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Tang Y, Gao L, Fei J. Light-triggered AND logic tetrapeptide dynamic covalent assembly. Colloids Surf B Biointerfaces 2024; 238:113885. [PMID: 38574405 DOI: 10.1016/j.colsurfb.2024.113885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/07/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
We demonstrate light-triggered dynamic covalent assembly of a linear short tetrapeptide containing two terminal cysteine residues in an AND logic manner. A photobase generator is introduced to accomplish light-mediated pH regulation to increase the reduction potential of thiols in the tetrapeptide, which activates its oxidative polymerization through disulfide bonds. Interestingly, it is elucidated that under light irradiation, mere co-existence of photobase generator and the oxidizing agent permits the polymerization performance of this tetrapeptide. Hence, a light-triggered AND logic dynamic covalent assembly of a tetrapeptide is achieved. Further, upon redox response, the reversible aggregation and disaggregation can be transformed for numerous times due to the dynamic covalent feature of disulfide bond. As a comparison, no assembly occurs for a short peptide containing one terminal cysteine residue under the same stimuli condition. This work offers a new approach to remotely control programmable molecular assembly of short linear peptides based on dynamic covalent bond, holding great potential in wide bioapplications.
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Affiliation(s)
- Yuhua Tang
- College of Materials Science and Engineering, Beijing University of Technology, Beijing 100124, China
| | - Liang Gao
- Department of Chemistry, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China.
| | - Jinbo Fei
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Yasamineh S, Nikben N, Hamed Ahmed M, Abdul Kareem R, Kadhim Al-Aridhy A, Hosseini Hooshiar M. Increasing the sensitivity and accuracy of detecting exosomes as biomarkers for cancer monitoring using optical nanobiosensors. Cancer Cell Int 2024; 24:189. [PMID: 38816782 PMCID: PMC11138050 DOI: 10.1186/s12935-024-03379-1] [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: 12/23/2023] [Accepted: 05/19/2024] [Indexed: 06/01/2024] Open
Abstract
The advancement of nanoscience and material design in recent times has facilitated the creation of point-of-care devices for cancer diagnosis and biomolecule sensing. Exosomes (EXOs) facilitate the transfer of bioactive molecules between cancer cells and diverse cells in the local and distant microenvironments, thereby contributing to cancer progression and metastasis. Specifically, EXOs derived from cancer are likely to function as biomarkers for early cancer detection due to the genetic or signaling alterations they transport as payload within the cancer cells of origin. It has been verified that EXOs circulate steadily in bodily secretions and contain a variety of information that indicates the progression of the tumor. However, acquiring molecular information and interactions regarding EXOs has presented significant technical challenges due to their nanoscale nature and high heterogeneity. Colorimetry, surface plasmon resonance (SPR), fluorescence, and Raman scattering are examples of optical techniques utilized to quantify cancer exosomal biomarkers, including lipids, proteins, RNA, and DNA. Many optically active nanoparticles (NPs), predominantly carbon-based, inorganic, organic, and composite-based nanomaterials, have been employed in biosensing technology. The exceptional physical properties exhibited by nanomaterials, including carbon NPs, noble metal NPs, and magnetic NPs, have facilitated significant progress in the development of optical nanobiosensors intended for the detection of EXOs originating from tumors. Following a summary of the biogenesis, biological functions, and biomarker value of known EXOs, this article provides an update on the detection methodologies currently under investigation. In conclusion, we propose some potential enhancements to optical biosensors utilized in detecting EXO, utilizing various NP materials such as silicon NPs, graphene oxide (GO), metal NPs, and quantum dots (QDs).
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Affiliation(s)
- Saman Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | | | | | | | - Ameer Kadhim Al-Aridhy
- College of Health and Medical Technology, National University of Science and Technology, Dhi Qar, 64001, Iraq
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Zhang X, Qiu C, Li F, Zhang X, Li MC, Xie J, de Hoop CF, Qi J, Huang X. Magnetic nanocellulose-based adsorbent for highly selective removal of malachite green from mixed dye solution. Int J Biol Macromol 2023; 253:126752. [PMID: 37678694 DOI: 10.1016/j.ijbiomac.2023.126752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Herein, a novel magnetic adsorbent (BC/AA/MN@Fe3O4) was successfully prepared from waste bamboo fiber tissue and montmorillonite, and subsequently applied for the highly selective removal of malachite green (MG, removal efficiency = 97.3 %) from the mixed dye solution of MG with methyl orange (MO, removal efficiency = 4.5 %). The magnetic adsorbent has a high porosity with abundant mesopores. In the single dye MG solution, the adsorbent could effectively remove MG over a wide pH range from 4 to 10, and the maximum adsorption capacity (qmax) was 2282.3 mg/g. Moreover, the magnetic adsorbent could remove MG from various solutions including mixed dye solution, high salinity solution, and real river water dye solution. The thermodynamic results proved that the adsorption process of MG was spontaneous and endothermic. The adsorption of MG was due to the comprehensive effects of electrostatic attraction, hydrogen bonding interactions and ions exchange, between the adsorbent and MG. Furthermore, the BC/AA/MN@Fe3O4 exhibited an excellent reusability with adsorption efficiency above 53.4 % after five consecutive cycles. Therefore, the prepared magnetic nanocellulose-based adsorbent was expected to be a promising material for highly selective adsorption and separation of MG from mixed dye solution.
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Affiliation(s)
- Xuelun Zhang
- College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Chongpeng Qiu
- College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Feng Li
- Research Institute of Characteristic Flowers and Trees, Chengdu Agricultural College, Chengdu 611130, China
| | - Xuefeng Zhang
- Department of Sustainable Bioproducts, Mississippi State University, MS 39762, USA
| | - Mei-Chun Li
- School of Petroleum Engineering, China University of Petroleum (East China), Qingdao, Shandong 266580, China
| | - Jiulong Xie
- College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Cornelis F de Hoop
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jinqiu Qi
- College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Xingyan Huang
- College of Forestry, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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Deng Z, Li L, Jia H, Li NF, He J, Li MD, Phillips DL, Li Y. Insights into the Photodynamics of Fluorescence Emission and Singlet Oxygen Generation of Fluorogen Activating Protein-Malachite Green Systems. Chemistry 2023; 29:e202203684. [PMID: 36453719 DOI: 10.1002/chem.202203684] [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: 11/25/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
The self-assembled fluorogen activating protein (FAP)-malachite green (MG) complex is a well-established protein-ligand system, which can realize binding-caused fluorescence turn-on of MG and singlet oxygen (1 O2 ) generation by MG iodination. To clarify the mechanism of fluorescence activation and 1 O2 generation, the photodynamics of different halogen-substituted MG derivatives and their corresponding FAP-MG complexes were studied by femtosecond transient absorption spectroscopy and theoretical computations. The results show that the rotation of MG is restricted by FAP binding, which prevents a rapid internal conversion to allow a longer lifetime for the excited MG to undergo fluorescence emission and intersystem crossing. Moreover, these FAP-MG complexes exhibit notably varied fluorescence quantum yields (ΦFL ) and 1 O2 yields. The study on the decay pathways indicates that such an anti-heavy atom effect predominately stems from the lifetimes of the excited-state species. The photodynamic mechanism study here will lead to more advanced FAP-MG systems with high spatiotemporal resolution.
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Affiliation(s)
- Ziqi Deng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Jia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Nga-Fong Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiaxing He
- Department of Chemistry and Key Laboratory for Preparation and, Application of Ordered Structure Materials of Guangdong Providence, Shantou University, Shantou, 515063, Guangdong, China
| | - Ming-De Li
- Department of Chemistry and Key Laboratory for Preparation and, Application of Ordered Structure Materials of Guangdong Providence, Shantou University, Shantou, 515063, Guangdong, China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ying Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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A Fluorescence Kinetic-Based Aptasensor Employing Stilbene Isomerization for Detection of Thrombin. MATERIALS 2021; 14:ma14226927. [PMID: 34832326 PMCID: PMC8624160 DOI: 10.3390/ma14226927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023]
Abstract
It is important to detect thrombin due to its physiological and pathological roles, where rapid and simple analytical approaches are needed. In this study, an aptasensor based on fluorescence attenuation kinetics for the detection of thrombin is presented, which incorporates the features of stilbene and aptamer. We designed and synthesized an aptasensor by one-step coupling of stilbene compound and aptamer, which employed the adaptive binding of the aptamer with thrombin to cause a change in stilbene fluorescence attenuation kinetics. The sensor realized detection of thrombin by monitoring the variation in apparent fluorescence attenuation rate constant (kapp), which could be further used for probing of enzyme–aptamer binding. In comprehensive studies, the developed aptasensor presented satisfactory performance on repeatability, specificity, and regeneration capacity, which realized rapid sensing (10 s) with a limit of detection (LOD) of 0.205 μM. The strategy was successful across seven variants of thrombin aptasensors, with tunable kapp depending on the SITS (4-Acetamido-4′-isothiocyanato-2,2′-stilbenedisulfonic acid disodium salt hydrate) grafting site. Analyte detection mode was demonstrated in diluted serum, requiring no separation or washing steps. The new sensing mode for thrombin detection paves a way for high-throughput kinetic-based sensors for exploiting aptamers targeted at clinically relevant proteins.
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Zhu X, Chen H, Zhou Y, Wu J, Ramakrishna S, Peng X, Nanda HS, Zhou Y. Recent advances in biosensors for detection of exosomes. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021. [DOI: 10.1016/j.cobme.2021.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zhou Y, Mahapatra C, Chen H, Peng X, Ramakrishna S, Nanda HS. Recent developments in fluorescent aptasensors for detection of antibiotics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020. [DOI: 10.1016/j.cobme.2019.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Gayen A, Kumar D, Matheshwaran S, Chandra M. Unveiling the Modulating Role of Extracellular pH in Permeation and Accumulation of Small Molecules in Subcellular Compartments of Gram-negative Escherichia coli using Nonlinear Spectroscopy. Anal Chem 2019; 91:7662-7671. [PMID: 30986344 DOI: 10.1021/acs.analchem.9b00574] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantitative evaluation of small molecule permeation and accumulation in Gram-negative bacteria is important for drug development against these bacteria. While these measurements are commonly performed at physiological pH, Escherichia coli and many other Enterobacteriaceae infect human gastrointestinal and urinary tracts, where they encounter different pH conditions. To understand how external pH affects permeation and accumulation of small molecules in E. coli cells, we apply second harmonic generation (SHG) spectroscopy using SHG-active antimicrobial compound malachite green as the probe molecule. Using SHG, we quantify periplasmic and cytoplasmic accumulations separately in live E. coli cells, which was never done before. Compartment-wise measurements reveal accumulation of the probe molecule in cytoplasm at physiological and alkaline pH, while entrapment in periplasm at weakly acidic pH and retention in external solution at highly acidic pH. Behind such disparity in localizations, up to 2 orders of magnitude reduction in permeability across the inner membrane at weakly acidic pH and outer membrane at highly acidic pH are found to play key roles. Our results unequivocally demonstrate the control of external pH over entry and compartment-wise distribution of small molecules in E. coli cells, which is a vital information and should be taken into account in antibiotic screening against E. coli and other Enterobacteriaceae members. In addition, our results demonstrate the ability of malachite green as an excellent SHG-indicator of changes of individual cell membrane and periplasm properties of live E. coli cells in response to external pH change from acidic to alkaline. This finding, too, has great importance, as there is barely any other molecular probe that can provide similar information.
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Zhou Y, Wu Y, Pokholenko O, Papper V, Marks RS, Steele TWJ. Design and optimisation of Photochrome Aptamer Switch Assay (PHASA). Anal Chim Acta 2019; 1061:134-141. [PMID: 30926032 DOI: 10.1016/j.aca.2019.01.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/10/2019] [Accepted: 01/24/2019] [Indexed: 02/07/2023]
Abstract
Photochrome Aptamer Switch Assay (PHASA) is our unique and recently developed fluorescent biosensing platform that exploits the combination of aptamer adaptive binding and photoisomerisation kinetics of stilbenes. The PHASA is based on converting any suitable stilbene-ligand-aptamer complex into a reversible biosensor. Binding affinity, aptamer concentration, and stilbene molecular structure determine the PHASA performance criteria. Consequently, understanding of the structure-activity relationship of the stilbene-ligand conjugate is extremely important when predicting and optimising the biosensor sensitivity. In the present manuscript, new analytical methods relating to calculation of the limit of detection (LOD) of the PHASA are proposed and discussed. Using these methods, it is possible to optimise the independent or dependent physicochemical parameters of the stilbene-ligand conjugates and evaluate their general sensing performance. The proposed analytical methods are based on the inter-dependent relationships between the sensitivity and the range of analyte detection and provide starting conditions for known aptamer binding constants in various PHASA applications.
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Affiliation(s)
- Yubin Zhou
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore; Department of Physiology and Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Yuanyuan Wu
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Oleksandr Pokholenko
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | | | - Robert S Marks
- Department of Biotechnology Engineering, Faculty of Engineering Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Be'er-Sheva, 84105, Israel
| | - Terry W J Steele
- School of Materials Science & Engineering, College of Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
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Saha S, Hetzke T, Prisner TF, Sigurdsson ST. Noncovalent spin-labeling of RNA: the aptamer approach. Chem Commun (Camb) 2018; 54:11749-11752. [PMID: 30276367 DOI: 10.1039/c8cc05597a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the first example of site-directed spin-labeling of unmodified RNA, a pyrrolidine-nitroxide derivative of tetramethylrosamine (TMR) was shown to bind with high affinity to the malachite green (MG) aptamer, as determined by continuous-wave (CW) electron paramagnetic resonance (EPR), pulsed electron-electron double resonance (PELDOR) and fluorescence spectroscopies.
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Affiliation(s)
- Subham Saha
- Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland.
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Current state of in vivo panning technologies: Designing specificity and affinity into the future of drug targeting. Adv Drug Deliv Rev 2018; 130:39-49. [PMID: 29964079 DOI: 10.1016/j.addr.2018.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 06/22/2018] [Indexed: 11/20/2022]
Abstract
Targeting ligands are used in drug delivery to improve drug distribution to desired cells or tissues and to facilitate cellular entry. In vivo biopanning, whereby billions of potential ligand sequences are screened in biologically-relevant and complex conditions, is a powerful method for identification of novel target ligands. This tool has impacted drug delivery technologies and expanded our arsenal of therapeutics and diagnostics. Within this review we will discuss current in vivo panning technologies and ways that these technologies can be improved to advance next-generation drug delivery strategies.
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Gao F, Djordjevic I, Pokholenko O, Zhang H, Zhang J, Steele TWJ. On-Demand Bioadhesive Dendrimers with Reduced Cytotoxicity. Molecules 2018; 23:E796. [PMID: 29601480 PMCID: PMC6017702 DOI: 10.3390/molecules23040796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 03/22/2018] [Accepted: 03/27/2018] [Indexed: 01/11/2023] Open
Abstract
Tissue adhesives based on polyamidoamine (PAMAM) dendrimer, grafted with UV-sensitive aryldiazirine (PAMAM-g-diazirine) are promising new candidates for light active adhesion on soft tissues. Diazirine carbene precursors form interfacial and intermolecular covalent crosslinks with tissues after UV light activation that requires no premixing or inclusion of free radical initiators. However, primary amines on the PAMAM dendrimer surface present a potential risk due to their cytotoxic and immunological effects. PAMAM-g-diazirine formulations with cationic pendant amines converted into neutral amide groups were evaluated. In vitro toxicity is reduced by an order of magnitude upon amine capping while retaining bioadhesive properties. The in vivo immunological response to PAMAM-g-diazirine formulations was found to be optimal in comparison to standard poly(lactic-co-glycolic acid) (PLGA) thin films.
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Affiliation(s)
- Feng Gao
- School of Material Science and Engineering, Beijing University of Chemistry Technology, North Third Ring Road 15, Chaoyang District, Beijing 100029, China.
| | - Ivan Djordjevic
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, NL, Mexico.
| | - Oleksandr Pokholenko
- School of Materials Science and Engineering, Division of Materials Technology, Nanyang Technological University, Singapore 639798, Singapore.
| | - Haobo Zhang
- School of Material Science and Engineering, Beijing University of Chemistry Technology, North Third Ring Road 15, Chaoyang District, Beijing 100029, China.
| | - Junying Zhang
- School of Material Science and Engineering, Beijing University of Chemistry Technology, North Third Ring Road 15, Chaoyang District, Beijing 100029, China.
| | - Terry W J Steele
- School of Materials Science and Engineering, Division of Materials Technology, Nanyang Technological University, Singapore 639798, Singapore.
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Yerramilli VS, Kim KH. Labeling RNAs in Live Cells Using Malachite Green Aptamer Scaffolds as Fluorescent Probes. ACS Synth Biol 2018. [PMID: 29513000 DOI: 10.1021/acssynbio.7b00237] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNAs mediate many different processes that are central to cellular function. The ability to quantify or image RNAs in live cells is very useful in elucidating such functions of RNA. RNA aptamer-fluorogen systems have been increasingly used in labeling RNAs in live cells. Here, we use the malachite green aptamer (MGA), an RNA aptamer that can specifically bind to malachite green (MG) dye and induces it to emit far-red fluorescence signals. Previous studies on MGA showed a potential for the use of MGA for genetically tagging other RNA molecules in live cells. However, these studies also exhibited low fluorescence signals and high background noise. Here we constructed and tested RNA scaffolds containing multiple tandem repeats of MGA as a strategy to increase the brightness of the MGA aptamer-fluorogen system as well as to make the system fluoresce when tagging various RNA molecules, in live cells. We demonstrate that our MGA scaffolds can induce fluorescence signals by up to ∼20-fold compared to the basal level as a genetic tag for other RNA molecules. We also show that our scaffolds function reliably as genetically encoded fluorescent tags for mRNAs of fluorescent proteins and other RNA aptamers.
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Affiliation(s)
- V. Siddartha Yerramilli
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
| | - Kyung Hyuk Kim
- Department of Bioengineering, University of Washington, Seattle, Washington 98105, United States
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Jia J, Yan S, Lai X, Xu Y, Liu T, Xiang Y. Colorimetric Aptasensor for Detection of Malachite Green in Fish Sample Based on RNA and Gold Nanoparticles. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-017-1144-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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