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Yari P, Liang S, Chugh VK, Rezaei B, Mostufa S, Krishna VD, Saha R, Cheeran MCJ, Wang JP, Gómez-Pastora J, Wu K. Nanomaterial-Based Biosensors for SARS-CoV-2 and Future Epidemics. Anal Chem 2023; 95:15419-15449. [PMID: 37826859 DOI: 10.1021/acs.analchem.3c01522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Affiliation(s)
- Parsa Yari
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Shuang Liang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Vinit Kumar Chugh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bahareh Rezaei
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Shahriar Mostufa
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Venkatramana Divana Krishna
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Renata Saha
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Maxim C-J Cheeran
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Jian-Ping Wang
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jenifer Gómez-Pastora
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Kai Wu
- Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, Texas 79409, United States
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Hastman DA, Chaturvedi P, Oh E, Melinger JS, Medintz IL, Vuković L, Díaz SA. Mechanistic Understanding of DNA Denaturation in Nanoscale Thermal Gradients Created by Femtosecond Excitation of Gold Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2022; 14:3404-3417. [PMID: 34982525 DOI: 10.1021/acsami.1c19411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There is significant interest in developing photothermal systems that can precisely control the structure and function of biomolecules through local temperature modulation. One specific application is the denaturation of double-stranded (ds) DNA through femtosecond (fs) laser pulse optical heating of gold nanoparticles (AuNPs); however, the mechanism of DNA melting in these systems is not fully understood. Here, we utilize 55 nm AuNPs with surface-tethered dsDNA, which are locally heated using fs laser pulses to induce DNA melting. By varying the dsDNA distance from the AuNP surface and the laser pulse energy fluence, this system is used to study how the nanosecond duration temperature increase and the steep temperature gradient around the AuNP affect dsDNA dehybridization. Through modifying the distance between the dsDNA and AuNP surface by 3.8 nm in total and the pulse energy fluence from 7.1 to 14.1 J/m2, the dehybridization rates ranged from 0.002 to 0.05 DNA per pulse, and the total amount of DNA released into solution was controlled over a range of 26-93% in only 100 s of irradiation. By shifting the dsDNA position as little as ∼1.1 nm, the average dsDNA dehybridization rate is altered up to 30 ± 2%, providing a high level of control over DNA melting and release. By comparing the theoretical temperature around the dsDNA to the experimentally derived temperature, we find that maximum or peak temperatures have a greater influence on the dehybridization rate when the dsDNA is closer to the AuNP surface and when lower laser pulse fluences are used. Furthermore, molecular dynamics simulations mimicking the photothermal heat pulse around a AuNP provide mechanistic insight into the stochastic nature of dehybridization and demonstrate increased base pair separation near the AuNP surface during laser pulse heating when compared to steady-state heating. Understanding how biological materials respond to the short-lived and non-uniform temperature increases innate to fs laser pulse optical heating of AuNPs is critical to improving the functionality and precision of this technique so that it may be implemented into more complex biological systems.
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Affiliation(s)
- David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Parth Chaturvedi
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
| | - Lela Vuković
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, Texas 79968, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
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Hastman DA, Melinger JS, Aragonés GL, Cunningham PD, Chiriboga M, Salvato ZJ, Salvato TM, Brown CW, Mathur D, Medintz IL, Oh E, Díaz SA. Femtosecond Laser Pulse Excitation of DNA-Labeled Gold Nanoparticles: Establishing a Quantitative Local Nanothermometer for Biological Applications. ACS NANO 2020; 14:8570-8583. [PMID: 32677822 DOI: 10.1021/acsnano.0c02899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Femtosecond (fs) laser pulsed excitation of plasmonic nanoparticle (NP)-biomolecule conjugates is a promising method to locally heat biological materials. Studies have demonstrated that fs pulses of light can modulate the activity of DNA or proteins when attached to plasmonic NPs; however, the precision over subsequent biological function remains largely undetermined. Specifically, the temperature the localized biomolecules "experience" remains unknown. We used 55 nm gold nanoparticles (AuNPs) displaying double-stranded (ds) DNA to examine how, for dsDNA with different melting temperatures, the laser pulse energy fluence and bulk solution temperature affect the rate of local DNA denaturation. A universal "template" single-stranded DNA was attached to the AuNP surface, and three dye-labeled probe strands, distinct in length and melting temperature, were hybridized to it creating three individual dsDNA-AuNP bioconjugates. The dye-labeled probe strands were used to quantify the rate and amount of DNA release after a given number of light pulses, which was then correlated to the dsDNA denaturation temperature, resulting in a quantitative nanothermometer. The localized DNA denaturation rate could be modulated by more than threefold over the biologically relevant range of 8-53 °C by varying pulse energy fluence, DNA melting temperature, and surrounding bath temperature. With a modified dissociation equation tailored for this system, a "sensed" temperature parameter was extracted and compared to simulated AuNP temperature profiles. Determining actual biological responses in such systems can allow researchers to design precision nanoscale photothermal heating sources.
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Affiliation(s)
- David A Hastman
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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4
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Carnevale KJF, Strouse GF. Intracellular DNA Cargo Release from a Gold Nanoparticle Modulated by the Nature of the Surface Coupling Functionality. Bioconjug Chem 2018; 29:3429-3440. [DOI: 10.1021/acs.bioconjchem.8b00575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kate J. F. Carnevale
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Geoffrey F. Strouse
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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5
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Carnevale KJF, Riskowski RA, Strouse GF. A Gold Nanoparticle Bio-Optical Transponder to Dynamically Monitor Intracellular pH. ACS NANO 2018; 12:5956-5968. [PMID: 29874043 DOI: 10.1021/acsnano.8b02200] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A pH-sensitive bio-optical transponder (pH-BOT) capable of simultaneously reporting the timing of intracellular DNA cargo release from a gold nanoparticle (AuNP) and the evolving intracellular pH (pH i) during endosomal maturation is demonstrated. The pH-BOT is designed with a triple-dye-labeled duplex DNA appended to a 6.6 nm AuNP, utilizing pH-responsive fluorescein paired with DyLight405 as a surface energy transfer (SET) coupled dye pair to ratiometrically report the pH at and after cargo release. A non-SET-coupled dye, DyLight 700, is used to provide dynamic tracking throughout the experiment. The pH-BOT beacon of the cargo uptake, release, and processing was visualized using live-cell confocal fluorescent microscopy in Chinese hamster ovary cells, and it was observed that while maturation of endosomes carrying pH-BOT is slowed significantly, the pH-BOT is distributed throughout the endolysosomal system while remaining at pH ∼6. This observed decoupling of endosomal maturation from acidification lends support to those models that propose that pH alone is not sufficient to explain endosomal maturation and may enable greater insight into our understanding of the fundamental processes of biology.
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Affiliation(s)
- Kate J F Carnevale
- Department of Chemistry and Biochemistry , The Florida State University , Tallahassee , Florida 32306 , United States
| | - Ryan A Riskowski
- Department of Chemistry and Biochemistry , The Florida State University , Tallahassee , Florida 32306 , United States
| | - Geoffrey F Strouse
- Department of Chemistry and Biochemistry , The Florida State University , Tallahassee , Florida 32306 , United States
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6
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Spectroscopic measurements of interactions between hydrophobic 1-pyrenebutyric acid and silver colloidal nanoparticles. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2017.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J Chem Theory Comput 2016; 12:6077-6097. [DOI: 10.1021/acs.jctc.6b00667] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Petr Stadlbauer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Departments of Physical
Chemistry, Faculty of Science, Palacký University, 17. listopadu
1192/12, 771 46 Olomouc, Czech Republic
| | - Liuba Mazzanti
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Tristan Cragnolini
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J. Wales
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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Bottomley A, Prezgot D, Coyle JP, Ianoul A. Dynamics of nanocubes embedding into polymer films investigated via spatially resolved plasmon modes. NANOSCALE 2016; 8:11168-11176. [PMID: 27180659 DOI: 10.1039/c6nr02604d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Integration of nanoparticles into thin films is essential for the development of functional materials, studies of fundamental interfacial processes, and exploitation of inherent properties from the particles themselves. In this work, we systematically investigate the process of incorporation of silver nanocubes into thin polystyrene films at temperatures just above the polymer glass transition. The process of nanocrystal incorporation can be precisely monitored via far-field spectroscopy to observe the response of spatially resolved hybrid plasmon modes. Each plasmon resonance has a distinct dynamic range and maximum sensitivity forming a complementary set of nanorulers that operates over a distance comparable to the edge length of the cubes. The approach explored in this work is a general robust method for the development of long-range polychromatic nanorulers.
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Affiliation(s)
- Adam Bottomley
- Department of Chemistry, Carleton University, 1125 Colonel By Dr., Ottawa, ON, Canada.
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Samanta A, Medintz IL. Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology. NANOSCALE 2016; 8:9037-95. [PMID: 27080924 DOI: 10.1039/c5nr08465b] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.
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Affiliation(s)
- Anirban Samanta
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA. and College of Science, George Mason University, Fairfax, Virginia 22030, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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Riskowski RA, Armstrong RE, Greenbaum NL, Strouse GF. Triangulating Nucleic Acid Conformations Using Multicolor Surface Energy Transfer. ACS NANO 2016; 10:1926-1938. [PMID: 26795549 DOI: 10.1021/acsnano.5b05764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Optical ruler methods employing multiple fluorescent labels offer great potential for correlating distances among several sites, but are generally limited to interlabel distances under 10 nm and suffer from complications due to spectral overlap. Here we demonstrate a multicolor surface energy transfer (McSET) technique able to triangulate multiple points on a biopolymer, allowing for analysis of global structure in complex biomolecules. McSET couples the competitive energy transfer pathways of Förster Resonance Energy Transfer (FRET) with gold-nanoparticle mediated Surface Energy Transfer (SET) in order to correlate systematically labeled points on the structure at distances greater than 10 nm and with reduced spectral overlap. To demonstrate the McSET method, the structures of a linear B-DNA and a more complex folded RNA ribozyme were analyzed within the McSET mathematical framework. The improved multicolor optical ruler method takes advantage of the broad spectral range and distances achievable when using a gold nanoparticle as the lowest energy acceptor. The ability to report distance information simultaneously across multiple length scales, short-range (10-50 Å), mid-range (50-150 Å), and long-range (150-350 Å), distinguishes this approach from other multicolor energy transfer methods.
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Affiliation(s)
- Ryan A Riskowski
- Molecular Biophysics Program, Florida State University , Tallahassee, Florida 32306, United States
| | - Rachel E Armstrong
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Nancy L Greenbaum
- Department of Chemistry and Biochemistry, Hunter College and The Graduate Center of the City University of New York , New York, New York 10065, United States
| | - Geoffrey F Strouse
- Molecular Biophysics Program, Florida State University , Tallahassee, Florida 32306, United States
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
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11
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Kotkowiak M, Dudkowiak A. Multiwavelength excitation of photosensitizers interacting with gold nanoparticles and its impact on optical properties of their hybrid mixtures. Phys Chem Chem Phys 2015; 17:27366-72. [DOI: 10.1039/c5cp04459f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Different behavior of the mixtures on excitation with the wavelengths from the Soret and Q bands of the dyes and with those corresponding to the surface plasmon resonance band of gold nanoparticles, was analyzed.
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Affiliation(s)
- Michał Kotkowiak
- Faculty of Technical Physics Poznan University of Technology
- 60-965 Poznań
- Poland
| | - Alina Dudkowiak
- Faculty of Technical Physics Poznan University of Technology
- 60-965 Poznań
- Poland
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