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Hastman DA, Hooe S, Chiriboga M, Díaz SA, Susumu K, Stewart MH, Green CM, Hildebrandt N, Medintz IL. Multiplexed DNA and Protease Detection with Orthogonal Energy Transfer on a Single Quantum Dot Scaffolded Biosensor. ACS Sens 2024; 9:157-170. [PMID: 38160434 DOI: 10.1021/acssensors.3c01812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Almost all pathogens, whether viral or bacterial, utilize key proteolytic steps in their pathogenesis. The ability to detect a pathogen's genomic material along with its proteolytic activity represents one approach to identifying the pathogen and providing initial evidence of its viability. Here, we report on a prototype biosensor design assembled around a single semiconductor quantum dot (QD) scaffold that is capable of detecting both nucleic acid sequences and proteolytic activity by using orthogonal energy transfer (ET) processes. The sensor consists of a central QD assembled via peptidyl-PNA linkers with multiple DNA sequences that encode complements to genomic sequences originating from the Ebola, Influenza, and COVID-19 viruses, which we use as surrogate targets. These are hybridized to complement strands labeled with a terbium (Tb) chelate, AlexaFluor647 (AF647), and Cy5.5 dyes, giving rise to two potential FRET cascades: the first includes Tb → QD → AF647 → Cy5.5 (→ = ET step), which is detected in a time-gated modality, and QD → AF647 → Cy5.5, which is detected from direct excitation. The labeled DNA-displaying QD construct is then further assembled with a RuII-modified peptide, which quenches QD photoluminescence by charge transfer and is recognized by a protease to yield the full biosensor. Each of the labeled DNAs and peptides can be ratiometrically assembled to the QD in a controllable manner to tune each of the ET pathways. Addition of a given target DNA displaces its labeled complement on the QD, disrupting that FRET channel, while protease addition disrupts charge transfer quenching of the central QD scaffold and boosts its photoluminescence and FRET relay capabilities. Along with characterizing the ET pathways and verifying biosensing in both individual and multiplexed formats, we also demonstrate the ability of this construct to function in molecular logic and perform Boolean operations; this highlights the construct's ability to discriminate and transduce signals between different inputs or pathogens. The potential application space for such a sensor device is discussed.
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Affiliation(s)
- David A Hastman
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
- American Society for Engineering Education, Washington ,District of Columbia20036, United States
| | - Shelby Hooe
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Matthew Chiriboga
- Northrop Grumman Corporation, Mission Systems, Baltimore, Maryland, 21240, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Michael H Stewart
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton L8S 4L7, Canada
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington ,District of Columbia20375, United States
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2
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Tsai HY, Robidillo CJT, Matharu GK, O'Connor K, Cheong IT, Ni C, Veinot JGC, Algar WR. Spectrotemporal characterization of photoluminescent silicon nanocrystals and their energy transfer to dyes. Nanoscale 2023. [PMID: 37449921 DOI: 10.1039/d3nr02461j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Silicon nanocrystals (SiNCs) are a promising material for applications in bioanalysis and imaging. Compared to other types of semiconductor nanocrystals, the development and characterization of energy transfer (ET) configurations with SiNCs has been far more limited, resulting in an equally limited understanding of this process and its SiNC-specific nuances. Here, we present a systematic and detailed study of ET between SiNCs and dyes. A combination of spectroelectrophoresis and time-gated and time-resolved photoluminescence measurements were used to characterize the photophysical properties of ensembles of SiNCs and gain insight into how these properties varied as a function of nanocrystal size. ET between SiNC donors and a series of non-fluorescent Black Hole Quencher (BHQ) dyes and fluorescent sulfo-Cyanine 5.5 dye acceptors was evaluated in terms of spectral properties, wavelength-resolved efficiencies, trends with spectral overlap integral, and differences between two methods of BHQ association with the SiNCs. The overall results were consistent with a Förster resonance energy transfer (FRET) mechanism where the polydispersity of the SiNCs had a significant impact on the observed ET: the choice of wavelength and timing parameters were important, and ensemble measurements represented an average of heterogeneous ET behaviors. Prospective advantages and disadvantages of SiNCs as ET donors are discussed. This study serves as a foundation for the continued and optimized development of ET configurations with SiNCs.
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Affiliation(s)
- Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z1.
| | - Christopher Jay T Robidillo
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Physical Sciences and Mathematics, University of the Philippines Manila, P. Faura Street, Ermita, Manila 1000, Philippines
| | - Gunwant K Matharu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Kevin O'Connor
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - I Teng Cheong
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Chuyi Ni
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Jonathan G C Veinot
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z1.
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3
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Darwish GH, Massey M, Daudet G, Alde LG, Algar WR. Tetrameric Antibody Complexes and Affinity Tag Peptides for the Selective Immobilization and Imaging of Single Quantum Dots. Bioconjug Chem 2023. [PMID: 37243625 DOI: 10.1021/acs.bioconjchem.3c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Colloidal semiconductor quantum dots (QDs) are of widespread interest as fluorescent labels for bioanalysis and imaging applications. Single-particle measurements have proven to be a very powerful tool for better understanding the fundamental properties and behaviors of QDs and their bioconjugates; however, a recurring challenge is the immobilization of QDs in a solution-like environment that minimizes interactions with a bulk surface. Immobilization strategies for QD-peptide conjugates are particularly underdeveloped within this context. Here, we present a novel strategy for the selective immobilization of single QD-peptide conjugates using a combination of tetrameric antibody complexes (TACs) and affinity tag peptides. A glass substrate is modified with an adsorbed layer of concanavalin A (ConA) that binds a subsequent layer of dextran that minimizes nonspecific binding. A TAC with anti-dextran and anti-affinity tag antibodies binds to the dextran-coated glass surface and to the affinity tag sequence of QD-peptide conjugates. The result is spontaneous and sequence-selective immobilization of single QDs without any chemical activation or cross-linking. Controlled immobilization of multiple colors of QDs is possible using multiple affinity tag sequences. Experiments confirmed that this approach positions the QD away from the bulk surface. The method supports real-time imaging of binding and dissociation, measurements of Förster resonance energy transfer (FRET), tracking of dye photobleaching, and detection of proteolytic activity. We anticipate that this immobilization strategy will be useful for studies of QD-associated photophysics, biomolecular interactions and processes, and digital assays.
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Affiliation(s)
- Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Gabrielle Daudet
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Luis G Alde
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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4
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Hildebrandt N, Lim M, Kim N, Choi DY, Nam JM. Plasmonic quenching and enhancement: metal-quantum dot nanohybrids for fluorescence biosensing. Chem Commun (Camb) 2023; 59:2352-2380. [PMID: 36727288 DOI: 10.1039/d2cc06178c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Plasmonic metal nanoparticles and semiconductor quantum dots (QDs) are two of the most widely applied nanomaterials for optical biosensing and bioimaging. While their combination for fluorescence quenching via nanosurface energy transfer (NSET) or Förster resonance energy transfer (FRET) offers powerful ways of tuning and amplifying optical signals and is relatively common, metal-QD nanohybrids for plasmon-enhanced fluorescence (PEF) have been much less prevalent. A major reason is the competition between fluorescence quenching and enhancement, which poses important challenges for optimizing distances, orientations, and spectral overlap toward maximum PEF. In this feature article, we discuss the interplay of the different quenching and enhancement mechanisms (a mixed distance dependence of quenching and enhancement - "quenchancement") to better understand the obstacles that must be overcome for the development of metal-QD nanohybrid-based PEF biosensors. The different nanomaterials, their combination within various surface and solution based design concepts, and their structural and photophysical characterization are reviewed and applications toward advanced optical biosensing and bioimaging are presented along with guidelines and future perspectives for sensitive, selective, and versatile bioanalytical research and biomolecular diagnostics with metal-QD nanohybrids.
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Affiliation(s)
- Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
| | - Mihye Lim
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
| | - Namjun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
| | - Da Yeon Choi
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea.
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5
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Milićević D, Hlaváč J. Triple-FRET multi-purpose fluorescent probe for three-protease detection. RSC Adv 2022; 12:28780-28787. [PMID: 36320525 PMCID: PMC9549473 DOI: 10.1039/d2ra05125g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022] Open
Abstract
A new, robust and reliable methodology for three-protease screening in a single-enzyme mode has been developed and verified, employing a multi-purpose peptide probe with three selectively cleavable sites furnished with four fluorophores. A triple-FRET-based single-excitation quadruple-emission concept for unambiguous sensing of trypsin, chymotrypsin and caspase-8 in the lowest detectable concentrations of 0.5 ng mL-1, 0.2 μg mL-1, and 2 U mL-1, respectively, has been applied and graphically depicted. Then the developed 4-dye probe has been also studied from the perspective of simultaneous two-protease screening, which was found only partially feasible, primarily due to unselective chymotrypsin cleavage.
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Affiliation(s)
- David Milićević
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc17. Listopadu 12771 46 OlomoucCzech Republic
| | - Jan Hlaváč
- Department of Organic Chemistry, Faculty of Science, Palacký University Olomouc17. Listopadu 12771 46 OlomoucCzech Republic
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Chen C, Wei X, Parsons MF, Guo J, Banal JL, Zhao Y, Scott MN, Schlau-Cohen GS, Hernandez R, Bathe M. Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. Nat Commun 2022; 13:4935. [PMID: 35999227 PMCID: PMC9399249 DOI: 10.1038/s41467-022-32662-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.
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Affiliation(s)
- Chi Chen
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Xingfei Wei
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Molly F. Parsons
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Jiajia Guo
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,grid.458489.c0000 0001 0483 7922Present Address: Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - James L. Banal
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA ,Present Address: Cache DNA, Inc., 200 Lincoln Centre Drive, Foster City, CA 94404 USA
| | - Yinong Zhao
- grid.21107.350000 0001 2171 9311Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Madelyn N. Scott
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Gabriela S. Schlau-Cohen
- grid.116068.80000 0001 2341 2786Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Rigoberto Hernandez
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Mark Bathe
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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7
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Abstract
Förster resonance energy transfer (FRET) is a widely used fluorescence-based sensing mechanism. To date, most implementations of FRET sensors have relied on a discrete donor-acceptor pair for detection of each analytical target. FRET networks are an emerging concept in which target recognition perturbs a set of interconnected FRET pathways between multiple emitters. Here, we review the energy transfer topologies and scaffold materials for FRET networks, propose a general nomenclature, and qualitatively summarize the dynamics of the competitive, sequential, homoFRET, and heteroFRET pathways that constitute FRET networks. Implementations of FRET networks for sensing are also described, including concentric FRET probes, other single-vector multiplexing, and logic gates and switches. Unresolved questions and future research directions for current systems are discussed, as are potential but currently unexplored applications of FRET networks in sensing.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada;
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada;
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8
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Abstract
Förster resonance energy transfer (FRET) is widely used for the development of biological probes and sensors. In this context, the norm for multiplexed detection is deployment of multiple probes, each a discrete donor-acceptor pair. Concentric FRET (cFRET) probes enable multiplexed sensing with a single vector but, to date, have only been developed around semiconductor quantum dots, which may limit the scope of biological applications for such probes. Here, we demonstrate that dendrimers labeled with a luminescent terbium complex (Tb) are a viable and advantageous alternative platform for cFRET probes. Polyamidoamine dendrimers were functionalized with Tb, biotin, NeutrAvidin, and three types of dye-labeled oligonucleotide probes to establish a network of competitive and sequential Tb-to-dye and dye-to-dye FRET pathways. These probes were characterized physically and photophysically, and a time-gated multiplexed assay for DNA targets was demonstrated. The time-gating offered by the Tb allowed the rejection of background autofluorescence from serum. More broadly, this dendrimer-based architecture shows that cFRET is a general concept and is an important step toward a new generation of probes for biological sensing.
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Affiliation(s)
- Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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9
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Periyathambi P, Balian A, Hu Z, Padro D, Hernandez LI, Uvdal K, Duarte J, Hernandez FJ. Activatable MRI probes for the specific detection of bacteria. Anal Bioanal Chem 2021; 413:7353-7362. [PMID: 34704109 PMCID: PMC8626403 DOI: 10.1007/s00216-021-03710-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/07/2021] [Accepted: 09/30/2021] [Indexed: 12/15/2022]
Abstract
Activatable fluorescent probes have been successfully used as molecular tools for biomedical research in the last decades. Fluorescent probes allow the detection of molecular events, providing an extraordinary platform for protein and cellular research. Nevertheless, most of the fluorescent probes reported are susceptible to interferences from endogenous fluorescence (background signal) and limited tissue penetration is expected. These drawbacks prevent the use of fluorescent tracers in the clinical setting. To overcome the limitation of fluorescent probes, we and others have developed activatable magnetic resonance probes. Herein, we report for the first time, an oligonucleotide-based probe with the capability to detect bacteria using magnetic resonance imaging (MRI). The activatable MRI probe consists of a specific oligonucleotide that targets micrococcal nuclease (MN), a nuclease derived from Staphylococcus aureus. The oligonucleotide is flanked by a superparamagnetic iron oxide nanoparticle (SPION) at one end, and by a dendron functionalized with several gadolinium complexes as enhancers, at the other end. Therefore, only upon recognition of the MRI probe by the specific bacteria is the probe activated and the MRI signal can be detected. This approach may be widely applied to detect bacterial infections or other human conditions with the potential to be translated into the clinic as an activatable contrast agent.
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Affiliation(s)
- Prabu Periyathambi
- Department of Physics, Chemistry and Biology, Linkӧping University, 58185, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Alien Balian
- Department of Physics, Chemistry and Biology, Linkӧping University, 58185, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology, Linkӧping University, 58185, Linköping, Sweden
| | - Daniel Padro
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), 20014, Donostia-San Sebastián, Spain
| | - Luiza I Hernandez
- Department of Clinical and Experimental Medicine, Linkӧping University, Linköping, Sweden
| | - Kajsa Uvdal
- Department of Physics, Chemistry and Biology, Linkӧping University, 58185, Linköping, Sweden
| | - Joao Duarte
- Department of Experimental Medical Science, Faculty of Medicine, Lund University, 22181, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linkӧping University, 58185, Linköping, Sweden. .,Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.
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10
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Mathur D, Samanta A, Ancona MG, Díaz SA, Kim Y, Melinger JS, Goldman ER, Sadowski JP, Ong LL, Yin P, Medintz IL. Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks. ACS Nano 2021; 15:16452-16468. [PMID: 34609842 PMCID: PMC8823280 DOI: 10.1021/acsnano.1c05871] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r4 energy transfer distance (r) dependency versus the 1/r6 dependency seen for a single donor-acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.
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Affiliation(s)
| | | | | | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Youngchan Kim
- Center for Materials Physics and Technology Code 6390, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S. Melinger
- Electronic Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - John Paul Sadowski
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States; American Society for Engineering Education, Washington, D.C. 20001, United States
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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11
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Krause KD, Tsai HY, Rees K, Kim H, Algar WR. Preparation and Characterization of Quantum Dot-Peptide Conjugates Based on Polyhistidine Tags. Methods Mol Biol 2021; 2355:175-218. [PMID: 34386960 DOI: 10.1007/978-1-0716-1617-8_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Quantum dots (QDs) offer bright and robust photoluminescence among several other advantages in comparison to fluorescent dyes. In order to leverage the advantageous properties of QDs for applications in bioanalysis and imaging, simple and reliable methods for bioconjugation are required. One such method for conjugating peptides to QDs is the use of polyhistidine tags, which spontaneously bind to the surface of QDs. We describe protocols for assembling polyhistidine-tagged peptides to QDs and for characterizing the resultant QD-peptide conjugates. The latter include both electrophoretic and FRET-based protocols for confirming successful peptide assembly, estimating the maximum peptide loading capacity, and measuring the assembly kinetics. Sensors for protease activity and intracellular delivery are briefly noted as prospective applications of QD-peptide conjugates.
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12
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Algar WR, Massey M, Rees K, Higgins R, Krause KD, Darwish GH, Peveler WJ, Xiao Z, Tsai HY, Gupta R, Lix K, Tran MV, Kim H. Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging. Chem Rev 2021; 121:9243-9358. [PMID: 34282906 DOI: 10.1021/acs.chemrev.0c01176] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rehan Higgins
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - William J Peveler
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Zhujun Xiao
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rupsa Gupta
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelsi Lix
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hyungki Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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Reynolds KA, Rosa-Molinar E, Ward RE, Zhang H, Urbanowicz BR, Settles AM. Accelerating biological insight for understudied genes. Integr Comp Biol 2021; 61:2233-2243. [PMID: 33970251 DOI: 10.1093/icb/icab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The vast majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.
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Affiliation(s)
- Kimberly A Reynolds
- The Green Center for Systems Biology and the Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eduardo Rosa-Molinar
- Department of Pharmacology & Toxicology, The University of Kansas, Lawrence, KS 66047, USA
| | - Robert E Ward
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Hongbin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - A Mark Settles
- Bioengineering Branch, NASA Ames Research Center, Moffett Field, CA USA
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