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Berndt D, Glaap D, Jennings T, Dose C, Werz DB, Reckert DNH. Water-Soluble Fluorescent Polymer Dyes with Tunable Emission Spectra for Flow Cytometry Applications. Angew Chem Int Ed Engl 2024; 63:e202402616. [PMID: 38488317 DOI: 10.1002/anie.202402616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Indexed: 04/04/2024]
Abstract
The application of spectrally unique, bright, and water-soluble fluorescent dyes is indispensable for the analysis of biological systems. Multiparameter flow cytometry is a powerful tool for characterization of mixed cell populations. To discriminate the different cell populations, they are typically stained by a set of fluorescent reagents, e.g., antibody-fluorophore conjugates. The number of parameters which can be studied simultaneously strongly depends on the availability of reagents which can be differentiated by their spectral properties. In this study a series of fluorescent polymer dyes was developed, that can be excited with a single violet laser (405 nm) but distinguished by their unique emission spectra. The polyfluorene-based polymers can be used on their own, or in combination with covalently bound small-molecule dyes to generate energy transfer constructs to red-shift the emission wavelength based on Förster resonance energy transfer (FRET). The polymer dyes were utilized in a biological flow cytometry assay by conjugating several of them to antibodies, demonstrating their effectiveness as reagents. This report represents the first systematic investigation of structure-property relationships for this type of fluorescent dyes.
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Affiliation(s)
- Daniel Berndt
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
- DFG Cluster of Excellence livMatS @FIT and Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie, Albertstraße 21, 79104, Freiburg, Germany
| | - Dorina Glaap
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Travis Jennings
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Christian Dose
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
| | - Daniel B Werz
- DFG Cluster of Excellence livMatS @FIT and Albert-Ludwigs-Universität Freiburg, Institut für Organische Chemie, Albertstraße 21, 79104, Freiburg, Germany
| | - Dirk N H Reckert
- Miltenyi Biotec BV & Co. KG, Department Chemical Biology, Friedrich-Ebert-Str. 68, 51429, Bergisch Gladbach, Germany
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2
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Sengupta P, Dutta A, Suseela YV, Roychowdhury T, Banerjee N, Dutta A, Halder S, Jana K, Mukherjee G, Chattopadhyay S, Govindaraju T, Chatterjee S. G-quadruplex structural dynamics at MAPK12 promoter dictates transcriptional switch to determine stemness in breast cancer. Cell Mol Life Sci 2024; 81:33. [PMID: 38214819 PMCID: PMC11073236 DOI: 10.1007/s00018-023-05046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 01/13/2024]
Abstract
P38γ (MAPK12) is predominantly expressed in triple negative breast cancer cells (TNBC) and induces stem cell (CSC) expansion resulting in decreased survival of the patients due to metastasis. Abundance of G-rich sequences at MAPK12 promoter implied the functional probability to reverse tumorigenesis, though the formation of G-Quadruplex (G4) structures at MAPK12 promoter is elusive. Here, we identified two evolutionary consensus adjacent G4 motifs upstream of the MAPK12 promoter, forming parallel G4 structures. They exist in an equilibria between G4 and duplex, regulated by the binding turnover of Sp1 and Nucleolin that bind to these G4 motifs and regulate MAPK12 transcriptional homeostasis. To underscore the gene-regulatory functions of G4 motifs, we employed CRISPR-Cas9 system to eliminate G4s from TNBC cells and synthesized a naphthalene diimide (NDI) derivative (TGS24) which shows high-affinity binding to MAPK12-G4 and inhibits MAPK12 transcription. Deletion of G4 motifs and NDI compound interfere with the recruitment of the transcription factors, inhibiting MAPK12 expression in cancer cells. The molecular basis of NDI-induced G4 transcriptional regulation was analysed by RNA-seq analyses, which revealed that MAPK12-G4 inhibits oncogenic RAS transformation and trans-activation of NANOG. MAPK12-G4 also reduces CD44High/CD24Low population in TNBC cells and downregulates internal stem cell markers, arresting the stemness properties of cancer cells.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Anindya Dutta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Y V Suseela
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, Karnataka, 560064, India
| | - Tanaya Roychowdhury
- Department of Cancer Biology and Inflammatory Disorder, IICB, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Dutta
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Satyajit Halder
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Kuladip Jana
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Gopeswar Mukherjee
- Barasat Cancer Research and Welfare Centre, Barasat, Kolkata, West Bengal, India
| | - Samit Chattopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, K. K. Birla Goa Campus, Goa, 403726, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru, Karnataka, 560064, India.
| | - Subhrangsu Chatterjee
- Department of Biological Sciences, Unified Academic Campus, Bose Institute, EN-80, Sector V, Salt Lake, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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3
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Zarandi MA, Pathak P, Beltrami N, Walker JN, Zhang F, Brodbelt JS, Schmehl R, Jayawickramarajah J. Heteromeric guanosine (G)-quadruplex derived antenna modules with directional energy transfer. NANOSCALE 2023; 15:19069-19073. [PMID: 37990645 DOI: 10.1039/d3nr04086k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
A heteromeric guanosine (G)-quadruplex centered self-assembly approach is developed to prepare compact light-harvesting antenna modules featuring multiple donor dyes and a single toehold region. Due to the mix-and-match nature of our approach, the number and placement of donor dyes can be readily fine-tuned via quadruplex assembly. Moreover, hybridization of the toehold with an acceptor containing sequence results in directional energy transfer ensembles with effective absorption coefficients in the 105 M-1 cm-1 range. These compact antennas exhibit system efficiencies that are comparable to much larger and elaborate DNA architectures containing numerous DNA strands.
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Affiliation(s)
| | - Pravin Pathak
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Noah Beltrami
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fengqi Zhang
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Russell Schmehl
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
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4
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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5
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Hamza AO, Al-Dulaimi A, Bouillard JSG, Adawi AM. Long-Range and High-Efficiency Plasmon-Assisted Förster Resonance Energy Transfer. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:21611-21616. [PMID: 37969925 PMCID: PMC10641858 DOI: 10.1021/acs.jpcc.3c04281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 11/17/2023]
Abstract
The development of a long-range and efficient Förster resonance energy transfer (FRET) process is essential for its application in key enabling optoelectronic and sensing technologies. Via controlling the delocalization of the donor's electric field and Purcell enhancements, we experimentally demonstrate long-range and high-efficiency Förster resonance energy transfer using a plasmonic nanogap formed between a silver nanoparticle and an extended silver film. Our measurements show that the FRET range can be extended to over 200 nm while keeping the FRET efficiency over 0.38, achieving an efficiency enhancement factor of ∼108 with respect to a homogeneous environment. Reducing Purcell enhancements by removing the extended silver film increases the FRET efficiency to 0.55, at the expense of the FRET rate. We support our experimental findings with numerical calculations based on three-dimensional finite difference time-domain calculations and treat the donor and acceptor as classical dipoles. Our enhanced FRET range and efficiency structures provide a powerful strategy to develop novel optoelectronic devices and long-range FRET imaging and sensing systems.
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Affiliation(s)
- Abdullah O. Hamza
- Department
of Physics, University of Hull, Cottingham Road, Hull HU6 7RX, U.K.
- G.
W. Gray Centre for Advanced Materials, University
of Hull, Cottingham Road, Hull HU6 7RX, U.K.
- Department
of Physics, College of Science, Salahaddin
University-Erbil, Erbil 44002, Kurdistan Region, Iraq
| | - Ali Al-Dulaimi
- Department
of Physics, University of Hull, Cottingham Road, Hull HU6 7RX, U.K.
- G.
W. Gray Centre for Advanced Materials, University
of Hull, Cottingham Road, Hull HU6 7RX, U.K.
| | - Jean-Sebastien G. Bouillard
- Department
of Physics, University of Hull, Cottingham Road, Hull HU6 7RX, U.K.
- G.
W. Gray Centre for Advanced Materials, University
of Hull, Cottingham Road, Hull HU6 7RX, U.K.
| | - Ali M. Adawi
- Department
of Physics, University of Hull, Cottingham Road, Hull HU6 7RX, U.K.
- G.
W. Gray Centre for Advanced Materials, University
of Hull, Cottingham Road, Hull HU6 7RX, U.K.
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6
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Kogikoski S, Ameixa J, Mostafa A, Bald I. Lab-on-a-DNA origami: nanoengineered single-molecule platforms. Chem Commun (Camb) 2023; 59:4726-4741. [PMID: 37000514 PMCID: PMC10111202 DOI: 10.1039/d3cc00718a] [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] [Received: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.
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Affiliation(s)
- Sergio Kogikoski
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - João Ameixa
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Amr Mostafa
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
| | - Ilko Bald
- Institute of Chemistry, Hybrid Nanostructures, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.
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7
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Adamczyk AK, Huijben TAPM, Sison M, Di Luca A, Chiarelli G, Vanni S, Brasselet S, Mortensen KI, Stefani FD, Pilo-Pais M, Acuna GP. DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation. ACS NANO 2022; 16:16924-16931. [PMID: 36065997 DOI: 10.1021/acsnano.2c06936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.
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Affiliation(s)
- Aleksandra K Adamczyk
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Teun A P M Huijben
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Miguel Sison
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Germán Chiarelli
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, FribourgCH-1700, Switzerland
| | - Sophie Brasselet
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, F-13013Marseille, France
| | - Kim I Mortensen
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800Kongens Lyngby, Denmark
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQDCiudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHACiudad Autónoma de Buenos Aires, Argentina
| | - Mauricio Pilo-Pais
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, FribourgCH-1700, Switzerland
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8
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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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9
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Morris MA, Vallmitjana A, Grein F, Schneider T, Arts M, Jones CR, Nguyen BT, Hashemian MH, Malek M, Gratton E, Nowick JS. Visualizing the Mode of Action and Supramolecular Assembly of Teixobactin Analogues in Bacillus subtilis. Chem Sci 2022; 13:7747-7754. [PMID: 35865902 PMCID: PMC9258396 DOI: 10.1039/d2sc01388f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022] Open
Abstract
Teixobactin has been the source of intensive study and interest as a promising antibiotic, because of its excellent activity against drug-resistant Gram-positive pathogens and its novel but not yet fully understood mechanism of action that precludes drug resistance. Recent studies have demonstrated that the mode of action of teixobactin is more complicated than initially thought, with supramolecular assembly of the antibiotic appearing to play a critical role in the binding process. Further studies of the interactions of teixobactin with bacteria and its molecular targets offer the promise of providing deeper insights into its novel mechanism of action and guiding the design of additional drug candidates and analogues. The current study reports the preparation and study of teixobactin analogues bearing a variety of fluorophores. Structured illumination microscopy of the fluorescent teixobactin analogues with B. subtilis enables super-resolution visualization of the interaction of teixobactin with bacterial cell walls and permits the observation of aggregated clusters of the antibiotic on the bacteria. Förster resonance energy transfer (FRET) microscopy further elucidates the supramolecular assembly by showing that fluorescent teixobactin molecules co-localize within a few nanometers on B. subtilis. Fluorescence microscopy over time with a fluorescent teixobactin analogue and propidium iodide in B. subtilis reveals a correlation between cell death and binding of the antibiotic to cellular targets, followed by lysis of cells. Collectively, these studies provide new insights into the binding of teixobactin to Gram-positive bacteria, its supramolecular mechanism of action, and the lysis of bacteria that follows. FRET microscopy experiments demonstrate supramolecular assembly of teixobactin molecules on Bacillus subtilis, providing further evidence that teixobactin is a supramolecular antibiotic.![]()
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Affiliation(s)
- Michael A Morris
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
| | - Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine Irvine California 92697 USA
| | - Fabian Grein
- Institute for Pharmaceutical Microbiology, University of Bonn, University Hospital Bonn Bonn 53115 Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne Bonn 53115 Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, University Hospital Bonn Bonn 53115 Germany
| | - Melina Arts
- Institute for Pharmaceutical Microbiology, University of Bonn, University Hospital Bonn Bonn 53115 Germany
| | - Chelsea R Jones
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
| | - Betty T Nguyen
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
| | - Mohammad H Hashemian
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
| | - Melody Malek
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine Irvine California 92697 USA
| | - James S Nowick
- Department of Chemistry, University of California, Irvine Irvine California 92697 USA
- Department of Pharmaceutical Sciences, University of California, Irvine Irvine California 92697 USA
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10
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Baier AS, Peterson CL. Fluorescence approaches for biochemical analysis of ATP-dependent chromatin remodeling enzymes. Methods Enzymol 2022; 673:1-17. [PMID: 35965003 PMCID: PMC10107425 DOI: 10.1016/bs.mie.2022.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The dynamic nature of chromatin is an essential mechanism by which gene expression is regulated. Chromatin is comprised of nucleosomes, an octamer of histone proteins wrapped by DNA, and manipulation of these structures is carried out by a family of proteins known as ATP-dependent chromatin remodeling enzymes. These enzymes carry out a diverse range of activities, from appropriately positioning and adjusting the density of nucleosomes on genes, to installation and removal of histones for sequence variants, to ejection from DNA. These activities have a critical role in the proper maintenance of chromatin architecture, and dysregulation of chromatin remodeling is directly linked to the pathophysiology of various diseases. Mechanistic understanding of chromatin remodeling enzymes is therefore desirable, both as the drivers of this essential cellular activity and as potentially novel therapeutic targets in disease. In this chapter we cover our current methods for characterization of remodeler substrate binding affinity and catalytic activity, leveraging fluorescence polarization and Förster resonance energy transfer assays.
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11
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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] [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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12
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Bourne Worster S, Feighan O, Manby FR. Reliable transition properties from excited-state mean-field calculations. J Chem Phys 2021; 154:124106. [DOI: 10.1063/5.0041233] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Susannah Bourne Worster
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Oliver Feighan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Frederick R. Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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13
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Hübner K, Joshi H, Aksimentiev A, Stefani FD, Tinnefeld P, Acuna GP. Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures. ACS NANO 2021; 15:5109-5117. [PMID: 33660975 DOI: 10.1021/acsnano.0c10259] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores' binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise double-stranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores' probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.
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Affiliation(s)
- Kristina Hübner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
| | - Guillermo P Acuna
- Department of Physics, University of Fribourg, Chemin du Musée 3, Fribourg CH-1700, Switzerland
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14
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Panniello A, Trapani M, Cordaro M, Dibenedetto CN, Tommasi R, Ingrosso C, Fanizza E, Grisorio R, Collini E, Agostiano A, Curri ML, Castriciano MA, Striccoli M. High-Efficiency FRET Processes in BODIPY-Functionalized Quantum Dot Architectures. Chemistry 2021; 27:2371-2380. [PMID: 32896940 DOI: 10.1002/chem.202003574] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 01/24/2023]
Abstract
Efficient FRET systems are developed combining colloidal CdSe quantum dots (QDs) donors and BODIPY acceptors. To promote effective energy transfer in FRET architectures, the distance between the organic fluorophore and the QDs needs to be optimized by a careful system engineering. In this context, BODIPY dyes bearing amino-terminated functionalities are used in virtue of the high affinity of amine groups in coordinating the QD surface. A preliminary QD surface treatment with a short amine ligand is performed to favor the interaction with the organic fluorophores in solution. The successful coordination of the dye to the QD surface, accomplishing a short donor-acceptor distance, provides effective energy transfer already in solution, with efficiency of 76 %. The efficiency further increases in the solid state where the QDs and the dye are deposited as single coordinated units from solution, with a distance between the fluorophores down to 2.2 nm, demonstrating the effectiveness of the coupling strategy.
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Affiliation(s)
- Annamaria Panniello
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Mariachiara Trapani
- Istituto per lo Studio dei Materiali Nanostrutturati del CNR (ISMN-CNR), c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed, Ambientali, Università degli Studi di Messina, Viale F. Stagno D'Alcontres31, 98166, Messina, Italy
| | - Massimiliano Cordaro
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed, Ambientali, Università degli Studi di Messina, Viale F. Stagno D'Alcontres31, 98166, Messina, Italy
| | - Carlo Nazareno Dibenedetto
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Raffaele Tommasi
- Dipartimento di Scienze Mediche di Base, Neuroscienze e Organi di Senso, Università degli Studi di Bari "Aldo Moro", Piazza G. Cesare 11, 70124, Bari, Italy
| | - Chiara Ingrosso
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Elisabetta Fanizza
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Roberto Grisorio
- Dipartimento di Ingegneria Civile, Ambientale, del Territorio, Edile e di, Chimica (DICATECh), Politecnico di Bari, Via Orabona, 4, 70126, Bari, Italy
| | - Elisabetta Collini
- Dipartimento Scienze Chimiche, Università di Padova, via Marzolo 1, 35131, Padova, Italy
| | - Angela Agostiano
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Maria Lucia Curri
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy.,Dipartimento Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
| | - Maria Angela Castriciano
- Istituto per lo Studio dei Materiali Nanostrutturati del CNR (ISMN-CNR), c/o Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed, Ambientali, Università degli Studi di Messina, Viale F. Stagno D'Alcontres31, 98166, Messina, Italy
| | - Marinella Striccoli
- Istituto per i Processi Chimico Fisici del CNR (IPCF-CNR), c/o Dipartimento di Chimica, Università degli Studi di Bari "Aldo Moro", Via Orabona, 4, 70126, Bari, Italy
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15
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Bos I, Timmerman M, Sprakel J. FRET-Based Determination of the Exchange Dynamics of Complex Coacervate Core Micelles. Macromolecules 2021; 54:398-411. [PMID: 33456072 PMCID: PMC7808214 DOI: 10.1021/acs.macromol.0c02387] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/08/2020] [Indexed: 02/07/2023]
Abstract
Complex coacervate core micelles (C3Ms) are nanoscopic structures formed by charge interactions between oppositely charged macroions and used to encapsulate a wide variety of charged (bio)molecules. In most cases, C3Ms are in a dynamic equilibrium with their surroundings. Understanding the dynamics of molecular exchange reactions is essential as this determines the rate at which their cargo is exposed to the environment. Here, we study the molecular exchange in C3Ms by making use of Förster resonance energy transfer (FRET) and derive an analytical model to relate the experimentally observed increase in FRET efficiency to the underlying macromolecular exchange rates. We show that equilibrated C3Ms have a broad distribution of exchange rates. The overall exchange rate can be strongly increased by increasing the salt concentration. In contrast, changing the unlabeled homopolymer length does not affect the exchange of the labeled homopolymers and an increase in the micelle concentration only affects the FRET increase rate at low micelle concentrations. Together, these results suggest that the exchange of these equilibrated C3Ms occurs mainly by expulsion and insertion, where the rate-limiting step is the breaking of ionic bonds to expel the chains from the core. These are important insights to further improve the encapsulation efficiency of C3Ms.
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Affiliation(s)
- Inge Bos
- Physical Chemistry and Soft
Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Marga Timmerman
- Physical Chemistry and Soft
Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft
Matter, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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16
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Oh I, Lee H, Kim TW, Kim CW, Jun S, Kim C, Choi EH, Rhee YM, Kim J, Jang W, Ihee H. Enhancement of Energy Transfer Efficiency with Structural Control of Multichromophore Light-Harvesting Assembly. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001623. [PMID: 33101863 PMCID: PMC7578888 DOI: 10.1002/advs.202001623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/24/2020] [Indexed: 06/11/2023]
Abstract
Multichromophore systems (MCSs) are envisioned as building blocks of molecular optoelectronic devices. While it is important to understand the characteristics of energy transfer in MCSs, the effect of multiple donors on energy transfer has not been understood completely, mainly due to the lack of a platform to investigate such an effect systematically. Here, a systematic study on how the number of donors (n D) and interchromophore distances affect the efficiency of energy transfer (η FRET) is presented. Specifically, η FRET is calculated for a series of model MCSs using simulations, a series of multiporphyrin dendrimers with systematic variation of n D and interdonor distances is synthesized, and η FRETs of those dendrimers using transient absorption spectroscopy are measured. The simulations predict η FRET in the multiporphyrin dendrimers well. In particular, it is found that η FRET is enhanced by donor-to-donor energy transfer only when structural heterogeneity exists in an MCS, and the relationships between the η FRET enhancement and the structural parameters of the MCS are revealed.
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Affiliation(s)
- Inhwan Oh
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Hosoowi Lee
- Department of ChemistryCollege of ScienceYonsei UniversitySeoul120‐749Republic of Korea
| | - Tae Wu Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Chang Woo Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Sunhong Jun
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
| | - Changwon Kim
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Eun Hyuk Choi
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Young Min Rhee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
| | - Jeongho Kim
- Department of ChemistryInha UniversityIncheon22212Republic of Korea
| | - Woo‐Dong Jang
- Department of ChemistryCollege of ScienceYonsei UniversitySeoul120‐749Republic of Korea
| | - Hyotcherl Ihee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- Center for Nanomaterials and Chemical ReactionsInstitute for Basic Science (IBS)Daejeon34141Republic of Korea
- KI for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
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17
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Gebrezgiabher M, Zalloum WA, Clarke DJ, Miles SM, Fedorova AA, Zenkova MA, Bichenkova EV. RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions. J Biomol Struct Dyn 2020; 39:2555-2574. [PMID: 32248755 DOI: 10.1080/07391102.2020.1751711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sequence-specific protein-based ribonucleases are not found in nature. Absolute sequence selectivity in RNA cleavage in vivo normally requires multi-component complexes that recruit a guide RNA or DNA for target recognition and a protein-RNA assembly for catalytic functioning (e.g. RNAi molecular machinery, RNase H). Recently discovered peptidyl-oligonucleotide synthetic ribonucleases selectively knock down pathogenic RNAs by irreversible cleavage to offer unprecedented opportunities for control of disease-relevant RNA. Understanding how to increase their potency, selectivity and catalytic turnover will open the translational pathway to successful therapeutics. Yet, very little is known about how these chemical ribonucleases bind, cleave and leave their target. Rational design awaits this understanding in order to control therapy, particularly how to overcome the trade-off between sequence specificity and potency through catalytic turnover. We illuminate this here by characterizing the interactions of these chemical RNases with both complementary and non-complementary RNAs using Tm profiles, fluorescence, UV-visible and NMR spectroscopies. Crucially, the level of counter cations, which are tightly-controlled within cellular compartments, also controlled these interactions. The oligonucleotide component dominated interaction between conjugates and complementary targets in the presence of physiological levels of counter cations (K+), sufficient to prevent repulsion between the complementary nucleic acid strands to allow Watson-Crick hydrogen bonding. In contrast, the positively-charged catalytic peptide interacted poorly with target RNA, when counter cations similarly screened the negatively-charged sugar-phosphate RNA backbones. The peptide only became the key player, when counter cations were insufficient for charge screening; moreover, only under such non-physiological conditions did conjugates form strong complexes with non-complementary RNAs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mengisteab Gebrezgiabher
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Waleed A Zalloum
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David J Clarke
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Steven M Miles
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antonina A Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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18
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Bourne Worster S, Stross C, Vaughan FMWC, Linden N, Manby FR. Structure and Efficiency in Bacterial Photosynthetic Light Harvesting. J Phys Chem Lett 2019; 10:7383-7390. [PMID: 31714789 DOI: 10.1021/acs.jpclett.9b02625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Photosynthetic organisms use networks of chromophores to absorb and deliver solar energy to reaction centers. We present a detailed model of the light-harvesting complexes in purple bacteria, including explicit interaction with sunlight, radiative and nonradiative energy loss, and dephasing and thermalizing effects of coupling to a vibrational bath. We capture the effect of slow vibrations by introducing time-dependent disorder. Our model describes the experimentally observed high efficiency of light harvesting, despite the absence of long-range quantum coherence. The one-exciton part of the quantum state fluctuates continuously but remains highly mixed at all times. These results suggest a relatively minor role for structure in determining efficiency. We build hypothetical models with randomly arranged chromophores but still observe high efficiency when nearest-neighbor distances are comparable to those in nature. This helps explain the high transport efficiency in organisms with widely differing antenna structures and suggests new design criteria for artificial light-harvesting devices.
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Affiliation(s)
- Susannah Bourne Worster
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
| | - Clement Stross
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
| | - Felix M W C Vaughan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
- Bristol Centre for Complexity Sciences , University of Bristol , Bristol BS2 8BB , U.K
| | - Noah Linden
- School of Mathematics , University of Bristol , Bristol BS8 1UG , U.K
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
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19
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Xu L, Wang Z, Wang R, Wang L, He X, Jiang H, Tang H, Cao D, Tang BZ. A Conjugated Polymeric Supramolecular Network with Aggregation‐Induced Emission Enhancement: An Efficient Light‐Harvesting System with an Ultrahigh Antenna Effect. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907678] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Linxian Xu
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Zaiyu Wang
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong Hong Kong
| | - Rongrong Wang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Lingyun Wang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Xuewen He
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong Hong Kong
| | - Huanfeng Jiang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Hao Tang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Derong Cao
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Ben Zhong Tang
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong Hong Kong
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20
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Xu L, Wang Z, Wang R, Wang L, He X, Jiang H, Tang H, Cao D, Tang BZ. A Conjugated Polymeric Supramolecular Network with Aggregation‐Induced Emission Enhancement: An Efficient Light‐Harvesting System with an Ultrahigh Antenna Effect. Angew Chem Int Ed Engl 2019; 59:9908-9913. [DOI: 10.1002/anie.201907678] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Linxian Xu
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Zaiyu Wang
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong Hong Kong
| | - Rongrong Wang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Lingyun Wang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Xuewen He
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong Hong Kong
| | - Huanfeng Jiang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Hao Tang
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Derong Cao
- State Key Laboratory of Luminescent Materials and DevicesSchool of Chemistry and Chemical EngineeringSouth China University of Technology Guangzhou 510641 China
| | - Ben Zhong Tang
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong Hong Kong
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21
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Bhattacharyya A, Makhal SC, Kumar Mandal S, Guchhait N. Exploring the hidden potential of a methoxy substituted HBT derivative as an efficient example of coupling of AIE and ESIPT processes and as an energy harvesting platform. NEW J CHEM 2019. [DOI: 10.1039/c9nj03340h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A methoxy substituted HBT derivative 2-(benzo[d]thiazol-2-yl)-6-methoxyphenol (TMP) showed coupling of AIE and ESIPT, underwent FRET with Rhodamine B and detected Sulfide in pure water by ratiometry.
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Affiliation(s)
| | | | | | - Nikhil Guchhait
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
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22
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Kogikoski S, Paschoalino WJ, Kubota LT. Supramolecular DNA origami nanostructures for use in bioanalytical applications. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Ashwin BCMA, Saravanan C, Stalin T, Muthu Mareeswaran P, Rajagopal S. FRET-based Solid-state Luminescent Glyphosate Sensor Using Calixarene-grafted Ruthenium(II)bipyridine Doped Silica Nanoparticles. Chemphyschem 2018; 19:2768-2775. [PMID: 29989285 DOI: 10.1002/cphc.201800447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Indexed: 12/11/2022]
Abstract
Calixarene-functionalized luminescent nanoparticles were successfully fabricated for the FRET-based selective and sensitive detection of the organophosphorus pesticide glyphosate (GP). p-Tert-butylcalix[4]arene was grafted on the surface of [Ru(bpy)3 ]2+ incorporated SiNps to produce self-assembled nanosensors (RSC). FRET was switched on in the presence of GP by means of energy transfer due to binding with p-tert-butylcalix[4]arene grafted on the surface of the RSC. The FRET efficiency of the GP-RSC system was increased gradually with the addition of GP. The FRET efficiency was evaluated as 87.69 % and a high binding affinity was established by the binding constant value, 1.16×107 M-1 , using a Langmuir binding isotherm plot. The estimated limit of detection (LOD) was 7.91×10-7 M, which was lower than the Environmental Protection Agency (EPA) recommendation. The probe also effectively responds to real sample analysis. The sensitivity and selectivity was realized due to the efficient FRET towards the fluorescence properties of the [Ru(bpy)3 ]2+ complex.
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Affiliation(s)
| | - Chokalingam Saravanan
- Department of Industrial Chemistry, Alagappa University, Karaikudi, Tamilnadu, India
| | - Thambusamy Stalin
- Department of Industrial Chemistry, Alagappa University, Karaikudi, Tamilnadu, India
| | | | - Seenivasan Rajagopal
- Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, Tamilnadu, India
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24
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Choi Y, Kotthoff L, Olejko L, Resch-Genger U, Bald I. DNA Origami-Based Förster Resonance Energy-Transfer Nanoarrays and Their Application as Ratiometric Sensors. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23295-23302. [PMID: 29916243 DOI: 10.1021/acsami.8b03585] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Förster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH-responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.
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Affiliation(s)
- Youngeun Choi
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
| | - Lisa Kotthoff
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
| | - Lydia Olejko
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
| | - Ute Resch-Genger
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
| | - Ilko Bald
- Department of Chemistry, Physical Chemistry , University of Potsdam , 14476 Potsdam , Germany
- BAM Federal Institute for Materials Research and Testing , 12489 Berlin , Germany
- School of Analytical Sciences Adlershof , Humboldt-Universität zu Berlin , 10099 Berlin , Germany
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25
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Bösch CD, Jevric J, Bürki N, Probst M, Langenegger SM, Häner R. Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties. Bioconjug Chem 2018; 29:1505-1509. [DOI: 10.1021/acs.bioconjchem.8b00263] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Caroline D. Bösch
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jovana Jevric
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Nutcha Bürki
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon M. Langenegger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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26
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Kuzyk A, Jungmann R, Acuna GP, Liu N. DNA Origami Route for Nanophotonics. ACS PHOTONICS 2018; 5:1151-1163. [PMID: 30271812 PMCID: PMC6156112 DOI: 10.1021/acsphotonics.7b01580] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/06/2018] [Accepted: 02/11/2018] [Indexed: 05/21/2023]
Abstract
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.
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Affiliation(s)
- Anton Kuzyk
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Department
of Neuroscience and Biomedical Engineering, Aalto University School of Science, P.O. Box 12200, FI-00076 Aalto, Finland
| | - Ralf Jungmann
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Guillermo P. Acuna
- Institute
for Physical & Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Na Liu
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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27
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Pilo-Pais M, Acuna GP, Tinnefeld P, Liedl T. Sculpting Light by Arranging Optical Components with DNA Nanostructures. MRS BULLETIN 2017; 42:936-942. [PMID: 31168224 PMCID: PMC6546597 DOI: 10.1557/mrs.2017.278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA nanotechnology has developed into a state where the design and assembly of complex nanoscale structures has become fast, reliable, cost-effective, and accessible to non-experts. Nanometer-precise positioning of organic (dyes, biomolecules, etc.) and inorganic (metal nanoparticles, colloidal quantum dots, etc.) components on DNA nanostructures is straightforward and modular. In this perspective article, we identify the opportunities and challenges that DNA-assembled devices and materials are facing for optical antennas, metamaterials, and sensing applications. With the abilities of arranging hybrid materials in defined geometries, plasmonic effects will, for example, amplify molecular recognition transduction so that single-molecule events will be measureable with simple devices. On the larger scale, DNA nanotechnology has the potential of breaking the symmetry of common self-assembled functional materials creating pre-defined optical properties such as refractive index tuning, Bragg reflection and topological insulation.
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Affiliation(s)
- Mauricio Pilo-Pais
- Faculty of Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Guillermo P Acuna
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig University of Technology, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Department for Chemistry and Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, 80539, München, Germany
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28
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Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Yamanaka Y, Ohya Y, Komiyama M. Allosteric control of nanomechanical DNA origami pinching devices for enhanced target binding. Chem Commun (Camb) 2017; 53:8276-8279. [DOI: 10.1039/c7cc03991c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Significant enhancement of single-molecular binding of specific targets was achieved by allosterically controlling nanomechanical DNA origami pinching devices.
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Affiliation(s)
- Akinori Kuzuya
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Yusuke Sakai
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Takahiro Yamazaki
- Research Center for Advanced Science and Technology
- The University of Tokyo
- Tokyo 153-8904
- Japan
| | - Yan Xu
- Department of Medical Sciences
- University of Miyazaki
- Miyazaki 889-1692
- Japan
| | - Yusei Yamanaka
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Yuichi Ohya
- Department of Chemistry and Materials Engineering
- Kansai University
- Suita
- Japan
| | - Makoto Komiyama
- International Center for Materials Nanoarchitectonics
- National Institute for Materials Science
- Tsukuba
- Japan
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