1
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Levin N, Hendler-Neumark A, Kamber D, Bisker G. Enhanced cellular internalization of near-infrared fluorescent single-walled carbon nanotubes facilitated by a transfection reagent. J Colloid Interface Sci 2024; 664:650-666. [PMID: 38490040 DOI: 10.1016/j.jcis.2024.03.039] [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: 12/17/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
Functionalized single-walled carbon nanotubes (SWCNTs) hold immense potential for diverse biomedical applications due to their biocompatibility and optical properties, including near-infrared fluorescence. Specifically, SWCNTs have been utilized to target cells as a vehicle for drug delivery and gene therapy, and as sensors for various intracellular biomarkers. While the main internalization route of SWCNTs into cells is endocytosis, methods for enhancing the cellular uptake of SWCNTs are of great importance. In this research, we demonstrate the use of a transfecting reagent for promoting cell internalization of functionalized SWCNTs. We explore different types of SWCNT functionalization, namely single-stranded DNA (ssDNA) or polyethylene glycol (PEG)-lipids, and two different cell types, embryonic kidney cells and adenocarcinoma cells. We show that internalizing PEGylated functionalized SWCNTs is enhanced in the presence of the transfecting reagent, where the effect is more pronounced for negatively charged PEG-lipid. However, ssDNA-SWCNTs tend to form aggregates in the presence of the transfecting reagent, rendering it unsuitable for promoting internalization. For all cases, cellular uptake is visualized by near-infrared fluorescence microscopy, showing that the SWCNTs are typically localized within the lysosome. Generally, cellular internalization was higher in the adenocarcinoma cells, thereby paving new avenues for drug delivery and sensing in malignant cells.
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Affiliation(s)
- Naamah Levin
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Adi Hendler-Neumark
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dotan Kamber
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel; Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel; Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel.
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2
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Basu S, Hendler-Neumark A, Bisker G. Monitoring Enzyme Activity Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes. ACS Sens 2024; 9:2237-2253. [PMID: 38669585 PMCID: PMC11129355 DOI: 10.1021/acssensors.4c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]
Abstract
Enzymes serve as pivotal biological catalysts that accelerate essential chemical reactions, thereby influencing a variety of physiological processes. Consequently, the monitoring of enzyme activity and inhibition not only yields crucial insights into health and disease conditions but also forms the basis of research in drug discovery, toxicology, and the understanding of disease mechanisms. In this context, near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) have emerged as effective tools for tracking enzyme activity and inhibition through diverse strategies. This perspective explores the physicochemical attributes of SWCNTs that render them well-suited for such monitoring. Additionally, we delve into the various strategies developed so far for successfully monitoring enzyme activity and inhibition, emphasizing the distinctive features of each principle. Furthermore, we contrast the benefits of SWCNT-based NIR probes with conventional gold standards in monitoring enzyme activity. Lastly, we highlight the current challenges faced in this field and suggest potential solutions to propel it forward. This perspective aims to contribute to the ongoing progress in biodiagnostics and seeks to engage the wider community in developing and applying enzymatic assays using SWCNTs.
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Affiliation(s)
- Srestha Basu
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Adi Hendler-Neumark
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel
Aviv University, Tel Aviv 6997801, Israel
- Center
for Light-Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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3
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Metternich JT, Hill B, Wartmann JAC, Ma C, Kruskop RM, Neutsch K, Herbertz S, Kruss S. Signal Amplification and Near-Infrared Translation of Enzymatic Reactions by Nanosensors. Angew Chem Int Ed Engl 2024; 63:e202316965. [PMID: 38100133 DOI: 10.1002/anie.202316965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Indexed: 01/18/2024]
Abstract
Enzymatic reactions are used to detect analytes in a range of biochemical methods. To measure the presence of an analyte, the enzyme is conjugated to a recognition unit and converts a substrate into a (colored) product that is detectable by visible (VIS) light. Thus, the lowest enzymatic turnover that can be detected sets a limit on sensitivity. Here, we report that substrates and products of horseradish peroxidase (HRP) and β-galactosidase change the near-infrared (NIR) fluorescence of (bio)polymer modified single-walled carbon nanotubes (SWCNTs). They translate a VIS signal into a beneficial NIR signal. Moreover, the affinity of the nanosensors leads to a higher effective local concentration of the reactants. This causes a non-linear sensor-based signal amplification and translation (SENSAT). We find signal enhancement up to ≈120x for the HRP substrate p-phenylenediamine (PPD), which means that reactions below the limit of detection in the VIS can be followed in the NIR (≈1000 nm). The approach is also applicable to other substrates such as 3,3'-5,5'-tetramethylbenzidine (TMB). An adsorption-based theoretical model fits the observed signals and corroborates the sensor-based enhancement mechanism. This approach can be used to amplify signals, translate them into the NIR and increase sensitivity of biochemical assays.
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Affiliation(s)
- Justus T Metternich
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
| | - Björn Hill
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Janus A C Wartmann
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Chen Ma
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Rebecca M Kruskop
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
| | - Krisztian Neutsch
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Svenja Herbertz
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
| | - Sebastian Kruss
- Department of Chemistry, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
- Biomedical Nanosensors, Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
- Center for Nanointegration Duisburg-Essen (CENIDE), Carl-Benz-Strasse 199, 47057, Duisburg, Germany
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4
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Ahsan A, Wagner D, Varaljay VA, Roman V, Kelley-Loughnane N, Reuel NF. Screening putative polyester polyurethane degrading enzymes with semi-automated cell-free expression and nitrophenyl probes. Synth Biol (Oxf) 2024; 9:ysae005. [PMID: 38414826 PMCID: PMC10898825 DOI: 10.1093/synbio/ysae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/26/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
Cell-free expression (CFE) has shown recent utility in prototyping enzymes for discovery efforts. In this work, CFE is demonstrated as an effective tool to screen putative polyester polyurethane degrading enzyme sequences sourced from metagenomic analysis of biofilms prospected on aircraft and vehicles. An automated fluid handler with a controlled temperature block is used to assemble the numerous 30 µL CFE reactions to provide more consistent results over human assembly. In sum, 13 putative hydrolase enzymes from the biofilm organisms as well as a previously verified, polyester-degrading cutinase were expressed using in-house E. coli extract and minimal linear templates. The enzymes were then tested for esterase activity directly in extract using nitrophenyl conjugated substrates, showing highest sensitivity to shorter substrates (4-nitrophenyl hexanoate and 4-nNitrophenyl valerate). This screen identified 10 enzymes with statistically significant activities against these substrates; however, all were lower in measured relative activity, on a CFE volume basis, to the established cutinase control. This approach portends the use of CFE and reporter probes to rapidly prototype, screen and design for synthetic polymer degrading enzymes from environmental consortia. Graphical Abstract.
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Affiliation(s)
- Afrin Ahsan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Dominique Wagner
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
- UES Inc., Dayton, OH, USA
| | - Vanessa A Varaljay
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Victor Roman
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH, USA
| | - Nigel F Reuel
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
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5
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Hendler-Neumark A, Wulf V, Bisker G. Single-Walled Carbon Nanotube Sensor Selection for the Detection of MicroRNA Biomarkers for Acute Myocardial Infarction as a Case Study. ACS Sens 2023; 8:3713-3722. [PMID: 37700465 PMCID: PMC10616859 DOI: 10.1021/acssensors.3c00633] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/01/2023] [Indexed: 09/14/2023]
Abstract
MicroRNAs (miRNAs) are single-stranded non-coding short ribonucleic acid sequences that take part in many cellular and biological processes. Recent studies have shown that altered expression of miRNAs is involved in pathological processes, and they can thus be considered biomarkers for the early detection of various diseases. Here, we demonstrate a selection and elimination process of fluorescent single-walled carbon nanotube (SWCNT) sensors for miRNA biomarkers based on RNA-DNA hybridization with a complementary DNA recognition unit bound to the SWCNT surface. We use known miRNA biomarkers for acute myocardial infarction (AMI), commonly known as a heart attack, as a case study. We have selected five possible miRNA biomarkers which are selective and specific to AMI and tested DNA-SWCNT sensor candidates with the target DNA and RNA sequences in different environments. Out of these five miRNA sensors, three could recognize the complementary DNA or RNA sequence in a buffer, showing fluorescence modulation of the SWCNT in response to the target sequence. Out of the three working sensors in buffer, only one could function in serum and was selected for further testing. The chosen sensor, SWCNT-miDNA208a, showed high specificity and selectivity toward the target sequence, with better performance in serum compared to a buffer environment. The SWCNT sensor selection pipeline highlights the importance of testing sensor candidates in the appropriate environment and can be extended to other libraries of biomarkers.
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Affiliation(s)
- Adi Hendler-Neumark
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Verena Wulf
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Department
of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Center
for Physics and Chemistry of Living Systems, Tel-Aviv University, Tel Aviv 6997801, Israel
- Center
for Nanoscience and Nanotechnology, Tel-Aviv
University, Tel Aviv 6997801, Israel
- Center
for Light-Matter Interaction, Tel-Aviv University, Tel Aviv 6997801, Israel
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6
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Kallmyer NE, Agarwal S, Eeg D, Khor R, Roby N, Vela Ramirez A, Hillier AC, Reuel NF. Lipid-Functionalized Single-Walled Carbon Nanotubes as Probes for Screening Cell Wall Disruptors. ACS APPLIED MATERIALS & INTERFACES 2023; 15:44621-44630. [PMID: 37721709 DOI: 10.1021/acsami.3c06592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Membrane-active molecules are of great importance to drug delivery and antimicrobials applications. While the ability to prototype new membrane-active molecules has improved greatly with the advent of automated chemistries and rapid biomolecule expression techniques, testing methods are still limited by throughput, cost, and modularity. Existing methods suffer from feasibility constraints of working with pathogenic living cells and by intrinsic limitations of model systems. Herein, we demonstrate an abiotic sensor that uses semiconducting single-walled carbon nanotubes (SWCNTs) as near-infrared fluorescent transducers to report membrane interactions. This sensor is composed of SWCNTs aqueously suspended in lipid, creating a cylindrical, bilayer corona; these SWCNT probes are very sensitive to solvent access (changes in permittivity) and thus report morphological changes to the lipid corona by modulation of fluorescent signals, where binding and disruption are reported as brightening and attenuation, respectively. This mechanism is first demonstrated with chemical and physical membrane-disruptive agents, including ethanol and sodium dodecyl sulfate, and application of electrical pulses. Known cell-penetrating and antimicrobial peptides are then used to demonstrate how the dynamic response of these sensors can be deconvoluted to evaluate different parallel mechanisms of interaction. Last, SWCNTs functionalized in several different bacterial lipopolysaccharides (Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli) are used to evaluate a panel of known membrane-disrupting antimicrobials to demonstrate that drug selectivity can be assessed by suspension of SWCNTs with different membrane materials.
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Affiliation(s)
- Nathaniel E Kallmyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Sparsh Agarwal
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Danielle Eeg
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Rachel Khor
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Nathan Roby
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Alma Vela Ramirez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Andrew C Hillier
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Nigel F Reuel
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
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7
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Kuo MT, Raffaelle JF, Waller EM, Varaljay VA, Wagner D, Kelley-Loughnane N, Reuel NF. Screening Enzymatic Degradation of Polyester Polyurethane with Fluorescent Single-walled Carbon Nanotube and Polymer Nanoparticle Conjugates. ACS NANO 2023; 17:17021-17030. [PMID: 37606935 DOI: 10.1021/acsnano.3c04347] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Enzymatic biodegradation is a promising method to reclaim plastic materials. However, to date, a high-throughput method for screening potential enzyme candidates for biodegradation is still lacking. Here, we propose a single-walled carbon nanotube (SWCNT) fluorescence sensor for screening the enzymatic degradation of polyester polyurethane nanoparticles. Through wrapping the SWCNT with cationic chitosan, an electrostatic bond is formed between the SWCNT and Impranil, a widely applied model substrate of polyester polyurethane. As Impranil is being degraded by the enzymes, a characteristic quenching at a short reaction time followed by a brightening at a longer reaction time in the fluorescence signal is observed. The time-dependent fluorescence response is compared with turbidity measurement, and we conclude that the brightening in fluorescence results from the binding of the degradation product with the SWCNT. The proposed SWCNT sensor design has the potential to screen enzyme candidates for selective degradation of other plastic particles.
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Affiliation(s)
- Mei-Tsan Kuo
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Jack F Raffaelle
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Ellise McKenna Waller
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Vanessa A Varaljay
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, Ohio 45433, United States
| | | | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, Ohio 45433, United States
| | - Nigel F Reuel
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
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8
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Ackermann J, Metternich JT, Herbertz S, Kruss S. Biosensing with Fluorescent Carbon Nanotubes. Angew Chem Int Ed Engl 2022; 61:e202112372. [PMID: 34978752 PMCID: PMC9313876 DOI: 10.1002/anie.202112372] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/28/2021] [Indexed: 12/23/2022]
Abstract
Biosensors are powerful tools for modern basic research and biomedical diagnostics. Their development requires substantial input from the chemical sciences. Sensors or probes with an optical readout, such as fluorescence, offer rapid, minimally invasive sensing of analytes with high spatial and temporal resolution. The near-infrared (NIR) region is beneficial because of the reduced background and scattering of biological samples (tissue transparency window) in this range. In this context, single-walled carbon nanotubes (SWCNTs) have emerged as versatile NIR fluorescent building blocks for biosensors. Here, we provide an overview of advances in SWCNT-based NIR fluorescent molecular sensors. We focus on chemical design strategies for diverse analytes and summarize insights into the photophysics and molecular recognition. Furthermore, different application areas are discussed-from chemical imaging of cellular systems and diagnostics to in vivo applications and perspectives for the future.
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Affiliation(s)
- Julia Ackermann
- Biomedical NanosensorsFraunhofer Institute for Microelectronic Circuits and SystemsFinkenstrasse 6147057DuisburgGermany
- Department EBSUniversity Duisburg-EssenBismarckstrasse 8147057DuisburgGermany
| | - Justus T. Metternich
- Physical ChemistryRuhr-University BochumUniversitätsstrasse 15044801BochumGermany
- Biomedical NanosensorsFraunhofer Institute for Microelectronic Circuits and SystemsFinkenstrasse 6147057DuisburgGermany
| | - Svenja Herbertz
- Biomedical NanosensorsFraunhofer Institute for Microelectronic Circuits and SystemsFinkenstrasse 6147057DuisburgGermany
| | - Sebastian Kruss
- Physical ChemistryRuhr-University BochumUniversitätsstrasse 15044801BochumGermany
- Biomedical NanosensorsFraunhofer Institute for Microelectronic Circuits and SystemsFinkenstrasse 6147057DuisburgGermany
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9
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Ackermann J, Metternich JT, Herbertz S, Kruss S. Biosensing with Fluorescent Carbon Nanotubes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julia Ackermann
- Biomedical Nanosensors Fraunhofer Institute for Microelectronic Circuits and Systems Finkenstrasse 61 47057 Duisburg Germany
- Department EBS University Duisburg-Essen Bismarckstrasse 81 47057 Duisburg Germany
| | - Justus T. Metternich
- Physical Chemistry Ruhr-University Bochum Universitätsstrasse 150 44801 Bochum Germany
- Biomedical Nanosensors Fraunhofer Institute for Microelectronic Circuits and Systems Finkenstrasse 61 47057 Duisburg Germany
| | - Svenja Herbertz
- Biomedical Nanosensors Fraunhofer Institute for Microelectronic Circuits and Systems Finkenstrasse 61 47057 Duisburg Germany
| | - Sebastian Kruss
- Physical Chemistry Ruhr-University Bochum Universitätsstrasse 150 44801 Bochum Germany
- Biomedical Nanosensors Fraunhofer Institute for Microelectronic Circuits and Systems Finkenstrasse 61 47057 Duisburg Germany
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10
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Agarwal S, Kallmyer NE, Vang DX, Ramirez AV, Islam MM, Hillier AC, Halverson L, Reuel NF. Single-Walled Carbon Nanotube Probes for the Characterization of Biofilm-Degrading Enzymes Demonstrated against Pseudomonas aeruginosa Extracellular Matrices. Anal Chem 2022; 94:856-865. [PMID: 34939783 PMCID: PMC9150823 DOI: 10.1021/acs.analchem.1c03633] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hydrolase co-therapies that degrade biofilm extracellular polymeric substances (EPS) allow for a better diffusion of antibiotics and more effective treatment; current methods for quantitatively measuring the enzymatic degradation of EPS are not amendable to high-throughput screening. Herein, we present biofilm EPS-functionalized single-walled carbon nanotube (SWCNT) probes for rapid screening of hydrolytic enzyme selectivity and activity on EPS. The extent of biofilm EPS degradation is quantified by monitoring the quenching of the SWCNT fluorescence. We used this platform to screen 16 hydrolases with varying bond breaking selectivity against a panel of wild-type Pseudomonas aeruginosa and mutants deficient or altered in one or more EPS. Next, we performed concentration-dependent studies of six enzymes on two common strains found in cystic fibrosis (CF) environments and, for each enzyme, extracted three first-order rate constants and their relative contributions by fitting a parallel, multi-site degradation model, with a good model fit (R2 from 0.65 to 0.97). Reaction rates (turnover rates) are dependent on the enzyme concentration and range from 6.67 × 10-11 to 2.80 × 10-3 *s-1 per mg/mL of enzymes. Lastly, we confirmed findings from this new assay using an established crystal-violet staining assay for a subset of hydrolase panels. In summary, our work shows that this modular sensor is amendable to the high-throughput screening of EPS degradation, thereby improving the rate of discovery and development of novel hydrolases.
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Affiliation(s)
- Sparsh Agarwal
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, United States
| | - Nathaniel E Kallmyer
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, United States
| | - Dua X Vang
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50011, United States,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa 50011, United States
| | - Alma V Ramirez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, United States
| | - Md Monirul Islam
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, United States
| | - Andrew C Hillier
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, United States
| | - Larry Halverson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, 50011, United States,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa 50011, United States
| | - Nigel F Reuel
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, 50011, United States,Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa 50011, United States,Corresponding Author: Prof. Nigel F Reuel, 2114 Sweeney Hall, 618 Bissell Rd, Iowa State University, Ames, IA, 50011, United States, , Ph: 515-294-4592
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11
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Algar WR, Massey M, Rees K, Higgins R, Krause KD, Darwish GH, Peveler WJ, Xiao Z, Tsai HY, Gupta R, Lix K, Tran MV, Kim H. Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging. Chem Rev 2021; 121:9243-9358. [PMID: 34282906 DOI: 10.1021/acs.chemrev.0c01176] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rehan Higgins
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - William J Peveler
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Zhujun Xiao
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rupsa Gupta
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelsi Lix
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hyungki Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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12
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Kallmyer NE, Abdennadher MS, Agarwal S, Baldwin-Kordick R, Khor RL, Kooistra AS, Peterson E, McDaniel MD, Reuel NF. Inexpensive Near-Infrared Fluorimeters: Enabling Translation of nIR-Based Assays to the Field. Anal Chem 2021; 93:4800-4808. [PMID: 33703890 DOI: 10.1021/acs.analchem.0c03732] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The practical impact of analytical probes that transduce in the near-infrared (nIR) has been dampened by the lack of cost-effective and portable nIR fluorimeters. Herein, we demonstrate straightforward designs for an inexpensive microplate reader and a portable fluorimeter. These instruments require minimally complex machining and fabrication and operate with an open-source programming language (Python). Complete wiring diagrams, assembly diagrams, and scripts are provided. To demonstrate the utility of these two instruments, we performed high-throughput and field-side measurements of soil samples to evaluate the effect of soil management strategies on extracellular proteolytic, cellulolytic, and lignin-modifying activities. This was accomplished with fluorescent enzyme probes that utilized uniquely sensitive transducers exclusive to the nIR spectrum, single-walled carbon nanotubes. We also used the portable fluorimeter to evaluate spatial variations of proteolytic activity within individual field plots, while minimizing the effects of soil storage and handling. These demonstrations indicate the utility of these fluorimeters for translating analytical probes that operate in the nIR beyond the laboratory and into actual use.
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Affiliation(s)
- Nathaniel E Kallmyer
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
| | - Mohamed Seddik Abdennadher
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
| | - Sparsh Agarwal
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
| | - Rebecca Baldwin-Kordick
- Department of Agronomy, Iowa State University, 716 Farm House Ln., Ames, Iowa 50011, United States
| | - Rachel L Khor
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
| | - Alex S Kooistra
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
| | - Erica Peterson
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
| | - Marshall D McDaniel
- Department of Agronomy, Iowa State University, 716 Farm House Ln., Ames, Iowa 50011, United States
| | - Nigel F Reuel
- Department of Chemical and Biological Engineering, Iowa State University, 618 Bissell Rd., Ames, Iowa 50011, United States
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Chio L, Del Bonis-O'Donnell JT, Kline MA, Kim JH, McFarlane IR, Zuckermann RN, Landry MP. Electrostatic Assemblies of Single-Walled Carbon Nanotubes and Sequence-Tunable Peptoid Polymers Detect a Lectin Protein and Its Target Sugars. NANO LETTERS 2019; 19:7563-7572. [PMID: 30958010 DOI: 10.1021/acs.nanolett.8b04955] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A primary limitation to real-time imaging of metabolites and proteins has been the selective detection of biomolecules that have no naturally occurring or stable molecular recognition counterparts. We present developments in the design of synthetic near-infrared fluorescent nanosensors based on the fluorescence modulation of single-walled carbon nanotubes (SWNTs) with select sequences of surface-adsorbed N-substituted glycine peptoid polymers. We assess the stability of the peptoid-SWNT nanosensor candidates under variable ionic strengths, protease exposure, and cell culture media conditions and find that the stability of peptoid-SWNTs depends on the composition and length of the peptoid polymer. From our library, we identify a peptoid-SWNT assembly that can detect lectin protein wheat germ agglutinin (WGA) with a sensitivity comparable to the concentration of serum proteins. To demonstrate the retention of nanosensor-bound protein activity, we show that WGA on the nanosensor produces an additional fluorescent signal modulation upon exposure to the lectin's target sugars, suggesting the lectin protein remains active and selectively binds its target sugars through ternary molecular recognition interactions relayed to the nanosensor. Our results inform design considerations for developing synthetic molecular recognition elements by assembling peptoid polymers on SWNTs and also demonstrate these assemblies can serve as optical nanosensors for lectin proteins and their target sugars. Together, these data suggest certain peptoid sequences can be assembled with SWNTs to serve as versatile optical probes to detect proteins and their molecular substrates.
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Affiliation(s)
- Linda Chio
- Department of Chemical and Biomolecular Engineering , University of California, Berkeley , Berkeley , California 94720 , United States
| | | | - Mark A Kline
- The Molecular Foundry , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Jae Hong Kim
- The Molecular Foundry , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Ian R McFarlane
- Department of Chemical and Biomolecular Engineering , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Ronald N Zuckermann
- The Molecular Foundry , Lawrence Berkeley National Laboratory , 1 Cyclotron Road , Berkeley , California 94720 , United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering , University of California, Berkeley , Berkeley , California 94720 , United States
- Chan-Zuckerberg Biohub , San Francisco , California 94158 , United States
- California Institute for Quantitative Biosciences (qb3) , University of California, Berkeley , Berkeley , California 94720 , United States
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14
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Nißler R, Mann FA, Preiß H, Selvaggio G, Herrmann N, Kruss S. Chirality enriched carbon nanotubes with tunable wrapping via corona phase exchange purification (CPEP). NANOSCALE 2019; 11:11159-11166. [PMID: 31149692 DOI: 10.1039/c9nr03258d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) have unique photophysical properties and serve as building blocks for biosensors, functional materials and devices. For many applications it is crucial to use chirality-pure SWCNTs, which requires sophisticated processes. Purification procedures such as wrapping by certain polymers, phase separation, density gradient centrifugation or gel chromatography have been developed and yield distinct SWCNT species wrapped by a specific polymer or surfactant. However, many applications require a different organic functionalization (corona) around the SWCNTs instead of the one used for the purification process. Here, we present a novel efficient and straightforward process to gain chirality pure SWCNTs with tunable functionalization. Our approach uses polyfluorene (PFO) polymers to enrich certain chiralities but the polymer is removed again and finally exchanged to any desired organic phase. We demonstrate this concept by dispersing SWCNTs in poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(6,6'-{2,2'-bipyridine})] (PFO-BPy), which is known to preferentially solubilize (6,5)-SWCNTs. Then PFO-BPy is removed and recycled, while letting the SWCNTs adsorb/agglomerate on sodium chloride (NaCl) crystals, which act as a toluene-stable but water-soluble filler material. In the last step these purified SWCNTs are redispersed in different polymers, surfactants and ssDNA. This corona phase exchange purification (CPEP) approach was also extended to other PFO variants to enrich and functionalize (7,5)-SWCNTs. CPEP purified and functionalized SWCNTs display monodisperse nIR spectra, which are important for fundamental studies and applications that rely on spectral changes. We show this advantage for SWCNT-based nIR fluorescent sensors for the neurotransmitter dopamine and red-shifted sp3 defect peaks . In summary, CPEP makes use of PFO polymers for chirality enrichment but provides access to chirality enriched SWCNTs functionalized in any desired polymer, surfactant or biopolymer.
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Affiliation(s)
- Robert Nißler
- Institute of Physical Chemistry, Göttingen University, Germany.
| | - Florian A Mann
- Institute of Physical Chemistry, Göttingen University, Germany.
| | - Helen Preiß
- Institute of Physical Chemistry, Göttingen University, Germany.
| | | | - Niklas Herrmann
- Institute of Physical Chemistry, Göttingen University, Germany.
| | - Sebastian Kruss
- Institute of Physical Chemistry, Göttingen University, Germany.
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Dopp JL, Rothstein SM, Mansell TJ, Reuel NF. Rapid prototyping of proteins: Mail order gene fragments to assayable proteins within 24 hours. Biotechnol Bioeng 2019; 116:667-676. [DOI: 10.1002/bit.26912] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/08/2018] [Accepted: 12/26/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Jared Lynn Dopp
- Iowa State University Chemical and Biological EngineeringAmes Iowa
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Charkhabi S, Beierle AM, McDaniel MD, Reuel NF. Resonant Sensors for Low-Cost, Contact-Free Measurement of Hydrolytic Enzyme Activity in Closed Systems. ACS Sens 2018; 3:1489-1498. [PMID: 30016082 DOI: 10.1021/acssensors.8b00267] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A passive, resonant sensor was developed that can be embedded in closed systems for wireless monitoring of hydrolytic enzyme activity. The resonators are rapidly prototyped from copper coated polyimide substrates that are masked using an indelible marker with an XY plotter and subsequently etched. The resonator's frequency response window is designed by the Archimedean coil length and pitch and is tuned for the 1-100 MHz range for better penetration through soil, water, and tissue. The resonant frequency is measured up to 5 cm stand-off distance by a coplanar, two-loop coil reader antenna attached to a vector network analyzer monitoring the S21 scattering parameter. The resonant frequency is modulated (up to 50 MHz redshift) by changing the relative permittivity of the medium in contact with the resonator (e.g., air to water). The resonant sensors are coated by an enzyme substrate, which, when degraded, causes a change in dielectric and a shift in resonant frequency (up to 7 MHz redshift). The activity (turnover rate, or kcat) of the enzyme is calculated by fitting the measured data via a custom transport and reaction model which simulates the radial digestion profile. This is used to test purified Subtilisin A and unpurified bacterial protease samples at concentrations of 30 mg/mL to 200 mg/mL with kcat ranges of 0.003-0.002 and 0.008-0.004 gsubstrate/ genzyme per second. The sensor response rate can be tuned by substrate composition (e.g., gelatin and glycerol plasticizer weight percentage). Finally, the utility of these sensors is demonstrated by wirelessly measuring the proteolytic activity of farm soil with a measured kcat of 0.00152 gsubstrate/( gsoil·s).
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