. [DOI: 10.1016/j.colsurfb.2015.03.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/27/2015] [Accepted: 03/10/2015] [Indexed: 11/20/2022]
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23
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de Puig H, Tam JO, Yen CW, Gehrke L, Hamad-Schifferli K. Extinction Coefficient of Gold Nanostars. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:17408-17415. [PMID: 28018519 PMCID: PMC5176261 DOI: 10.1021/acs.jpcc.5b03624] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Gold nanostars (NStars) are highly attractive for biological applications due to their surface chemistry, facile synthesis and optical properties. Here, we synthesize NStars in HEPES buffer at different HEPES/Au ratios, producing NStars of different sizes and shapes, and therefore varying optical properties. We measure the extinction coefficient of the synthesized NStars at their maximum surface plasmon resonances (SPR), which range from 5.7 × 108 to 26.8 × 108 M-1cm-1. Measured values correlate with those obtained from theoretical models of the NStars using the discrete dipole approximation (DDA), which we use to simulate the extinction spectra of the nanostars. Finally, because NStars are typically used in biological applications, we conjugate DNA and antibodies to the NStars and calculate the footprint of the bound biomolecules.
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Affiliation(s)
- Helena de Puig
- Dept. of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Justina O. Tam
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology Cambridge, MA USA 02139
- Winchester Engineering Analytical Center, Food and Drug Administration. Winchester MA USA 01890
| | - Chun-Wan Yen
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology Cambridge, MA USA 02139
- Winchester Engineering Analytical Center, Food and Drug Administration. Winchester MA USA 01890
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology Cambridge, MA USA 02139
- Dept. of Microbiology and Immunobiology, Harvard Medical School, Boston 02115
- Corresponding Authors: Kimberly Hamad-Schifferli, , Lee Gehrke,
| | - Kimberly Hamad-Schifferli
- Dept. of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Corresponding Authors: Kimberly Hamad-Schifferli, , Lee Gehrke,
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24
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Uddayasankar U, Krull UJ. Energy Transfer Assays Using Quantum Dot-Gold Nanoparticle Complexes: Optimizing Oligonucleotide Assay Configuration Using Monovalently Conjugated Quantum Dots. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:8194-204. [PMID: 26154687 DOI: 10.1021/acs.langmuir.5b01932] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The energy transfer between quantum dots (QDs) and gold nanoparticles (AuNPs) represents a popular transduction scheme in analytical assays that use nanomaterials. The impact of the spatial arrangement of the two types of nanoparticles on analytical performance has now been evaluated using a nucleic acid strand displacement assay. The first spatial arrangement (configuration 1) involved the assembly of a number of monovalently functionalized QD-oligonucleotide conjugates around a single central AuNP that was functionalized with complementary oligonucleotide sequences. The assembly of these complexes, and subsequent disassembly via target oligonucleotide-mediated displacement, were used to evaluate energy transfer efficiencies. Furthermore, the inner filter effect of AuNPs on the fluorescence intensity of the QD was studied. AuNPs of three different diameters (6, 13, and 30 nm) were used in these studies. Configuration 2 was based on the placement of monovalently functionalized AuNP-oligonucleotide conjugates around a single QD that was functionalized with a complementary oligonucleotide. The optimal assay configuration, established by evaluating energy transfer efficiencies and inner filter effects, was obtained by arranging at most 15 QDs around the 13 nm AuNP (configuration 1). These assays provided a 2.5-fold change in fluorescence intensity in the presence of target oligonucleotides. To obtain the same response with configuration 2 required the placement of three 6 nm AuNPs around the QD. This resulted in configuration 2 having a 5-fold lower fluorescence intensity when compared to configuration 1. The use of low-cost detection systems (digital camera) further emphasized the higher analytical performance of configuration 1. Response curves obtained using these detection systems demonstrated that configuration 1 had a 10-fold higher sensitivity when compared to configuration 2. This study provides an important framework for the development of sensitive assays using gold nanoparticles and quantum dots.
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Affiliation(s)
- Uvaraj Uddayasankar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L1C6
| | - Ulrich J Krull
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L1C6
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25
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Yao D, Wang B, Xiao S, Song T, Huang F, Liang H. What Controls the "Off/On Switch" in the Toehold-Mediated Strand Displacement Reaction on DNA Conjugated Gold Nanoparticles? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:7055-7061. [PMID: 26057346 DOI: 10.1021/acs.langmuir.5b01671] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In DNA dynamic nanotechnology, a toehold-mediated DNA strand-displacement reaction has demonstrated its capability in building complex autonomous system. In most cases, the reaction is performed in pure DNA solution that is essentially a one-phase system. In the present work, we systematically investigated the reaction in a heterogeneous media, in which the strand that implements a displacing action is conjugated on gold nanoparticles. By monitoring the kinetics of spherical nucleic acid (SNA) assembly driven by toehold-mediated strand displacement reaction, we observed significant differences, i.e., the abrupt jump in behavior of an "off/on switch", in the reaction rate when the invading toehold was extended to eight bases from seven bases. These phenomena are attributed to the effect of steric hindrance arising from the high density of invading strand conjugated to AuNPs. Based on these studies, an INHIBIT logic gate presenting good selectivity was developed.
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Affiliation(s)
- Dongbao Yao
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Bei Wang
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shiyan Xiao
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Tingjie Song
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Fujian Huang
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Haojun Liang
- †CAS Key Laboratory of Soft Matter Chemistry, ‡iChEM, Department of Polymer Science and Engineering, and §Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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26
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Brown KA, Song Q, Mulder DW, King PW. Diameter dependent electron transfer kinetics in semiconductor-enzyme complexes. ACS NANO 2014; 8:10790-8. [PMID: 25244026 DOI: 10.1021/nn504561v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Excited state electron transfer (ET) is a fundamental step for the catalytic conversion of solar energy into chemical energy. To understand the properties controlling ET between photoexcited nanoparticles and catalysts, the ET kinetics were measured for solution-phase complexes of CdTe quantum dots and Clostridium acetobutylicum [FeFe]-hydrogenase I (CaI) using time-resolved photoluminescence spectroscopy. Over a 2.0-3.5 nm diameter range of CdTe nanoparticles, the observed ET rate (kET) was sensitive to CaI concentration. To account for diameter effects on CaI binding, a Langmuir isotherm and two geometric binding models were created to estimate maximal CaI affinities and coverages at saturating concentrations. Normalizing the ET kinetics to CaI surface coverage for each CdTe diameter led to k(ET) values that were insensitive to diameter, despite a decrease in the free energy for photoexcited ET (ΔGET) with increasing diameter. The turnover frequency (TOF) of CaI in CdTe-CaI complexes was measured at several molar ratios. Normalization for diameter-dependent changes in CaI coverage showed an increase in TOF with diameter. These results suggest that k(ET) and H2 production for CdTe-CaI complexes are not strictly controlled by ΔG(ET) and that other factors must be considered.
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Affiliation(s)
- Katherine A Brown
- Biosciences Center, National Renewable Energy Laboratory , Golden, Colorado 80401, United States
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27
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Wang W, Ding X, He M, Wang J, Lou X. Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering. Anal Chem 2014; 86:10186-92. [PMID: 25222203 PMCID: PMC4204920 DOI: 10.1021/ac502440h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The
kinetic adsorption profile at the DNA–gold nanoparticle
(AuNP) interface is probed by following the binding and organization
of thiolated linear DNA and aptamers of varying chain lengths (15,
30, 44, and 51 mer) to the surface of AuNPs (13.0 ± 1.0 nm diameter).
A systematic investigation utilizing dynamic light scattering has
been performed to directly measure the changes in particle size during
the course of a typical aging-salting thiolated DNA/AuNP preparation
procedure. We discuss the effect of DNA chain length, composition,
salt concentration, and secondary structure on the kinetics and conformation
at the DNA–AuNP interface. The adsorption kinetics are chain-length
dependent, composition independent, and not diffusion rate limited
for the conditions we report here. The kinetic data support a mechanism
of stepwise adsorption of thiols to the surface of AuNPs and reorganization
of the thiols at the interface. Very interestingly, the kinetic increases
of the particle sizes are modeled accurately by the pseudo-second-order
rate model, suggesting that DNA could possess the statistically well-defined
conformational evolution. Together with other experimental evidence,
we propose a dynamic inner-layer and outer-tail (DILOT) model to describe
the evolution of the DNA conformation after the initial adsorption
of a single oligonucleotide layer. According to this model, the length
of the tails that extend from the surface of AuNPs, capable for hybridization
or molecular recognition, can be conveniently calculated. Considering
the wide applications of DNA/AuNPs, the results should have important
implications in sensing and DNA-directed nanoparticle assembly.
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Affiliation(s)
- Wenjie Wang
- Department of Chemistry, Capital Normal University , Xisanhuan North Road. 105, Beijing 100048, China
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28
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Taylor U, Rehbock C, Streich C, Rath D, Barcikowski S. Rational design of gold nanoparticle toxicology assays: a question of exposure scenario, dose and experimental setup. Nanomedicine (Lond) 2014; 9:1971-89. [DOI: 10.2217/nnm.14.139] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many studies have evaluated the toxicity of gold nanoparticles, although reliable predictions based on these results are rare. In order to overcome this problem, this article highlights strategies to improve comparability and standardization of nanotoxicological studies. To this end, it is proposed that we should adapt the nanomaterial to the addressed exposure scenario, using ligand-free nanoparticle references in order to differentiate ligand effects from size effects. Furthermore, surface-weighted particle dosing referenced to the biologically relevant parameter (e.g., cell number or organ mass) is proposed as the gold standard. In addition, it is recommended that we should shift the focus of toxicological experiments from ‘live–dead’ assays to the assessment of cell function, as this strategy allows observation of bioresponses at lower doses that are more relevant for in vivo scenarios.
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Affiliation(s)
- Ulrike Taylor
- Institute of Farm Animal Genetics, Friedrich-Löffler-Institut, Federal Research Institute of Animal Health, Höltystraße 10, 31535 Mariensee, Germany
| | - Christoph Rehbock
- Technical Chemistry I & Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Carmen Streich
- Technical Chemistry I & Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
| | - Detlef Rath
- Institute of Farm Animal Genetics, Friedrich-Löffler-Institut, Federal Research Institute of Animal Health, Höltystraße 10, 31535 Mariensee, Germany
| | - Stephan Barcikowski
- Technical Chemistry I & Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen, Universitätsstraße 7, 45141 Essen, Germany
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29
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Singh G, Babele PK, Kumar A, Srivastava A, Sinha RP, Tyagi MB. Synthesis of ZnO nanoparticles using the cell extract of the cyanobacterium, Anabaena strain L31 and its conjugation with UV-B absorbing compound shinorine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:55-62. [PMID: 24911272 DOI: 10.1016/j.jphotobiol.2014.04.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 04/23/2014] [Accepted: 04/26/2014] [Indexed: 12/20/2022]
Abstract
In the present work, we describe a cheap, unexplored and simple procedure for the synthesis of zinc oxide nanoparticles (ZnONPs) using the cell extract of the cyanobacterium, Anabaena strain L31. An attempt was also made to conjugate synthesized ZnONPs with a UV-absorbing water soluble compound shinorine. UV-vis spectroscopy, X-ray diffraction (XRD), Fourier transform infra-red (FTIR) spectroscopy, transmission electron microscopy (TEM) and TEM-selected area electron diffraction (SAED) analyses were made to elucidate the formation and characterization of ZnONPs and ZnONPs-shinorine conjugate. The synthesized ZnONPs were characterized by a sharp peak at 370 nm in UV-vis spectrum. TEM images showed the formation of spherical shaped nanoparticles with an average size of 80 nm. Results of selective area electron diffraction (SAED) pattern showed a set of rings which suggested uniform shape with hexagonal structure of ZnONPs. XRD spectra confirmed the crystalline structure of particles. Conjugation of ZnONPs with shinorine was successfully achieved at pH 7.0 and 10mM concentration of shinorine. The conjugate showed a zeta potential value of -3.75 mV as compared to +30.25 mV of ZnONPs. The change in zeta potential value of ZnONPs-shinorine conjugate was attributed to the changes in the surface functionalities after conjugation. The generation of in vivo reactive oxygen species (ROS) by Anabaena strain L31 with treatment of ZnONPs-shinorine conjugate showed approximately 75% less ROS generation as compared to ZnONPs. Properties exhibited by the ZnONPs-shinorine conjugate suggest that it may be used as a potential agent in developing environmental-friendly sunscreen filters of biological origin.
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Affiliation(s)
- Garvita Singh
- School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Piyoosh K Babele
- School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Ashok Kumar
- School of Biotechnology, Banaras Hindu University, Varanasi 221005, India.
| | - Anup Srivastava
- School of Biotechnology, Banaras Hindu University, Varanasi 221005, India
| | - Rajeshwar P Sinha
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
| | - Madhu B Tyagi
- Department of Botany, MMV, Banaras Hindu University, Varanasi 221005, India
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Riaz S, Qu L, Fodjo EK, Ma W, Long YT. Thioanisole induced size-selective fragmentation of gold nanoparticles. RSC Adv 2014. [DOI: 10.1039/c4ra00528g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The size-selective fragmentation of gold nanoparticles (AuNPs) by thioanisole showed that large particles are more susceptible to fragmentation than the smaller ones.
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Affiliation(s)
- Sara Riaz
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai, P.R. China
| | - LuLu Qu
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai, P.R. China
| | - Essy Kouadio Fodjo
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai, P.R. China
| | - Wei Ma
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai, P.R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- East China University of Science and Technology
- Shanghai, P.R. China
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31
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Li F, Zhang H, Dever B, Li XF, Le XC. Thermal stability of DNA functionalized gold nanoparticles. Bioconjug Chem 2013; 24:1790-7. [PMID: 24102258 PMCID: PMC3836601 DOI: 10.1021/bc300687z] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Therapeutic
uses of DNA functionalized gold nanoparticles (DNA-AuNPs)
have shown great potential and exciting opportunities for disease
diagnostics and treatment. Maintaining stable conjugation between
DNA oligonucleotides and gold nanoparticles under thermally stressed
conditions is one of the critical aspects for any of the practical
applications. We systematically studied the thermal stability of DNA-AuNPs
as affected by organosulfur anchor groups and packing densities. Using
a fluorescence assay to determine the kinetics of releasing DNA molecules
from DNA-AuNPs, we observed an opposite trend between the temperature-induced
and chemical-induced release of DNA from DNA-AuNPs when comparing
the DNA-AuNPs that were constructed with different anchor groups.
Specifically, the bidentate Au–S bond formed with cyclic disulfide
was thermally less stable than those formed with thiol or acyclic
disulfide. However, the same bidentate Au–S bond was chemically
more stable under the treatment of competing thiols (mercaptohexanol
or dithiothreitol). DNA packing density on AuNPs influenced the thermal
stability of DNA-AuNPs at 37 °C, but this effect was minimum
as temperature increased to 85 °C. With the improved understanding
from these results, we were able to design a strategy to enhance the
stability of DNA-AuNPs by conjugating double-stranded DNA to AuNPs
through multiple thiol anchors.
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Affiliation(s)
- Feng Li
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G2
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32
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Uddayasankar U, Krull UJ. Analytical performance of molecular beacons on surface immobilized gold nanoparticles of varying size and density. Anal Chim Acta 2013; 803:113-22. [DOI: 10.1016/j.aca.2013.07.059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 06/28/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022]
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Heuer-Jungemann A, Harimech PK, Brown T, Kanaras AG. Gold nanoparticles and fluorescently-labelled DNA as a platform for biological sensing. NANOSCALE 2013; 5:9503-9510. [PMID: 23982570 DOI: 10.1039/c3nr03707j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In the past decade gold nanoparticle-nucleic acid conjugates became progressively important for biomedical applications. Fluorophores attached to nucleic acid-gold nanoparticle conjugates have opened up a new era of biological sensing. The most promising advancement in this field was the invention of the so-called 'nano-flare' systems. These systems are capable of detecting specific endocellular targets such as mRNAs, microRNAs or small molecules in real time. In this minireview, we discuss the current progress in the field of DNA-nanoparticles as sensors, their properties, stability, cellular uptake and cytotoxicity.
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Affiliation(s)
- Amelie Heuer-Jungemann
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK.
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34
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Ravan H, Kashanian S, Sanadgol N, Badoei-Dalfard A, Karami Z. Strategies for optimizing DNA hybridization on surfaces. Anal Biochem 2013; 444:41-6. [PMID: 24121011 DOI: 10.1016/j.ab.2013.09.032] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 01/15/2023]
Abstract
Specific and predictable hybridization of the polynucleotide sequences to their complementary counterparts plays a fundamental role in the rational design of new nucleic acid nanodevices. Generally, nucleic acid hybridization can be performed using two major strategies, namely hybridization of DNA or RNA targets to surface-tethered oligonucleotide probes (solid-phase hybridization) and hybridization of the target nucleic acids to randomly distributed probes in solution (solution-phase hybridization). Investigations into thermodynamic and kinetic parameters of these two strategies showed that hybridization on surfaces is less favorable than that of the same sequence in solution. Indeed, the efficiency of DNA hybridization on surfaces suffers from three constraints: (1) electrostatic repulsion between DNA strands on the surface, (2) steric hindrance between tethered DNA probes, and (3) nonspecific adsorption of the attached oligonucleotides to the solid surface. During recent years, several strategies have been developed to overcome the problems associated with DNA hybridization on surfaces. Optimizing the probe surface density, application of a linker between the solid surface and the DNA-recognizing sequence, optimizing the pH of DNA hybridization solutions, application of thiol reagents, and incorporation of a polyadenine block into the terminal end of the recognizing sequence are among the most important strategies for enhancing DNA hybridization on surfaces.
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Affiliation(s)
- Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University, 76169-14111 Kerman, Iran.
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35
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Pekcevik IC, Poon LCH, Wang MCP, Gates BD. Tunable loading of single-stranded DNA on gold nanorods through the displacement of polyvinylpyrrolidone. Anal Chem 2013; 85:9960-7. [PMID: 24016255 DOI: 10.1021/ac4027737] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A quantitative and tunable loading of single-stranded (ss-DNA) molecules onto gold nanorods was achieved through a new method of surfactant exchange. This new method involves the exchange of cetyltrimethylammonium bromide surfactants for an intermediate stabilizing layer of polyvinylpyrrolidone and sodium dodecylsulfate. The intermediate layer of surfactants on the anisotropic gold particles was easily displaced by thiolated ss-DNA, forming a tunable density of single-stranded DNA molecules on the surfaces of the gold nanorods. The success of this ligand exchange process was monitored in part through the combination of extinction, X-ray photoelectron, and infrared absorption spectroscopies. The number of ss-DNA molecules per nanorod for nanorods with a high density of ss-DNA molecules was quantified through a combination of fluorescence measurements and elemental analysis, and the functionality of the nanorods capped with dense monolayers of DNA was assessed using a hybridization assay. Core-satellite assemblies were successfully prepared from spherical particles containing a probe DNA molecule and a nanorod core capped with complementary ss-DNA molecules. The methods demonstrated herein for quantitatively fine tuning and maximizing, or otherwise optimizing, the loading of ss-DNA in monolayers on gold nanorods could be a useful methodology for decorating gold nanoparticles with multiple types of biofunctional molecules.
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Affiliation(s)
- Idah C Pekcevik
- Department of Chemistry and 4D LABS, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6 Canada
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Reynolds M, Marradi M, Imberty A, Penadés S, Pérez S. Influence of ligand presentation density on the molecular recognition of mannose-functionalised glyconanoparticles by bacterial lectin BC2L-A. Glycoconj J 2013; 30:747-57. [PMID: 23666402 DOI: 10.1007/s10719-013-9478-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 04/24/2013] [Indexed: 01/09/2023]
Abstract
Polyvalent carbohydrate-protein interactions play a key role in bio- and pathological processes, including cell-cell communication and pathogen invasion. In order to study, control and manipulate these interactions gold nanoparticles have been employed as a 3D scaffold, presenting carbohydrate ligands in a multivalent fashion for use as high affinity binding partners and a model system for oligosaccharide presentation at biomacromolecular surfaces. In this study, the binding of a series of mannose-functionalised gold nanoparticles to the dimeric BC2L-A lectin from Burkholderia cenocepacia has been evaluated. BC2L-A is known to exhibit a high specificity for (oligo)mannosides. Due to the unique structure and binding nature of this lectin, it provides a useful tool to study (oligo)saccharides presented on multivalent scaffolds. Surface plasmon resonance and isothermal titration calorimetric assays were used to investigate the effect of ligand presentation density towards binding to the bacterial lectin. We show how a combination of structural complementarities between ligand presentation and lectin architecture and statistical re-binding effects are important for increasing the avidity of multivalent ligands for recognition by their protein receptors; further demonstrating the application of glyconanotechnology towards fundamental glycobiology research as well as a potential towards biomedical diagnostics and therapeutic treatments.
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Affiliation(s)
- Michael Reynolds
- Centre de Recherche sur les Macromolécules Végétales (CERMAV - CNRS), affiliated with Université Joseph Fourier Grenoble and ICMG, BP 53, 38041, Grenoble, France
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37
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Doane T, Burda C. Nanoparticle mediated non-covalent drug delivery. Adv Drug Deliv Rev 2013; 65:607-21. [PMID: 22664231 DOI: 10.1016/j.addr.2012.05.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 05/19/2012] [Accepted: 05/21/2012] [Indexed: 12/18/2022]
Abstract
The use of nanoparticles (NPs) for enhanced drug delivery has been heavily explored during the last decade. Within the field, it is has become increasingly apparent that the physical properties of the particles themselves dictate their efficacy, and the relevant non-covalent chemistry at the NP interface also influences how drugs are immobilized and delivered. In this review, we reflect on the physical chemistry of NP mediated drug delivery (and more specifically, non-covalent drug delivery) at the three main experimental stages of drug loading, NP-drug conjugate transport, and the resulting cellular drug delivery. Through a critical evaluation of advances in drug delivery within the last decade, an outlook for biomedical applications of nanoscale transport vectors will be presented.
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38
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Brown PK, Qureshi AT, Moll AN, Hayes DJ, Monroe WT. Silver nanoscale antisense drug delivery system for photoactivated gene silencing. ACS NANO 2013; 7:2948-59. [PMID: 23473419 DOI: 10.1021/nn304868y] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The unique photophysical properties of noble metal nanoparticles contribute to their potential as photoactivated drug delivery vectors. Here we demonstrate the synthesis and characterization of 60-80 nm silver nanoparticles (SNPs) decorated with thiol-terminated photolabile DNA oligonucleotides. In vitro assays and fluorescent confocal microscopy of treated cell cultures show efficient UV-wavelength photoactivation of surface-tethered caged ISIS2302 antisense oligonucleotides possessing internal photocleavable linkers. As a demonstration of the advantages of these novel nanocarriers, we investigate properties including: enhanced stability to nucleases, increased hybridization activity upon photorelease, and efficient cellular uptake as compared to commercial transfection vectors. Their potential as multicomponent delivery agents for oligonucleotide therapeutics is shown through regulation of ICAM-1 (Intracellular Adhesion Molecule-1) silencing. Our results suggest a means to achieve light-triggered, spatiotemporally controlled gene silencing via nontoxic silver nanocarriers, which hold promise as tailorable platforms for nanomedicine, gene expression studies, and genetic therapies.
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Affiliation(s)
- Paige K Brown
- Biological and Agricultural Engineering, Louisiana State University and LSU AgCenter, Baton Rouge, Louisiana 70803, United States
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39
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Rianasari I, de Jong MP, Huskens J, van der Wiel WG. Covalent Coupling of Nanoparticles with Low-Density Functional Ligands to Surfaces via Click Chemistry. Int J Mol Sci 2013; 14:3705-17. [PMID: 23434666 PMCID: PMC3588066 DOI: 10.3390/ijms14023705] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 02/02/2013] [Accepted: 02/05/2013] [Indexed: 11/16/2022] Open
Abstract
We demonstrate the application of the 1,3-dipolar cycloaddition (“click” reaction) to couple gold nanoparticles (Au NPs) functionalized with low densities of functional ligands. The ligand coverage on the citrate-stabilized Au NPs was adjusted by the ligand:Au surface atom ratio, while maintaining the colloidal stability of the Au NPs in aqueous solution. A procedure was developed to determine the driving forces governing the selectivity and reactivity of citrate-stabilized and ligand-functionalized Au NPs on patterned self-assembled monolayers. We observed selective and remarkably stable chemical bonding of the Au NPs to the complimentarily functionalized substrate areas, even when estimating that only 1–2 chemical bonds are formed between the particles and the substrate.
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Affiliation(s)
| | | | - Jurriaan Huskens
- Authors to whom correspondence should be addressed; E-Mails: (J.H.); (W.G.W.); Tel.: +31-53-489-2995 (J.H.); +31-53-489-2873 (W.G.W.); Fax: +31-53-489-4645 (J.H.); +31-53-489-4571 (W.G.W.)
| | - Wilfred G. van der Wiel
- Authors to whom correspondence should be addressed; E-Mails: (J.H.); (W.G.W.); Tel.: +31-53-489-2995 (J.H.); +31-53-489-2873 (W.G.W.); Fax: +31-53-489-4645 (J.H.); +31-53-489-4571 (W.G.W.)
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40
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Liu YC, Li YJ, Huang CC. Information Derived from Cluster Ions from DNA-Modified Gold Nanoparticles under Laser Desorption/Ionization: Analysis of Coverage, Structure, and Single-Nucleotide Polymorphism. Anal Chem 2012; 85:1021-8. [DOI: 10.1021/ac302847n] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Chih-Ching Huang
- School of Pharmacy, College of
Pharmacy, Kaohsiung Medical University,
Kaohsiung, 80708, Taiwan
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41
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Abstract
For over half a century, alternating electric fields have been used to induce particle transport, furnishing the ζ-potential of analytes with sizes ranging from a few nanometers to several micrometers. Concurrent advances in nanotechnology have provided new materials for catalysis, self-assembly, and biomedical applications, all of which benefit from a thorough understanding of particle surface charge. Therefore, the measurement of the ζ-potential via electrophoretic light scattering (ELS) has become essential for nanoparticle (NP) research. However, the interpretation of NP electrophoretic mobility, especially that of ligand-coated NPs, can be a complex undertaking. Despite the inherent intricacy of these data, key concepts from colloidal science can help to distill valuable information from ELS. In this Account, we adopt PEGylated Au NPs as an illustrative example to explore extensions of the classical theories of Smoluchowski, Hückel, and Henry to more contemporary theories for ligand-coated NP systems such as those from Ohshima, and Hill, Saville, and Russel. First, we review the basic experimental considerations necessary to understand NP electrophoretic mobility, identifying when O'Brien and White's numerical solution of the standard electrokinetic model should be adopted over Henry's closed-form analytical approximation. Next, we explore recent developments in the theory of ligand-coated particle electrophoresis, and how one can furnish accurate and meaningful relationships between measured NP mobility, ζ-potential, and surface charge. By identifying key ligand-coated NP parameters (e.g., coating thickness, permeability, molecular mass, and hydrodynamic segment size), we present a systematic method for quantitatively interpreting NP electrophoretic mobility. In addition to reviewing theoretical foundations, we describe our recent results that examine how the unique surface curvature of NPs alters and controls their properties. These data provide guidelines that can expedite the rational design of NPs for advanced uses, such as heterogeneous catalysis and in vivo drug delivery. As a practical demonstration of these concepts, we apply the ligand-coated theory to a recently developed noncovalent PEGylated Au NP drug-delivery system. Our analysis suggests that anion adsorption on the Au NP core may enhance the stability of these NP-drug conjugates in solution. In addition to providing useful nanochemistry insights, the information in this Account will be useful to biomedical and materials engineers, who use ELS and ζ-potentials for understanding NP dynamics.
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Affiliation(s)
- Tennyson L. Doane
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Chi-Hung Chuang
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Reghan J. Hill
- Department of Chemical Engineering, McGill University, 3610 University Street, Montreal, QC, Canada H3A 2B2
| | - Clemens Burda
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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42
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Broderick AH, Lockett MR, Buck ME, Yuan Y, Smith LM, Lynn DM. In situ Synthesis of Oligonucleotide Arrays on Surfaces Coated with Crosslinked Polymer Multilayers. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2012; 24:939-945. [PMID: 22611305 PMCID: PMC3352262 DOI: 10.1021/cm202720q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report an approach to the in situ synthesis of oligonucleotide arrays on surfaces coated with crosslinked polymer multilayers. Our approach makes use of methods for the 'reactive' layer-by-layer assembly of thin, amine-reactive multilayers using branched polyethyleneimine (PEI) and the azlactone-functionalized polymer poly(2-vinyl-4,4'-dimethylazlactone) (PVDMA). Post-fabrication treatment of film-coated glass substrates with d-glucamine or 4-amino-1-butanol yielded hydroxyl-functionalized films suitable for the Maskless Array Synthesis (MAS) of oligonucleotide arrays. Glucamine-functionalized films yielded arrays of oligonucleotides with fluorescence intensities and signal-to-noise ratios (after hybridization with fluorescently labeled complementary strands) comparable to those of arrays fabricated on conventional silanized glass substrates. These arrays could be exposed to multiple hybridization-dehybridization cycles with only moderate loss of hybridization density. The versatility of the layer-by-layer approach also permitted synthesis directly on thin sheets of film-coated poly(ethylene terephthalate) (PET) to yield flexible oligonucleotide arrays that could be readily manipulated (e.g., bent) and cut into smaller arrays. To our knowledge, this work presents the first use of polymer multilayers as a substrate for the multi-step synthesis of complex molecules. Our results demonstrate that these films are robust and able to withstand the ~450 individual chemical processing steps associated with MAS (as well as manipulations required to hybridize, image, and dehybridize the arrays) without large-scale cracking, peeling, or delamination of the thin films. The combination of layer-by-layer assembly and MAS provides a means of fabricating functional oligonucleotide arrays on a range of different materials and substrates. This approach may also prove useful for the fabrication of supports for the solid-phase synthesis and screening of other macromolecular or small-molecule agents.
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Affiliation(s)
- Adam H Broderick
- Department of Chemical and Biological Engineering, 1415 Engineering Drive, University of Wisconsin - Madison, Madison, WI 53706
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43
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Synthesis, properties, and optical applications of noble metal nanoparticle-biomolecule conjugates. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11434-011-4747-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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44
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Fenoglio I, Fubini B, Ghibaudi EM, Turci F. Multiple aspects of the interaction of biomacromolecules with inorganic surfaces. Adv Drug Deliv Rev 2011; 63:1186-209. [PMID: 21871508 DOI: 10.1016/j.addr.2011.08.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/01/2011] [Accepted: 08/02/2011] [Indexed: 12/19/2022]
Abstract
The understanding of the mechanisms involved in the interaction of biological systems with inorganic materials is of interest in both fundamental and applied disciplines. The adsorption of proteins modulates the formation of biofilms onto surfaces, a process important in infections associated to medical implants, in dental caries, in environmental technologies. The interaction with biomacromolecules is crucial to determine the beneficial/adverse response of cells to foreign inorganic materials as implants, engineered or accidentally produced inorganic nanoparticles. A detailed knowledge of the surface/biological fluids interface processes is needed for the design of new biocompatible materials. Researchers involved in the different disciplines face up with similar difficulties in describing and predicting phenomena occurring at the interface between solid phases and biological fluids. This review represents an attempt to integrate the knowledge from different research areas by focussing on the search for determinants driving the interaction of inorganic surfaces with biological matter.
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45
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Tsai DH, DelRio FW, Keene AM, Tyner KM, MacCuspie RI, Cho TJ, Zachariah MR, Hackley VA. Adsorption and conformation of serum albumin protein on gold nanoparticles investigated using dimensional measurements and in situ spectroscopic methods. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2464-77. [PMID: 21341776 DOI: 10.1021/la104124d] [Citation(s) in RCA: 263] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The adsorption and conformation of bovine serum albumin (BSA) on gold nanoparticles (AuNPs) were interrogated both qualitatively and quantitatively via complementary physicochemical characterization methods. Dynamic light scattering (DLS), asymmetric-flow field flow fractionation (AFFF), fluorescence spectrometry, and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy were combined to characterize BSA-AuNP conjugates under fluid conditions, while conjugates in the aerosol state were characterized by electrospray-differential mobility analysis (ES-DMA). The presence of unbound BSA molecules interferes with DLS analysis of the conjugates, particularly as the AuNP size decreases (i.e., below 30 nm in diameter). Under conditions where the γ value is high, where γ is defined as the ratio of scattering intensity by AuNPs to the scattering intensity by unbound BSA, DLS size results are consistent with results obtained after fractionation by AFFF. Additionally, the AuNP hydrodynamic size exhibits a greater proportional increase due to BSA conjugation at pH values below 2.5 compared with less acidic pH values (3.4-7.3), corresponding with the reversibly denatured (E or F form) conformation of BSA below pH 2.5. Over the pH range from 3.4 to 7.3, the hydrodynamic size of the conjugate is nearly constant, suggesting conformational stability over this range. Because of the difference in the measurement environment, a larger increase of AuNP size is observed following BSA conjugation when measured in the wet state (i.e., by DLS and AFFF) compared to the dry state (by ES-DMA). Molecular surface density for BSA is estimated based on ES-DMA and fluorescence measurements. Results from the two techniques are consistent and similar, but slightly higher for ES-DMA, with an average adsorbate density of 0.015 nm(-2). Moreover, from the change of particle size, we determine the extent of adsorption for BSA on AuNPs using DLS and ES-DMA at 21 °C, which show that increasing the concentration of BSA increases the measured change in AuNP size. Using ES-DMA, we observe that the BSA surface density reaches 90% of saturation at a solution phase concentration between 10 and 30 μmol/L, which is roughly consistent with fluorescence and ATR-FTIR results. The equilibrium binding constant for BSA on AuNPs is calculated by applying the Langmuir equation, with resulting values ranging from 0.51 × 10(6) to 1.65 × 10(6) L/mol, suggesting a strong affinity due to bonding between the single free exterior thiol on N-form BSA (associated with a cysteine residue) and the AuNP surface. Moreover, the adsorption interaction induces a conformational change in BSA secondary structure, resulting in less α-helix content and more open structures (β-sheet, random, or expanded).
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Affiliation(s)
- De-Hao Tsai
- Material Measurement Laboratory, National Institute of Standards and Technology , Gaithersburg, Maryland 20899-8520, United States
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Roskamp M, Enders S, Pfrengle F, Yekta S, Dekaris V, Dernedde J, Reissig HU, Schlecht S. Multivalent interaction and selectivities in selectin binding of functionalized gold colloids decorated with carbohydrate mimetics. Org Biomol Chem 2011; 9:7448-56. [DOI: 10.1039/c1ob05583f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cederquist KB, Keating CD. Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18273-80. [PMID: 21038880 PMCID: PMC2994276 DOI: 10.1021/la1031703] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/13/2010] [Indexed: 05/22/2023]
Abstract
Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.
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Affiliation(s)
- Kristin B. Cederquist
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Quantitative investigation of the influence of gold nanoparticles on the dynamics of DNA hybridization using a programmed multi-channel quartz crystal microbalance system. Colloids Surf A Physicochem Eng Asp 2010. [DOI: 10.1016/j.colsurfa.2010.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Liu G, Sun C, Li D, Song S, Mao B, Fan C, Tian Z. Gating of redox currents at gold nanoelectrodes via DNA hybridization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:2148-2150. [PMID: 20376817 DOI: 10.1002/adma.200903590] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Gang Liu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
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Barhoumi A, Huschka R, Bardhan R, Knight MW, Halas NJ. Light-induced release of DNA from plasmon-resonant nanoparticles: Towards light-controlled gene therapy. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.076] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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