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Rosenberg DJ, Cunningham FJ, Hubbard JD, Goh NS, Wang JWT, Nishitani S, Hayman EB, Hura GL, Landry MP, Pinals RL. Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry. J Am Chem Soc 2024; 146:386-398. [PMID: 38158616 DOI: 10.1021/jacs.3c09549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Single-walled carbon nanotubes (SWCNTs) with adsorbed single-stranded DNA (ssDNA) are applied as sensors to investigate biological systems, with potential applications ranging from clinical diagnostics to agricultural biotechnology. Unique ssDNA sequences render SWCNTs selectively responsive to target analytes such as (GT)n-SWCNTs recognizing the neuromodulator, dopamine. It remains unclear how the ssDNA conformation on the SWCNT surface contributes to functionality, as observations have been limited to computational models or experiments under dehydrated conditions that differ substantially from the aqueous biological environments in which the nanosensors are applied. We demonstrate a direct mode of measuring in-solution ssDNA geometries on SWCNTs via X-ray scattering interferometry (XSI), which leverages the interference pattern produced by AuNP tags conjugated to ssDNA on the SWCNT surface. We employ XSI to quantify distinct surface-adsorbed morphologies for two (GT)n ssDNA oligomer lengths (n = 6, 15) that are used on SWCNTs in the context of dopamine sensing and measure the ssDNA conformational changes as a function of ionic strength and during dopamine interaction. We show that the shorter oligomer, (GT)6, adopts a more periodically ordered ring structure along the SWCNT axis (inter-ssDNA distance of 8.6 ± 0.3 nm), compared to the longer (GT)15 oligomer (most probable 5'-to-5' distance of 14.3 ± 1.1 nm). During molecular recognition, XSI reveals that dopamine elicits simultaneous axial elongation and radial constriction of adsorbed ssDNA on the SWCNT surface. Our approach using XSI to probe solution-phase morphologies of polymer-functionalized SWCNTs can be applied to yield insights into sensing mechanisms and inform future design strategies for nanoparticle-based sensors.
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Affiliation(s)
- Daniel J Rosenberg
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Joshua D Hubbard
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jeffrey Wei-Ting Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Shoichi Nishitani
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Emily B Hayman
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, California 95064, 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
- Innovative Genomics Institute (IGI), Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California 94720, United States
| | - Rebecca L Pinals
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Gong X, Cho SY, Kuo S, Ogunlade B, Tso K, Salem DP, Strano MS. Divalent Metal Cation Optical Sensing Using Single-Walled Carbon Nanotube Corona Phase Molecular Recognition. Anal Chem 2022; 94:16393-16401. [DOI: 10.1021/acs.analchem.2c03648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xun Gong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Soo-Yeon Cho
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sydney Kuo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Babatunde Ogunlade
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kathryn Tso
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel P. Salem
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael S. Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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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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4
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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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5
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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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6
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Yaari Z, Horoszko CP, Antman-Passig M, Kim M, Nguyen FT, Heller DA. Emerging technologies in cancer detection. Cancer Biomark 2022. [DOI: 10.1016/b978-0-12-824302-2.00011-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Card M, Gravely M, M Madani SZ, Roxbury D. A Spin-Coated Hydrogel Platform Enables Accurate Investigation of Immobilized Individual Single-Walled Carbon Nanotubes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:31986-31995. [PMID: 34197074 DOI: 10.1021/acsami.1c06562] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) have been used in a variety of sensing and imaging applications over the past few years due to their unique optical properties. In the solution phase, SWCNTs are employed as near-infrared (NIR) fluorescence-based sensors of target analytes via modulations in emission intensity and/or wavelength. In an effort to lower the limit of detection, research has been conducted into isolating SWCNTs adhered to surfaces for potential single molecule analyte detection. However, it is known that SWCNT fluorescence is adversely affected by the inherently rough surfaces that are conventionally used for their observation (e.g., glass coverslip), potentially interfering with fluorescence-based analyte detection. Here, using a spin-coating method with thin films of alginate and SWCNTs, we demonstrate that a novel hydrogel platform can be created to investigate immobilized individual SWCNTs without significantly perturbing their optical properties as compared to solution-phase values. In contrast to the glass coverslip, which red-shifted DNA-functionalized (6,5)-SWCNTs by an average of 3.4 nm, the hydrogel platform reported emission wavelengths that statistically matched the solution-phase values. Additionally, the heterogeneity in the wavelength measurements, as determined from the width of created histograms, was reduced nearly by a factor of 3 for the SWCNTs in the hydrogel platform when compared to glass coverslips. Using long SWCNTs, i.e., those with an average length above the diffraction limit of our microscope, we show that a glass coverslip can induce optical heterogeneity along the length of a single SWCNT regardless of its surface functionalization. This is again significantly mitigated when examining the long SWCNTs in the hydrogel platform. Finally, we show that upon the addition of a model analyte (calcium chloride), the optical response can be spatially resolved along the length of a single SWCNT, enabling localized analyte detection on the surface of a single nanoscale sensor.
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Affiliation(s)
- Matthew Card
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Mitchell Gravely
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - S Zahra M Madani
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel Roxbury
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
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8
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Yaari Z, Cheung JM, Baker HA, Frederiksen RS, Jena PV, Horoszko CP, Jiao F, Scheuring S, Luo M, Heller DA. Nanoreporter of an Enzymatic Suicide Inactivation Pathway. NANO LETTERS 2020; 20:7819-7827. [PMID: 33119310 PMCID: PMC8177003 DOI: 10.1021/acs.nanolett.0c01858] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Enzymatic suicide inactivation, a route of permanent enzyme inhibition, is the mechanism of action for a wide array of pharmaceuticals. Here, we developed the first nanosensor that selectively reports the suicide inactivation pathway of an enzyme. The sensor is based on modulation of the near-infrared fluorescence of an enzyme-bound carbon nanotube. The nanosensor responded selectively to substrate-mediated suicide inactivation of the tyrosinase enzyme via bathochromic shifting of the nanotube emission wavelength. Mechanistic investigations revealed that singlet oxygen generated by the suicide inactivation pathway induced the response. We used the nanosensor to quantify the degree of enzymatic inactivation by measuring response rates to small molecule tyrosinase modulators. This work resulted in a new capability of interrogating a specific route of enzymatic death. Potential applications include drug screening and hit-validation for compounds that elicit or inhibit enzymatic inactivation and single-molecule measurements to assess population heterogeneity in enzyme activity.
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Affiliation(s)
- Zvi Yaari
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Justin M. Cheung
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Hanan A. Baker
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Rune S. Frederiksen
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Prakrit V. Jena
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Christopher, P. Horoszko
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Fang Jiao
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Simon Scheuring
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Minkui Luo
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Daniel A. Heller
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
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9
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Interfacing DNA with nanoparticles: Surface science and its applications in biosensing. Int J Biol Macromol 2020; 151:757-780. [DOI: 10.1016/j.ijbiomac.2020.02.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
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10
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Tardani F, Sarti S, Sennato S, Leo M, Filetici P, Casciardi S, Schiavi PG, Bordi F. Experimental Evidence of Single-Stranded DNA Adsorption on Multiwalled Carbon Nanotubes. J Phys Chem B 2020; 124:2514-2525. [PMID: 32134663 DOI: 10.1021/acs.jpcb.0c00882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncovalent DNA functionalization is one of the most used routes for the easy dispersion of carbon nanotubes (CNTs) yielding DNA-CNTs complexes with promising applications. Definition of the structure of adsorbed DNA is crucial, but the organization of polymer at the carbon interface is far from being understood. In comparison to single-walled nanotubes, not much effort has been devoted to assessing the structure of the adsorbed DNA on multiwalled carbon nanotubes (MWCNTs), where their metallic nature, large size, and polydispersity represent serious obstacles for both experimental and theoretical studies. As a contribution to fill this lack in these aspects, we investigated DNA-MWCNT complexes by dielectric spectroscopy (DS) which is sensitive to even small changes in the charge distribution at charged interfaces and was largely employed in studying the electric and conformational properties of polyelectrolytes, such as DNA, in aqueous solutions and at interfaces. The dielectric relaxation in the MHz range is the signature of DNA adsorption on CNTs and sheds light on its conformational properties. A detailed analysis of the conductivity of the DNA-MWCNT suspensions unequivocally proves that DNA is adsorbed in a single-stranded conformation while excess DNA reassociates without interfering with the stability of the complexes.
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Affiliation(s)
- Franco Tardani
- Istituto dei Sistemi Complessi (ISC) - CNR, UOS Roma Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | | | - Simona Sennato
- Istituto dei Sistemi Complessi (ISC) - CNR, UOS Roma Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | | | | | - Stefano Casciardi
- Dipartimento di Medicina, Epidemiologi, Igiene del Lavoro e Ambientale, Istituto Nazionale per l'Assicurazione contro gli Infortuni sul Lavoro, Via Fontana Candida 1, 00078 Monte Porzio Catone RM, Italy
| | | | - Federico Bordi
- Istituto dei Sistemi Complessi (ISC) - CNR, UOS Roma Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
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11
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Hofferber EM, Stapleton JA, Adams J, Kuss M, Duan B, Iverson NM. Implantable Nanotube Sensor Platform for Rapid Analyte Detection. Macromol Biosci 2019; 19:e1800469. [PMID: 30942955 PMCID: PMC6827871 DOI: 10.1002/mabi.201800469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/26/2019] [Indexed: 11/12/2022]
Abstract
The use of nanoparticles within living systems is a growing field, but the long-term effects of introducing nanoparticles to a biological system are unknown. If nanoparticles remain localized after in vivo implantation unanticipated side effects due to unknown biodistribution can be avoided. Unfortunately, stabilization and retention of nanoparticles frequently alters their function.[1] In this work multiple hydrogel platforms are developed to look at long-term localization of nanoparticle sensors with the goal of developing a sensor platform that will stabilize and localize the nanoparticles without altering their function. Two different hydrogel platforms are presented, one with a liquid core of sensors and another with sensors decorating the hydrogel's exterior, that are capable of localizing the nanoparticles without inhibiting their function. With the use of these new hydrogel platforms nanoparticle sensors can be easily implanted in vivo and utilized without concerns of nanoparticle impact on the animal.
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Affiliation(s)
- Eric M. Hofferber
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, 233 L. W. Chase Hall, Lincoln, NE 68583-0726
| | - Joseph A. Stapleton
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, 233 L. W. Chase Hall, Lincoln, NE 68583-0726
| | - Janelle Adams
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, 233 L. W. Chase Hall, Lincoln, NE 68583-0726
| | - Mitchell Kuss
- Regenerative Medicine Program, University of Nebraska Medical Center, DRC II 6035, UNMC, Omaha, NE 68198-5965
| | - Bin Duan
- Regenerative Medicine Program, University of Nebraska Medical Center, DRC II 6035, UNMC, Omaha, NE 68198-5965
| | - Nicole M. Iverson
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, 233 L. W. Chase Hall, Lincoln, NE 68583-0726
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12
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Wang M, Meng H, Wang D, Yin Y, Stroeve P, Zhang Y, Sheng Z, Chen B, Zhan K, Hou X. Dynamic Curvature Nanochannel-Based Membrane with Anomalous Ionic Transport Behaviors and Reversible Rectification Switch. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805130. [PMID: 30633407 DOI: 10.1002/adma.201805130] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/29/2018] [Indexed: 05/08/2023]
Abstract
Biological nanochannels control the movements of different ions through cell membranes depending on not only those channels' static inherent configurations, structures, inner surface's physicochemical properties but also their dynamic shape changes, which are required in various essential functions of life processes. Inspired by ion channels, many artificial nanochannel-based membranes for nanofluidics and biosensing applications have been developed to regulate ionic transport behaviors by using the functional molecular modifications at the inner surface of nanochannel to achieve a stimuli-responsive layer. Here, the concept of a dynamic nanochannel system is further developed, which is a new way to regulate ion transport in nanochannels by using the dynamic change in the curvature of channels to adjust ionic rectification in real time. The dynamic curvature nanochannel-based membrane displays the advanced features of the anomalous effect of voltage, concentration, and ionic size for applying simultaneous control over the curvature-tunable asymmetric and reversible ionic rectification switching properties. This dynamic approach can be used to build smart nanochannel-based systems, which have strong implications for flexible nanofluidics, ionic rectifiers, and power generators.
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Affiliation(s)
- Miao Wang
- Research Institute for Soft Matter and Biomimetics, College of Physical Science and Technology, Xiamen University, Xiamen, 361005, P. R. China
| | - Haiqiang Meng
- Research Institute for Soft Matter and Biomimetics, College of Physical Science and Technology, Xiamen University, Xiamen, 361005, P. R. China
| | - Dan Wang
- State Key Laboratory of Mechanics and Control of Mechanical Structures, College of Aerospace Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, P. R. China
| | - Yajun Yin
- School of Aerospace Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Pieter Stroeve
- Department of Chemical Engineering and Materials Science, University of California, Davis, Davis, CA, 95616, USA
| | - Yunmao Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Zhizhi Sheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Baiyi Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Kan Zhan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
| | - Xu Hou
- Research Institute for Soft Matter and Biomimetics, College of Physical Science and Technology, Xiamen University, Xiamen, 361005, P. R. China
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China
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13
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Gillen AJ, Kupis-Rozmysłowicz J, Gigli C, Schuergers N, Boghossian AA. Xeno Nucleic Acid Nanosensors for Enhanced Stability Against Ion-Induced Perturbations. J Phys Chem Lett 2018; 9:4336-4343. [PMID: 30004705 DOI: 10.1021/acs.jpclett.8b01879] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The omnipresence of salts in biofluids creates a pervasive challenge in designing sensors suitable for in vivo applications. Fluctuations in ion concentrations have been shown to affect the sensitivity and selectivity of optical sensors based on single-walled carbon nanotubes wrapped with single-stranded DNA (ssDNA-SWCNTs). We herein observe fluorescence wavelength shifting for ssDNA-SWCNT-based optical sensors in the presence of divalent cations at concentrations above 3.5 mM. In contrast, no shifting was observed for concentrations up to 350 mM for sensors bioengineered with increased rigidity using xeno nucleic acids (XNAs). Transient fluorescence measurements reveal distinct optical transitions for ssDNA- and XNA-based wrappings during ion-induced conformation changes, with XNA-based sensors showing increased permanence in conformational and signal stability. This demonstration introduces synthetic biology as a complementary means for enhancing nanotube optoelectronic behavior, unlocking previously unexplored possibilities for developing nanobioengineered sensors with augmented capabilities.
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Affiliation(s)
- Alice J Gillen
- École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015 , Switzerland
| | | | - Carlo Gigli
- Politecnico di Torino , Turin 10129 , Italy
- Université Denis Diderot (Paris VII) , Paris 75013 , France
| | - Nils Schuergers
- École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne 1015 , Switzerland
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14
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Yao H, Wynendaele E, Xu X, Kosgei A, De Spiegeleer B. Circular dichroism in functional quality evaluation of medicines. J Pharm Biomed Anal 2018; 147:50-64. [DOI: 10.1016/j.jpba.2017.08.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/18/2017] [Accepted: 08/19/2017] [Indexed: 12/31/2022]
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15
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Budhathoki-Uprety J, Langenbacher RE, Jena PV, Roxbury D, Heller DA. A Carbon Nanotube Optical Sensor Reports Nuclear Entry via a Noncanonical Pathway. ACS NANO 2017; 11:3875-3882. [PMID: 28398031 PMCID: PMC5511501 DOI: 10.1021/acsnano.7b00176] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Single-walled carbon nanotubes are of interest in biomedicine for imaging and molecular sensing applications and as shuttles for various cargos such as chemotherapeutic drugs, peptides, proteins, and oligonucleotides. Carbon nanotube surface chemistry can be modulated for subcellular targeting while preserving photoluminescence for label-free visualization in complex biological environments, making them attractive materials for such studies. The cell nucleus is a potential target for many pathologies including cancer and infectious diseases. Understanding mechanisms of nanomaterial delivery to the nucleus may facilitate diagnostics, drug development, and gene-editing tools. Currently, there are no systematic studies to understand how these nanomaterials gain access to the nucleus. Herein, we developed a carbon nanotube based hybrid material that elucidate a distinct mechanism of nuclear translocation of a nanomaterial in cultured cells. We developed a nuclear-targeted probe via cloaking photoluminescent single-walled carbon nanotubes in a guanidinium-functionalized helical polycarbodiimide. We found that the nuclear entry of the nanotubes was mediated by the import receptor importin β without the aid of importin α and not by the more common importin α/β pathway. Additionally, the nanotube photoluminescence exhibited distinct red-shifting upon entry to the nucleus, potentially functioning as a reporter of the importin β-mediated nuclear transport process. This work delineates a noncanonical mechanism for nanomaterial delivery to the nucleus and provides a reporter for the study of nucleus-related pathologies.
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Affiliation(s)
| | - Rachel E. Langenbacher
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Weill Cornell Medical College, New York, New York 10065, United States
| | - Prakrit V. Jena
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Daniel Roxbury
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, United States
| | - Daniel A. Heller
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Weill Cornell Medical College, New York, New York 10065, United States
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16
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Umemura K. Hybrids of Nucleic Acids and Carbon Nanotubes for Nanobiotechnology. NANOMATERIALS (BASEL, SWITZERLAND) 2015; 5:321-350. [PMID: 28347014 PMCID: PMC5312852 DOI: 10.3390/nano5010321] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/25/2015] [Accepted: 03/05/2015] [Indexed: 12/17/2022]
Abstract
Recent progress in the combination of nucleic acids and carbon nanotubes (CNTs) has been briefly reviewed here. Since discovering the hybridization phenomenon of DNA molecules and CNTs in 2003, a large amount of fundamental and applied research has been carried out. Among thousands of papers published since 2003, approximately 240 papers focused on biological applications were selected and categorized based on the types of nucleic acids used, but not the types of CNTs. This survey revealed that the hybridization phenomenon is strongly affected by various factors, such as DNA sequences, and for this reason, fundamental studies on the hybridization phenomenon are important. Additionally, many research groups have proposed numerous practical applications, such as nanobiosensors. The goal of this review is to provide perspective on biological applications using hybrids of nucleic acids and CNTs.
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Affiliation(s)
- Kazuo Umemura
- Biophysics Section, Department of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 1628601, Japan.
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17
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Mo R, Jiang T, Sun W, Gu Z. ATP-responsive DNA-graphene hybrid nanoaggregates for anticancer drug delivery. Biomaterials 2015; 50:67-74. [PMID: 25736497 DOI: 10.1016/j.biomaterials.2015.01.053] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/07/2015] [Accepted: 01/20/2015] [Indexed: 12/23/2022]
Abstract
Stimuli-triggered drug delivery systems are primarily focused on the applications of the tumor microenvironmental or cellular physiological cues to enhance the release of drugs at the target site. In this study, we applied adenosine-5'-triphosphate (ATP), the primary "energy molecule", as a trigger for enhanced release of preloaded drugs responding to the intracellular ATP concentration that is significantly higher than the extracellular level. A new ATP-responsive anticancer drug delivery strategy utilizing DNA-graphene crosslinked hybrid nanoaggregates as carriers was developed for controlled release of doxorubicin (DOX), which consists of graphene oxide (GO), two single-stranded DNA (ssDNA, denoted as DNA1 and DNA2) and ATP aptamer. The single-stranded DNA1 and DNA2 together with the ATP aptamer serve as the linkers upon hybridization for controlled assembly of the DNA-GO nanoaggregates, which effectively inhibited the release of DOX from the GO nanosheets. In the presence of ATP, the responsive formation of the ATP/ATP aptamer complex causes the dissociation of the aggregates, which promoted the release of DOX in the environment with a high ATP concentration such as cytosol compared with that in the ATP-deficient extracellular fluid. This supports the development of a novel ATP-responsive platform for targeted on-demand delivery of anticancer drugs inside specific cells.
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Affiliation(s)
- Ran Mo
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Tianyue Jiang
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wujin Sun
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhen Gu
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Center for Nanotechnology in Drug Delivery and Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Jain A, Homayoun A, Bannister CW, Yum K. Single-walled carbon nanotubes as near-infrared optical biosensors for life sciences and biomedicine. Biotechnol J 2015; 10:447-59. [DOI: 10.1002/biot.201400168] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/26/2014] [Accepted: 01/02/2015] [Indexed: 12/14/2022]
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19
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Budhathoki-Uprety J, Jena PV, Roxbury D, Heller DA. Helical polycarbodiimide cloaking of carbon nanotubes enables inter-nanotube exciton energy transfer modulation. J Am Chem Soc 2014; 136:15545-50. [PMID: 25343218 PMCID: PMC4227803 DOI: 10.1021/ja505529n] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Indexed: 01/18/2023]
Abstract
The use of single-walled carbon nanotubes (SWCNTs) as near-infrared optical probes and sensors require the ability to simultaneously modulate nanotube fluorescence and functionally derivatize the nanotube surface using noncovalent methods. We synthesized a small library of polycarbodiimides to noncovalently encapsulate SWCNTs with a diverse set of functional coatings, enabling their suspension in aqueous solution. These polymers, known to adopt helical conformations, exhibited ordered surface coverage on the nanotubes and allowed systematic modulation of nanotube optical properties, producing up to 12-fold differences in photoluminescence efficiency. Polymer cloaking of the fluorescent nanotubes facilitated the first instance of controllable and reversible internanotube exciton energy transfer, allowing kinetic measurements of dynamic self-assembly and disassembly.
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Affiliation(s)
| | - Prakrit V. Jena
- Memorial
Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Daniel Roxbury
- Memorial
Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Daniel A. Heller
- Memorial
Sloan Kettering Cancer Center, New York, New York 10065, United States
- Weill
Cornell Medical College, New York, New York 10065, United States
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20
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Ulissi Z, Sen F, Gong X, Sen S, Iverson N, Boghossian A, Godoy LC, Wogan GN, Mukhopadhyay D, Strano MS. Spatiotemporal intracellular nitric oxide signaling captured using internalized, near-infrared fluorescent carbon nanotube nanosensors. NANO LETTERS 2014; 14:4887-94. [PMID: 25029087 PMCID: PMC4134139 DOI: 10.1021/nl502338y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Indexed: 05/04/2023]
Abstract
Fluorescent nanosensor probes have suffered from limited molecular recognition and a dearth of strategies for spatial-temporal operation in cell culture. In this work, we spatially imaged the dynamics of nitric oxide (NO) signaling, important in numerous pathologies and physiological functions, using intracellular near-infrared fluorescent single-walled carbon nanotubes. The observed spatial-temporal NO signaling gradients clarify and refine the existing paradigm of NO signaling based on averaged local concentrations. This work enables the study of transient intracellular phenomena associated with signaling and therapeutics.
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Affiliation(s)
- Zachary
W. Ulissi
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Fatih Sen
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- Department
of Biochemistry, Dumlupinar University, Kutahya, 43100, Turkey
| | - Xun Gong
- Department
of Biomedical Engineering and Physiology, Mayo College of Medicine, Rochester, Minnesota 55905, United States
| | - Selda Sen
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicole Iverson
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Ardemis
A. Boghossian
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Luiz C. Godoy
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gerald N. Wogan
- Department
of Biological Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Debabrata Mukhopadhyay
- Department
of Biomedical Engineering and Physiology, Mayo College of Medicine, Rochester, Minnesota 55905, United States
- Department
of Biochemistry and Molecular Biology, Mayo
College of Medicine, Rochester, Minnesota 55905, United States
| | - Michael S. Strano
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
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21
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Yum K, McNicholas TP, Mu B, Strano MS. Single-walled carbon nanotube-based near-infrared optical glucose sensors toward in vivo continuous glucose monitoring. J Diabetes Sci Technol 2013; 7:72-87. [PMID: 23439162 PMCID: PMC3692218 DOI: 10.1177/193229681300700109] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This article reviews research efforts on developing single-walled carbon nanotube (SWNT)-based near-infrared (NIR) optical glucose sensors toward long-term in vivo continuous glucose monitoring (CGM). We first discuss the unique optical properties of SWNTs and compare SWNTs with traditional organic and nanoparticle fluorophores regarding in vivo glucose-sensing applications. We then present our development of SWNT-based glucose sensors that use glucose-binding proteins and boronic acids as a high-affinity molecular receptor for glucose and transduce binding events on the receptors to modulate SWNT fluorescence. Finally, we discuss opportunities and challenges in translating the emerging technology of SWNT-based NIR optical glucose sensors into in vivo CGM for practical clinical use.
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Affiliation(s)
- Kyungsuk Yum
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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22
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Reuel NF, Ahn JH, Kim JH, Zhang J, Boghossian AA, Mahal LK, Strano MS. Transduction of Glycan–Lectin Binding Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes for Glycan Profiling. J Am Chem Soc 2011; 133:17923-33. [DOI: 10.1021/ja2074938] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nigel F. Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jin-Ho Ahn
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jong-Ho Kim
- Department of Chemical Engineering, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jingqing Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ardemis A. Boghossian
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lara K. Mahal
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael S. Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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23
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Boghossian AA, Zhang J, Barone PW, Reuel NF, Kim JH, Heller DA, Ahn JH, Hilmer AJ, Rwei A, Arkalgud JR, Zhang CT, Strano MS. Near-infrared fluorescent sensors based on single-walled carbon nanotubes for life sciences applications. CHEMSUSCHEM 2011; 4:848-63. [PMID: 21751417 DOI: 10.1002/cssc.201100070] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Many properties of single-walled carbon nanotubes (SWCNTs) make them ideal candidates for sensors, particularly for biological systems. Both their fluorescence in the near-infrared range of 820-1600 nm, where absorption by biological tissues is often minimal, and their inherent photostability are desirable attributes for the design of in vitro and in vivo sensors. The mechanisms by which a target molecule can selectively alter the fluorescent emission include primarily changes in emission wavelength (i.e., solvatochromism) and intensity, including effects such as charge-transfer transition bleaching and exciton quenching. The central challenge lies in engineering the nanotube interface to be selective for the analyte of interest. In this work, we review the recent development in this area over the past few years, and describe the design rules that we have developed for detecting various analytes, ranging from stable small molecules and reactive oxygen species (ROS) or reactive nitrogen species (RNS) to macromolecules. Applications to in vivo sensor measurements using these sensors are also described. In addition, the emerging field of SWCNT-based single-molecule detection using band gap fluorescence and the recent efforts to accurately quantify and utilize this unique class of stochastic sensors are also described in this article.
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Affiliation(s)
- Ardemis A Boghossian
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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Huang H, Zou M, Xu X, Liu F, Li N, Wang X. Near-infrared fluorescence spectroscopy of single-walled carbon nanotubes and its applications. Trends Analyt Chem 2011. [DOI: 10.1016/j.trac.2011.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Peptide secondary structure modulates single-walled carbon nanotube fluorescence as a chaperone sensor for nitroaromatics. Proc Natl Acad Sci U S A 2011; 108:8544-9. [PMID: 21555544 DOI: 10.1073/pnas.1005512108] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A class of peptides from the bombolitin family, not previously identified for nitroaromatic recognition, allows near-infrared fluorescent single-walled carbon nanotubes to transduce specific changes in their conformation. In response to the binding of specific nitroaromatic species, such peptide-nanotube complexes form a virtual "chaperone sensor," which reports modulation of the peptide secondary structure via changes in single-walled carbon nanotubes, near-infrared photoluminescence. A split-channel microscope constructed to image quantized spectral wavelength shifts in real time, in response to nitroaromatic adsorption, results in the first single-nanotube imaging of solvatochromic events. The described indirect detection mechanism, as well as an additional exciton quenching-based optical nitroaromatic detection method, illustrate that functionalization of the carbon nanotube surface can result in completely unique sites for recognition, resolvable at the single-molecule level.
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26
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Feigel IM, Vedala H, Star A. Biosensors based on one-dimensional nanostructures. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm10521c] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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27
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Zhang J, Boghossian AA, Barone PW, Rwei A, Kim JH, Lin D, Heller DA, Hilmer AJ, Nair N, Reuel NF, Strano MS. Single molecule detection of nitric oxide enabled by d(AT)15 DNA adsorbed to near infrared fluorescent single-walled carbon nanotubes. J Am Chem Soc 2010; 133:567-81. [PMID: 21142158 DOI: 10.1021/ja1084942] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT)(15) oligonucleotides, adsorbed to an array of near-infrared fluorescent semiconducting single-walled carbon nanotubes (AT(15)-SWNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)(15) imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT(15)-SWNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in the estimated rate constants is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-site NO adsorption rate constant is 0.001 s(-1) μM NO(-1). The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation.
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Affiliation(s)
- Jingqing Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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28
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Cheung W, Pontoriero F, Taratula O, Chen AM, He H. DNA and carbon nanotubes as medicine. Adv Drug Deliv Rev 2010; 62:633-49. [PMID: 20338203 DOI: 10.1016/j.addr.2010.03.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 02/03/2010] [Indexed: 12/25/2022]
Abstract
The identification of disease-related genes and their complete nucleotide sequence through the human genome project provides us with a remarkable opportunity to combat a large number of diseases with designed genes as medicine. However, gene therapy relies on the efficient and nontoxic transport of therapeutic genetic medicine through the cell membranes, and this process is very inefficient. Carbon nanotubes, due to their large surface areas, unique surface properties, and needle-like shape, can deliver a large amount of therapeutic agents, including DNA and siRNAs, to the target disease sites. In addition, due to their unparalleled optical and electrical properties, carbon nanotubes can deliver DNA/siRNA not only into cells, which include difficult transfecting primary-immune cells and bacteria, they can also lead to controlled release of DNA/siRNA for targeted gene therapy. Furthermore, due to their wire shaped structure with a diameter matching with that of DNA/siRNA and their remarkable flexibility, carbon nanotubes can impact on the conformational structure and the transient conformational change of DNA/RNA, which can further enhance the therapeutic effects of DNA/siRNA. Synergistic combination of the multiple capabilities of carbon nanotubes to deliver DNA/siRNAs will lead to the development of powerful multifunctional nanomedicine to treat cancer or other difficult diseases. In this review, we summarized the current studies in using CNT as unique vehicles in the field of gene therapy.
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29
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Rotkin SV. Electronic Properties of Nonideal Nanotube Materials: Helical Symmetry Breaking in DNA Hybrids. Annu Rev Phys Chem 2010; 61:241-61. [DOI: 10.1146/annurev.physchem.012809.103304] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Slava V. Rotkin
- Physics Department and Center for Advanced Materials and Nanotechnology, Lehigh University, Bethlehem, Pennsylvania 18015;
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30
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Jeng ES, Nelson JD, Prather KLJ, Strano MS. Detection of a single nucleotide polymorphism using single-walled carbon-nanotube near-infrared fluorescence. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:40-43. [PMID: 19911391 DOI: 10.1002/smll.200900944] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Esther S Jeng
- 77 Massachusetts Avenue, Building 66-566, Cambridge, MA 02139-4307, USA
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31
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Kim JH, Heller DA, Jin H, Barone PW, Song C, Zhang J, Trudel LJ, Wogan GN, Tannenbaum SR, Strano MS. The rational design of nitric oxide selectivity in single-walled carbon nanotube near-infrared fluorescence sensors for biological detection. Nat Chem 2009; 1:473-81. [DOI: 10.1038/nchem.332] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 07/14/2009] [Indexed: 12/29/2022]
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32
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Johnson RR, Kohlmeyer A, Johnson ATC, Klein ML. Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics. NANO LETTERS 2009; 9:537-41. [PMID: 19161335 DOI: 10.1021/nl802645d] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The DNA-carbon nanotube hybrid (DNA-CN) consists of a single-wall carbon nanotube (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Recent experiments have demonstrated that this nanomaterial is ideal for numerous nanotechnological applications. Despite this importance, the structure of this material remains poorly understood. Molecular dynamics (MD) simulations have provided information about the self-assembly mechanisms and ssDNA conformations that characterize DNA-CN. However, MD simulations of biopolymers at low temperatures (T approximately 300 K) result in kinetic trapping that limits conformational sampling. Here, we present results of a large-scale replica exchange molecular dynamics (REMD) simulation that provides extensive sampling of the entire ensemble of oligonucleotide conformations in a (GT)(7)-SWCN hybrid. We calculate the free energy landscape and find minima corresponding to six distinct conformations, with a nonhelical loop structure as the global minimum. The hybrid contains significant structural disorder, with desorbed bases as an important structural feature. These results expand our understanding of DNA-CN and indicate the relevance of REMD for explorations of the physical properties of organic-inorganic multifunctional nanomaterials.
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Affiliation(s)
- Robert R Johnson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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33
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Heller DA, Jin H, Martinez BM, Patel D, Miller BM, Yeung TK, Jena PV, Höbartner C, Ha T, Silverman SK, Strano MS. Multimodal optical sensing and analyte specificity using single-walled carbon nanotubes. NATURE NANOTECHNOLOGY 2009; 4:114-20. [PMID: 19197314 DOI: 10.1038/nnano.2008.369] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 10/13/2008] [Indexed: 05/18/2023]
Abstract
Nanoscale sensing elements offer promise for single-molecule analyte detection in physically or biologically constrained environments. Single-walled carbon nanotubes have several advantages when used as optical sensors, such as photostable near-infrared emission for prolonged detection through biological media and single-molecule sensitivity. Molecular adsorption can be transduced into an optical signal by perturbing the electronic structure of the nanotubes. Here, we show that a pair of single-walled nanotubes provides at least four modes that can be modulated to uniquely fingerprint agents by the degree to which they alter either the emission band intensity or wavelength. We validate this identification method in vitro by demonstrating the detection of six genotoxic analytes, including chemotherapeutic drugs and reactive oxygen species, which are spectroscopically differentiated into four distinct classes, and also demonstrate single-molecule sensitivity in detecting hydrogen peroxide. Finally, we detect and identify these analytes in real time within live 3T3 cells, demonstrating multiplexed optical detection from a nanoscale biosensor and the first label-free tool to optically discriminate between genotoxins.
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34
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Jin H, Heller DA, Sharma R, Strano MS. Size-dependent cellular uptake and expulsion of single-walled carbon nanotubes: single particle tracking and a generic uptake model for nanoparticles. ACS NANO 2009; 3:149-58. [PMID: 19206261 DOI: 10.1021/nn800532m] [Citation(s) in RCA: 357] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cellular uptake and expulsion rates of length-fractionated single-walled carbon nanotubes (SWNT) from 130 to 660 nm in NIH-3T3 cells were measured via single particle tracking of their intrinsic photoluminescence. We develop a quantitative model to correlate endocytosis rate with nanoparticle geometry that accurately describes this data set and also literature results for Au nanoparticles. The model asserts that nanoparticles cluster on the cell membrane to form a size sufficient to generate a large enough enthalpic contribution via receptor ligand interactions to overcome the elastic energy and entropic barriers associated with vesicle formation. Interestingly, the endocytosis rate constant of SWNT (10(-3) min(-1)) is found to be nearly 1000 times that of Au nanoparticles (10(-6) min(-1)) but the recycling (exocytosis) rate constants are similar in magnitude (10(-4) to 10(-3) min(-1)) for poly(d,l-lactide-co-glycolide), SWNT, and Au nanoparticles across distinct cell lines. The total uptake of both SWNT and Au nanoparticles is maximal at a common radius of 25 nm when scaled using an effective capture dimension for membrane diffusion. The ability to understand and predict the cellular uptake of nanoparticles quantitatively should find utility in designing nanosystems with controlled toxicity, efficacy, and functionality.
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Affiliation(s)
- Hong Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Building 66-566, 77 Massachusettes Avenue, Cambridge, Massachusetts 02139-4307, USA
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Jin H, Heller DA, Kim JH, Strano MS. Stochastic analysis of stepwise fluorescence quenching reactions on single-walled carbon nanotubes: single molecule sensors. NANO LETTERS 2008; 8:4299-4304. [PMID: 19367966 DOI: 10.1021/nl802010z] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The 1D quantum confinement of photogenerated excitons in single-walled carbon nanotubes (SWNT) can amplify the detection of molecular adsorption to where single-molecule discrimination is realizable, even from within living cells and tissues. Toward this aim, we present a type 1 collagen film, similar to those used as 3D cell scaffolds for tissue engineering, containing embedded SWNT capable of reporting single-molecule adsorption of quenching molecules. We utilize hidden Markov modeling to link single-molecule adsorption events to rate constants for H2O2, H+, and Fe(CN)6(3-). Among the three kinds of reactant molecules studied, H2O2 has the highest quenching equilibrium constant of 1.59 at 20 microM, whereas H+ is so insensitive that a similar equilibrium constant is achieved only with a concentration of 0.1 M (pH 1). The results were self-consistent because reverse (unquenching) rate constants (600 micros(-1) for H2O2, 1130 micros(-1) for H+ and 4000 micros(-1) for Fe(CN)6(3-)) were observed to be concentration-independent and the forward (quenching) rate constants varied monotonically with concentration. The quenching rate constants also increased with an increase in the redox potential of the quencher, indicating that electron transfer increases the adsorption equilibrium constant on the nanotube surface and, hence, the dwell time of the quencher. These developments provide the material, analytical, and mechanistic groundwork for SWNT to function as single-molecule stochastic biosensors.
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Affiliation(s)
- Hong Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Strano MS, Jin H. Where is it heading? Single-particle tracking of single-walled carbon nanotubes. ACS NANO 2008; 2:1749-1752. [PMID: 19206412 DOI: 10.1021/nn800550u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-particle tracking of individual single-walled carbon nanotubes (SWNTs) using their near-infrared band gap fluorescence is a powerful tool for understanding how these Brownian rods diffuse and interact with various molecular force potentials, including living systems. Pioneered by the Weisman laboratory at Rice University, the method is one of the only available to study single SWNT molecules in solution over extended periods since SWNTs have no apparent irreversible photobleaching threshold at moderate fluence and no intrinsic blinking mechanism. Recent progress by Tsyboulski et al. shows how real-time measurement of rotational and transitional diffusivities can provide information about rod length and mechanical properties. Recently, Jin et al. used single-particle tracking to map the trajectories of SWNTs as they are incorporated into and expelled from NIH-3T3 cells in real time. The technique has provided the first evidence of nanoparticle exocytosis in this case and demonstrates an expulsion rate that closely matches the endocytosis rate. The ability to track and to analyze single molecules in this way may lead to new technologies that utilize as their platform a single, freely diffusing nanotube.
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Affiliation(s)
- Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Qian H, Araujo PT, Georgi C, Gokus T, Hartmann N, Green AA, Jorio A, Hersam MC, Novotny L, Hartschuh A. Visualizing the local optical response of semiconducting carbon nanotubes to DNA-wrapping. NANO LETTERS 2008; 8:2706-2711. [PMID: 18671438 DOI: 10.1021/nl801038t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We studied the local optical response of semiconducting single-walled carbon nanotubes to wrapping by DNA segments using high resolution tip-enhanced near-field microscopy. Photoluminescence (PL) near-field images of single nanotubes reveal large DNA-wrapping-induced red shifts of the exciton energy that are two times higher than indicated by spatially averaging confocal microscopy. Near-field PL spectra taken along nanotubes feature two distinct PL bands resulting from DNA-wrapped and unwrapped nanotube segments. The transition between the two energy levels occurs on a length scale smaller than our spatial resolution of about 15 nm.
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Affiliation(s)
- Huihong Qian
- Department Chemie and Biochemie and CeNS, Ludwig-Maximilians-Universitat Munchen, 81377 Munchen, Germany
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Mauter MS, Elimelech M. Environmental applications of carbon-based nanomaterials. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:5843-59. [PMID: 18767635 DOI: 10.1021/es8006904] [Citation(s) in RCA: 656] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The unique and tunable properties of carbon-based nanomaterials enable new technologies for identifying and addressing environmental challenges. This review critically assesses the contributions of carbon-based nanomaterials to a broad range of environmental applications: sorbents, high-flux membranes, depth filters, antimicrobial agents, environmental sensors, renewable energy technologies, and pollution prevention strategies. In linking technological advance back to the physical, chemical, and electronic properties of carbonaceous nanomaterials, this article also outlines future opportunities for nanomaterial application in environmental systems.
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Affiliation(s)
- Meagan S Mauter
- Department of Chemical Engineering, Environmental Engineering Program, Yale University, P.O. Box 208286, New Haven, Connecticut 06520-8286, USA
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Jin H, Heller DA, Strano MS. Single-particle tracking of endocytosis and exocytosis of single-walled carbon nanotubes in NIH-3T3 cells. NANO LETTERS 2008; 8:1577-1585. [PMID: 18491944 DOI: 10.1021/nl072969s] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Over 10000 individual trajectories of nonphotobleaching single-walled carbon nanotubes (SWNT) were tracked as they are incorporated into and expelled from NIH-3T3 cells in real time on a perfusion microscope stage. An analysis of mean square displacement allows the complete construction of the mechanistic steps involved from single duration experiments. We observe the first conclusive evidence of SWNT exocytosis and show that the rate closely matches the endocytosis rate with negligible temporal offset. We identify and study the endocytosis and exocytosis pathway that leads to the previously observed aggregation and accumulation of SWNT within the cells.
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Affiliation(s)
- Hong Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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Qian H, Georgi C, Anderson N, Green AA, Hersam MC, Novotny L, Hartschuh A. Exciton energy transfer in pairs of single-walled carbon nanotubes. NANO LETTERS 2008; 8:1363-1367. [PMID: 18366189 DOI: 10.1021/nl080048r] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We studied the exciton energy transfer in pairs of semiconducting nanotubes using high-resolution optical microscopy and spectroscopy on the nanoscale. Photoluminescence from large band gap nanotubes within bundles is observed with spatially varying intensities due to distance-dependent internanotube transfer. The range of efficient energy transfer is found to be limited to a few nanometers because of competing fast nonradiative relaxation responsible for low photoluminescence quantum yield.
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Affiliation(s)
- Huihong Qian
- Department Chemie and Biochemie and CeNS, Ludwig-Maximilians-Universität München, 81377 München, Germany
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