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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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2
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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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3
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Mass OA, Watt DR, Patten LK, Pensack RD, Lee J, Turner DB, Yurke B, Knowlton WB. Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer. Phys Chem Chem Phys 2023; 25:28437-28451. [PMID: 37843877 PMCID: PMC10599410 DOI: 10.1039/d3cp01634j] [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: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment-protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments-secured by noncovalent bonding to a protein template-enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC) featuring stability, high structural modularity, and spectral properties advantageous for exciton-based devices. The BC dimer was covalently templated by DNA, a stable and highly programmable scaffold. To achieve exciton delocalization in the absence of pigment-protein interactions critical for the Bchla dimer, we relied on the strong transition dipole moment in BC enabled by two auxochromes along the Qy transition, and omitting the central metal and isocyclic ring. The spectral properties of the synthetic "free" BC closely resembled those of Bchla in an organic solvent. Applying spectroscopic modeling, the exciton delocalization in the DNA-templated BC dimer was evaluated by extracting the excitonic hopping parameter, J to be 214 cm-1 (26.6 meV). For comparison, the same method applied to the natural protein-templated Bchla dimer yielded J of 286 cm-1 (35.5 meV). The smaller value of J in the BC dimer likely arose from the partial bacteriochlorin intercalation and the difference in medium effect between DNA and protein.
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Affiliation(s)
- Olga A Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Devan R Watt
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Lance K Patten
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
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4
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Barcenas G, Biaggne A, Mass OA, Knowlton WB, Yurke B, Li L. Molecular Dynamic Studies of Dye-Dye and Dye-DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions. Int J Mol Sci 2023; 24:ijms24044059. [PMID: 36835471 PMCID: PMC9967300 DOI: 10.3390/ijms24044059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye-DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was initialized in parallel and antiparallel arrangements in the DNA HJ. The MD results, validated by experimental measurements, suggested that the adjacent dimer promotes stronger excitonic coupling and less dye-DNA interaction than the transverse dimer. Additionally, we found that SQ dyes with specific functional groups (i.e., substituents) facilitate a closer degree of aggregate packing via hydrophobic effects, leading to a stronger excitonic coupling. This work advances a fundamental understanding of the impacts of dye-DNA interactions on aggregate orientation and excitonic coupling.
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Affiliation(s)
- German Barcenas
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Olga A. Mass
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
- Correspondence:
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5
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Sinha R, Das SK, Ghosh M, Chowdhury J. Fabrication of gold nanoparticles tethered in heat-cooled calf thymus-deoxyribonucleic acid Langmuir-Blodgett film as effective surface-enhanced Raman scattering sensing platform. Front Chem 2022; 10:1034060. [DOI: 10.3389/fchem.2022.1034060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
SERS active substrate fabricated through self-assembly of Gold nanoparticles on the disjointed networks of Heat-cooled Calf Thymus DNA (HC-Ct DNA) Langmuir-Blodgett (LB) film has been reported. Adsorption kinetics of HC-Ct DNA molecules at the air-water interface has been studied explicitly. The UV-Vis electronic absorption spectra in conjunction with the FESEM images collectively suggest the presence of H- type aggregated domains most likely owing to plane-to-plane self-association of the HC-Ct DNA molecules aligned vertically on the surface of the LB film. Elemental composition and the morphological features of the as-prepared substrate (APS) are explored from XPS analysis and the FESEM, AFM images respectively. The SERS efficacy of the APS has been tested with trace concentrations of 4-Mercaptopyridine molecule. Finally, this SERS active substrate has also been used for the detection of malathion at ultrasensitive concentrations.
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6
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Takada T, Shimobaki N, Naruo M, Nakamura M, Yamana K. Photoresponsive porphyrin‐DNA complexes constructed through intercalation‐like binding. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tadao Takada
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry 2167 Shosha 671-2280 Himeji, Hyogo JAPAN
| | - Nao Shimobaki
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Moe Naruo
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Mitsunobu Nakamura
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
| | - Kazushige Yamana
- University of Hyogo: Hyogo Kenritsu Daigaku Department of applied chemistry JAPAN
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7
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Barcenas G, Biaggne A, Mass OA, Wilson CK, Obukhova OM, Kolosova OS, Tatarets AL, Terpetschnig E, Pensack RD, Lee J, Knowlton WB, Yurke B, Li L. First-principles studies of substituent effects on squaraine dyes. RSC Adv 2021; 11:19029-19040. [PMID: 35478639 PMCID: PMC9033489 DOI: 10.1039/d1ra01377g] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/17/2021] [Indexed: 01/21/2023] Open
Abstract
Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used ab initio theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored via conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications. Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.![]()
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Affiliation(s)
- German Barcenas
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Olga A Mass
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Christopher K Wilson
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Olena M Obukhova
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine
| | - Olga S Kolosova
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine
| | - Anatoliy L Tatarets
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine.,SETA BioMedicals Urbana IL 61802 USA
| | | | - Ryan D Pensack
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Chemistry and Biochemistry, Boise State University Boise ID 83725 USA
| | - William B Knowlton
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Electrical and Computer Engineering, Boise State University Boise ID 83725 USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Electrical and Computer Engineering, Boise State University Boise ID 83725 USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Center for Advanced Energy Studies Idaho Falls ID 83401 USA
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8
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Dass M, Gür FN, Kołątaj K, Urban MJ, Liedl T. DNA Origami-Enabled Plasmonic Sensing. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:5969-5981. [PMID: 33828635 PMCID: PMC8016175 DOI: 10.1021/acs.jpcc.0c11238] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Indexed: 05/02/2023]
Abstract
The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.
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Affiliation(s)
- Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Fatih N. Gür
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Karol Kołątaj
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Maximilian J. Urban
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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9
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Tarabara U, Kirilova E, Kirilov G, Vus K, Zhytniakivska O, Trusova V, Gorbenko G. Benzanthrone dyes as mediators of cascade energy transfer in insulin amyloid fibrils. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115102] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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10
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Mass OA, Wilson CK, Roy SK, Barclay MS, Patten LK, Terpetschnig EA, Lee J, Pensack RD, Yurke B, Knowlton WB. Exciton Delocalization in Indolenine Squaraine Aggregates Templated by DNA Holliday Junction Scaffolds. J Phys Chem B 2020; 124:9636-9647. [PMID: 33052691 DOI: 10.1021/acs.jpcb.0c06480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Exciton delocalization plays a prominent role in the photophysics of molecular aggregates, ultimately governing their particular function or application. Deoxyribonucleic acid (DNA) is a compelling scaffold in which to template molecular aggregates and promote exciton delocalization. As individual dye molecules are the basis of exciton delocalization in molecular aggregates, their judicious selection is important. Motivated by their excellent photostability and spectral properties, here, we examine the ability of squaraine dyes to undergo exciton delocalization when aggregated via a DNA Holliday junction (HJ) template. A commercially available indolenine squaraine dye was chosen for the study given its strong structural resemblance to Cy5, a commercially available cyanine dye previously shown to undergo exciton delocalization in DNA HJs. Three types of DNA-dye aggregate configurations-transverse dimer, adjacent dimer, and tetramer-were investigated. Signatures of exciton delocalization were observed in all squaraine-DNA aggregates. Specifically, strong blue shift and Davydov splitting were observed in steady-state absorption spectroscopy and exciton-induced features were evident in circular dichroism (CD) spectroscopy. Strongly suppressed fluorescence emission provided additional, indirect evidence for exciton delocalization in the DNA-templated squaraine dye aggregates. To quantitatively evaluate and directly compare the excitonic Coulombic coupling responsible for exciton delocalization, the strength of excitonic hopping interactions between the dyes was obtained by simultaneously fitting the experimental steady-state absorption and CD spectra via a Holstein-like Hamiltonian, in which, following the theoretical approach of Kühn, Renger, and May, the dominant vibrational mode is explicitly considered. The excitonic hopping strength within indolenine squaraines was found to be comparable to that of the analogous Cy5 DNA-templated aggregate. The squaraine aggregates adopted primarily an H-type (dyes oriented parallel to each other) spatial arrangement. Extracted geometric details of the dye mutual orientation in the aggregates enabled a close comparison of aggregate configurations and the elucidation of the influence of dye angular relationship on excitonic hopping interactions in squaraine aggregates. These results encourage the application of squaraine-based aggregates in next-generation systems driven by molecular excitons.
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Affiliation(s)
| | | | | | | | | | - Ewald A Terpetschnig
- SETA BioMedicals, LLC, 2014 Silver Court East, Urbana, Illinois 61801, United States
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11
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Mazuski RJ, Díaz SA, Wood RE, Lloyd LT, Klein WP, Mathur D, Melinger JS, Engel GS, Medintz IL. Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency. J Phys Chem Lett 2020; 11:4163-4172. [PMID: 32391695 DOI: 10.1021/acs.jpclett.0c01020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.
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Affiliation(s)
- Richard J Mazuski
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ryan E Wood
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Divita Mathur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joseph S Melinger
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory S Engel
- Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, 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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Loretan M, Domljanovic I, Lakatos M, Rüegg C, Acuna GP. DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E2185. [PMID: 32397498 PMCID: PMC7254321 DOI: 10.3390/ma13092185] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022]
Abstract
DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.
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Affiliation(s)
- Morgane Loretan
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland; (M.L.); (G.P.A.)
| | - Ivana Domljanovic
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland;
| | - Mathias Lakatos
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland; (M.L.); (G.P.A.)
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland;
| | - Guillermo P. Acuna
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland; (M.L.); (G.P.A.)
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13
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Mizuno H, Kitamatsu M, Imai Y, Fukuhara G. Smart Fluorescence Materials that Are Controllable by Hydrostatic Pressure: Peptide−Pyrene Conjugates. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hiroaki Mizuno
- Department of ChemistryTokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
| | - Mizuki Kitamatsu
- Department of Applied ChemistryFaculty of Science and EngineeringKindai University 3-4-1 Kowakae Higashi-Osaka Osaka 577-8502 Japan
| | - Yoshitane Imai
- Department of Applied ChemistryFaculty of Science and EngineeringKindai University 3-4-1 Kowakae Higashi-Osaka Osaka 577-8502 Japan
| | - Gaku Fukuhara
- Department of ChemistryTokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
- JST, PRESTO 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
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14
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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15
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Mishra S, Feng Y, Endo M, Sugiyama H. Advances in DNA Origami–Cell Interfaces. Chembiochem 2019; 21:33-44. [DOI: 10.1002/cbic.201900481] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Shubham Mishra
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Yihong Feng
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Masayuki Endo
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
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16
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Gorbenko G, Trusova V, Deligeorgiev T, Gadjev N, Mizuguchi C, Saito H. Two-step FRET as a tool for probing the amyloid state of proteins. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Bortolus M, Ribaudo G, Toffoletti A, Carbonera D, Zagotto G. Photo-induced spin switching in a modified anthraquinone modulated by DNA binding. Photochem Photobiol Sci 2019; 18:2199-2207. [PMID: 30838367 DOI: 10.1039/c8pp00586a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
An anthraquinone modified with a nitroxide radical and able to intercalate into DNA has been synthesized to obtain a molecule the spin state of which can be manipulated by visible light and DNA binding. The doublet ground state of the molecule can be photo-switched to either a strongly coupled spin state (quartet + doublet), when isolated, or to an uncoupled spin state (triplet and doublet), when bound to DNA. The different spin state that is obtained upon photoexcitation depends on the intercalation of the quinonic core into double-stranded DNA which changes the conformation of the molecule, thereby altering the exchange interaction between the excited state localized on the quinonic core and the nitroxide radical. The spin state of the system has been investigated using both continuous-wave and time-resolved EPR spectroscopy.
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Affiliation(s)
- Marco Bortolus
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Giovanni Ribaudo
- Department of Pharmaceutical Sciences, University of Padova, via Marzolo 5, 35131, Padova, Italy
| | - Antonio Toffoletti
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
| | - Giuseppe Zagotto
- Department of Pharmaceutical Sciences, University of Padova, via Marzolo 5, 35131, Padova, Italy
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18
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Pathak P, Yao W, Hook KD, Vik R, Winnerdy FR, Brown JQ, Gibb BC, Pursell ZF, Phan AT, Jayawickramarajah J. Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns. J Am Chem Soc 2019; 141:12582-12591. [PMID: 31322869 DOI: 10.1021/jacs.9b03250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.
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Affiliation(s)
- Pravin Pathak
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Wei Yao
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Katherine Delaney Hook
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Ryan Vik
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Jonathon Quincy Brown
- Department of Biomedical Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Bruce C Gibb
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Janarthanan Jayawickramarajah
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
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19
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Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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20
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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21
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Kownacki M, Langenegger SM, Liu SX, Häner R. Integrating DNA Photonic Wires into Light-Harvesting Supramolecular Polymers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809914] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mariusz Kownacki
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Simon M. Langenegger
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Shi-Xia Liu
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
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22
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Kownacki M, Langenegger SM, Liu SX, Häner R. Integrating DNA Photonic Wires into Light-Harvesting Supramolecular Polymers. Angew Chem Int Ed Engl 2018; 58:751-755. [DOI: 10.1002/anie.201809914] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Mariusz Kownacki
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Simon M. Langenegger
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Shi-Xia Liu
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry; University of Bern; Freiestrasse 3 3012 Bern Switzerland
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23
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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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24
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Towards efficient solid-state triplet–triplet annihilation based photon upconversion: Supramolecular, macromolecular and self-assembled systems. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.02.011] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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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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Volkov IL, Reveguk ZV, Serdobintsev PY, Ramazanov RR, Kononov AI. DNA as UV light-harvesting antenna. Nucleic Acids Res 2018; 46:3543-3551. [PMID: 29186575 PMCID: PMC6283424 DOI: 10.1093/nar/gkx1185] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/08/2017] [Accepted: 11/15/2017] [Indexed: 12/23/2022] Open
Abstract
The ordered structure of UV chromophores in DNA resembles photosynthetic light-harvesting complexes in which quantum coherence effects play a major role in highly efficient directional energy transfer. The possible role of coherent excitons in energy transport in DNA remains debated. Meanwhile, energy transport properties are greatly important for understanding the mechanisms of photochemical reactions in cellular DNA and for DNA-based artificial nanostructures. Here, we studied energy transfer in DNA complexes formed with silver nanoclusters and with intercalating dye (acridine orange). Steady-state fluorescence measurements with two DNA templates (15-mer DNA duplex and calf thymus DNA) showed that excitation energy can be transferred to the clusters from 21 and 28 nucleobases, respectively. This differed from the DNA-acridine orange complex for which energy transfer took place from four neighboring bases only. Fluorescence up-conversion measurements showed that the energy transfer took place within 100 fs. The efficient energy transport in the Ag-DNA complexes suggests an excitonic mechanism for the transfer, such that the excitation is delocalized over at least four and seven stacked bases, respectively, in one strand of the duplexes stabilizing the clusters. This result demonstrates that the exciton delocalization length in some DNA structures may not be limited to just two bases.
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Affiliation(s)
- Ivan L Volkov
- St. Petersburg State University, St. Petersburg 199034, Russia
| | | | - Pavel Yu Serdobintsev
- St. Petersburg State University, St. Petersburg 199034, Russia
- St. Petersburg State Polytechnic University, St. Petersburg 195251, Russia
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27
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Kaminska I, Bohlen J, Mackowski S, Tinnefeld P, Acuna GP. Strong Plasmonic Enhancement of a Single Peridinin-Chlorophyll a-Protein Complex on DNA Origami-Based Optical Antennas. ACS NANO 2018; 12:1650-1655. [PMID: 29353479 DOI: 10.1021/acsnano.7b08233] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this contribution, we fabricate hybrid constructs based on a natural light-harvesting complex, peridinin-chlorophyll a-protein, coupled to dimer optical antennas self-assembled with the help of the DNA origami technique. This approach enables controlled positioning of individual complexes at the hotspot of the optical antennas based on large, colloidal gold and silver nanoparticles. Our approach allows us to selectively excite the different pigments present in the harvesting complex, reaching a fluorescence enhancement of 500-fold. This work expands the range of self-assembled functional hybrid constructs for harvesting sunlight and can be further developed for other pigment-proteins and proteins.
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Affiliation(s)
- Izabela Kaminska
- Institute for Physical & Theoretical Chemistry, and Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology , 38106 Braunschweig, Germany
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University , Grudziadzka 5, 87-100 Torun, Poland
| | - Johann Bohlen
- Institute for Physical & Theoretical Chemistry, and Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology , 38106 Braunschweig, Germany
- Department Chemie and Center for NanoScience (CeNS), Ludwig-Maximilians-Universitaet Muenchen , Butenandtstr. 5-13 Haus E, 81377 Muenchen, Germany
| | - Sebastian Mackowski
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University , Grudziadzka 5, 87-100 Torun, Poland
| | - Philip Tinnefeld
- Institute for Physical & Theoretical Chemistry, and Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology , 38106 Braunschweig, Germany
- Department Chemie and Center for NanoScience (CeNS), Ludwig-Maximilians-Universitaet Muenchen , Butenandtstr. 5-13 Haus E, 81377 Muenchen, 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 , 38106 Braunschweig, Germany
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28
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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29
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Arora AA, de Silva C. Beyond the smiley face: applications of structural DNA nanotechnology. NANO REVIEWS & EXPERIMENTS 2018; 9:1430976. [PMID: 30410711 PMCID: PMC6171786 DOI: 10.1080/20022727.2018.1430976] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/17/2018] [Indexed: 01/27/2023]
Abstract
Since the development of DNA origami by Paul Rothemund in 2006, the field of structural DNA nanotechnology has undergone tremendous growth. Through DNA origami and related approaches, self-assembly of specified DNA sequences allows for the ‘bottom-up’ construction of diverse nanostructures. By utilizing different sets of small ‘staple’ DNA strands to direct the folding of a long scaffold strand in diverse ways, DNA origami has particularly been incorporated into a variety of prototypical applications beyond the two-dimensional (2D) smiley face. In this review, the basis of DNA nanotechnology, methods of self-assembly, and Rothemund’s DNA origami breakthrough are discussed first. Next, some of the most promising applications of structural DNA nanotechnology since 2006 are summarized. These include utilizing DNA origami as a tool for creating 3D nanostructures (including DNA bricks), as well as structural (ligand capsid binding, viral capsid binding, DNA NanoOctahedron, DNA mold, photonic devices, energy transfer units), and dynamic (DNA box-with-lid, DNA nano-robot, DNA barges, amphipathic DNA structures, DNA nanocircuits) applications of DNA origami.
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30
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Nicoli F, Barth A, Bae W, Neukirchinger F, Crevenna AH, Lamb DC, Liedl T. Directional Photonic Wire Mediated by Homo-Förster Resonance Energy Transfer on a DNA Origami Platform. ACS NANO 2017; 11:11264-11272. [PMID: 29063765 PMCID: PMC6546591 DOI: 10.1021/acsnano.7b05631] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Elaborating efficient strategies and deepening the understanding of light transport at the nanoscale is of great importance for future designs of artificial light-harvesting assemblies and dye-based photonic circuits. In this work, we focus on studying the phenomenon of Förster resonance energy transfer (FRET) among fluorophores of the same kind (homo-FRET) and its implications for energy cascades containing two or three different dye molecules. Utilizing the spatial programmability of DNA origami, we arranged a chain of cyanine 3 (Cy3) dyes flanked at one end with a dye of lower excitation energy, cyanine 5 (Cy5), with or without an additional dye of higher excitation energy, Alexa488, at the other end. We characterized the response of our fluorophore assemblies with bulk and single-molecule spectroscopy and support our measurements by Monte Carlo modeling of energy transfer within the system. We find that, depending on the arrangement of the fluorophores, homo-FRET between the Cy3 dyes can lead to an overall enhanced energy transfer to the acceptor fluorophore. Furthermore, we systematically analyzed the homo-FRET system by addressing the fluorescence lifetime and anisotropy. Finally, we built a homo-FRET-mediated photonic wire capable of transferring energy through the homo-FRET system from the blue donor dye (Alexa488) to the red acceptor fluorophore (Cy5) across a total distance of 16 nm.
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Affiliation(s)
- Francesca Nicoli
- Department of Physics and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Anders Barth
- Department of Chemistry and Biochemistry and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Wooli Bae
- Department of Physics and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Fabian Neukirchinger
- Department of Physics and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Alvaro H. Crevenna
- Department of Chemistry and Biochemistry and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Don C. Lamb
- Department of Chemistry and Biochemistry and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
- Correspondence to and
| | - Tim Liedl
- Department of Physics and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
- Correspondence to and
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31
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Chiral multichromophoric supramolecular nanostructures assembled by single stranded DNA and RNA templates. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.08.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Liu Q, Wang H, Shi X, Wang ZG, Ding B. Self-Assembled DNA/Peptide-Based Nanoparticle Exhibiting Synergistic Enzymatic Activity. ACS NANO 2017; 11:7251-7258. [PMID: 28657711 DOI: 10.1021/acsnano.7b03195] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Designing enzyme-mimicking active sites in artificial systems is key to achieving catalytic efficiencies rivaling those of natural enzymes and can provide valuable insight in the understanding of the natural evolution of enzymes. Here, we report the design of a catalytic hemin-containing nanoparticle with self-assembled guanine-rich nucleic acid/histidine-rich peptide components that mimics the active site and peroxidative activity of hemoproteins. The chemical complementarities between the folded nucleic acid and peptide enable the spatial arrangement of essential elements in the active site and effective activation of hemin. As a result, remarkable synergistic effects of nucleic acid and peptide on the catalytic performances were observed. The turnover number of peroxide reached the order of that of natural peroxidase, and the catalytic efficiency is comparable to that of myoglobin. These results have implications in the precise design of supramolecular enzyme mimetics, particularly those with hierarchical active sites. The assemblies we describe here may also resemble an intermediate in the evolution of contemporary enzymes from the catalytic RNA of primitive cells.
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Affiliation(s)
- Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Hui Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
| | - Xinghua Shi
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchial Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology , Beijing 100190, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
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33
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Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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34
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Hatae T, Koshiyama T, Ohba M. Domain Size Dependent Fluorescence Resonance Energy Transfer in Lipid Domain Incorporated Fluorophores. CHEM LETT 2017. [DOI: 10.1246/cl.170104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tatsuru Hatae
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395
| | - Tomomi Koshiyama
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395
| | - Masaaki Ohba
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395
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35
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Amado AM, Pazin WM, Ito AS, Kuzmin VA, Borissevitch IE. Acridine orange interaction with DNA: Effect of ionic strength. Biochim Biophys Acta Gen Subj 2017; 1861:900-909. [DOI: 10.1016/j.bbagen.2017.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 12/31/2016] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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36
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Andreoni A, Lin S, Liu H, Blankenship RE, Yan H, Woodbury NW. Orange Carotenoid Protein as a Control Element in an Antenna System Based on a DNA Nanostructure. NANO LETTERS 2017; 17:1174-1180. [PMID: 28081606 DOI: 10.1021/acs.nanolett.6b04846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Taking inspiration from photosynthetic mechanisms in natural systems, we introduced a light-sensitive photo protective quenching element to an artificial light-harvesting antenna model to control the flow of energy as a function of light intensity excitation. The orange carotenoid protein (OCP) is a nonphotochemical quencher in cyanobacteria: under high-light conditions, the protein undergoes a spectral shift, and by binding to the phycobilisome, it absorbs excess light and dissipates it as heat. By the use of DNA as a scaffold, an antenna system made of organic dyes (Cy3 and Cy5) was constructed, and OCP was assembled on it as a modulated quenching element. By controlling the illumination intensity, it is possible to switch the direction of excitation energy transfer from the donor Cy3 to either of two acceptors. Under low-light conditions, energy is transferred from Cy3 to Cy5, and under intense illumination, energy is partially transferred to OCP as well. These results demonstrate the feasibility of controlling the pathway of energy transfer using light intensity in an engineered light-harvesting system.
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Affiliation(s)
| | - Su Lin
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | | | | | - Hao Yan
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Neal W Woodbury
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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37
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Chatelain G, Clavé G, Saint-Pierre C, Gasparutto D, Campidelli S. Self-assembly of porphyrin–DNA hybrids into large flat nanostructures. Org Biomol Chem 2017; 15:6257-6263. [DOI: 10.1039/c7ob01267e] [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
Two complementary 21-mer oligonucleotide/porphyrin hybrids were synthesized and assembled into nanostructures.
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Affiliation(s)
| | - G. Clavé
- LICSEN
- NIMBE
- CEA
- CNRS
- Université Paris-Saclay
| | - C. Saint-Pierre
- Université Grenoble Alpes
- INAC-SyMMES/UMR 5819 CEA-CNRS-UGA
- CEA-Grenoble
- F-38000 Grenoble
- France
| | - D. Gasparutto
- Université Grenoble Alpes
- INAC-SyMMES/UMR 5819 CEA-CNRS-UGA
- CEA-Grenoble
- F-38000 Grenoble
- France
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38
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Olejko L, Bald I. FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems. RSC Adv 2017. [DOI: 10.1039/c7ra02114c] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Artificial light harvesting complexes find applications in photosynthesis, photovoltaics and chemical sensors. Here, we present the characterization and optimization of a multi-color artificial light harvesting system on DNA origami structures.
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Affiliation(s)
- L. Olejko
- Department of Chemistry
- Physical Chemistry
- University of Potsdam
- 14476 Potsdam
- Germany
| | - I. Bald
- Department of Chemistry
- Physical Chemistry
- University of Potsdam
- 14476 Potsdam
- Germany
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39
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Probst M, Aeschimann W, Chau TTH, Langenegger SM, Stocker A, Häner R. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease. Nucleic Acids Res 2016; 44:7079-89. [PMID: 27422870 PMCID: PMC5009758 DOI: 10.1093/nar/gkw644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023] Open
Abstract
The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.
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Affiliation(s)
- Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Walter Aeschimann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Thi T H Chau
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
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40
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Mutsamwira S, Ainscough EW, Partridge AC, Derrick PJ, Filichev VV. G-Quadruplex Supramolecular Assemblies in Photochemical Upconversion. Chemistry 2016; 22:10376-81. [DOI: 10.1002/chem.201601353] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/04/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Saymore Mutsamwira
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
| | - Eric W. Ainscough
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
| | - Ashton C. Partridge
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
- Department of Physics and School of Engineering; The University of Auckland; 20 Symonds Street Auckland New Zealand
| | - Peter J. Derrick
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
- Department of Physics and School of Engineering; The University of Auckland; 20 Symonds Street Auckland New Zealand
| | - Vyacheslav V. Filichev
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
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41
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Olejko L, Cywiński PJ, Bald I. An ion-controlled four-color fluorescent telomeric switch on DNA origami structures. NANOSCALE 2016; 8:10339-10347. [PMID: 27138897 DOI: 10.1039/c6nr00119j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The folding of single-stranded telomeric DNA into guanine (G) quadruplexes is a conformational change that plays a major role in sensing and drug targeting. The telomeric DNA can be placed on DNA origami nanostructures to make the folding process extremely selective for K(+) ions even in the presence of high Na(+) concentrations. Here, we demonstrate that the K(+)-selective G-quadruplex formation is reversible when using a cryptand to remove K(+) from the G-quadruplex. We present a full characterization of the reversible switching between single-stranded telomeric DNA and G-quadruplex structures using Förster resonance energy transfer (FRET) between the dyes fluorescein (FAM) and cyanine3 (Cy3). When attached to the DNA origami platform, the G-quadruplex switch can be incorporated into more complex photonic networks, which is demonstrated for a three-color and a four-color FRET cascade from FAM over Cy3 and Cy5 to IRDye700 with G-quadruplex-Cy3 acting as a switchable transmitter.
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Affiliation(s)
- L Olejko
- Department of Chemistry, Physical Chemistry, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
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42
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Hemmig EA, Creatore C, Wünsch B, Hecker L, Mair P, Parker MA, Emmott S, Tinnefeld P, Keyser UF, Chin AW. Programming Light-Harvesting Efficiency Using DNA Origami. NANO LETTERS 2016; 16:2369-74. [PMID: 26906456 PMCID: PMC5003508 DOI: 10.1021/acs.nanolett.5b05139] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The remarkable performance and quantum efficiency of biological light-harvesting complexes has prompted a multidisciplinary interest in engineering biologically inspired antenna systems as a possible route to novel solar cell technologies. Key to the effectiveness of biological "nanomachines" in light capture and energy transport is their highly ordered nanoscale architecture of photoactive molecules. Recently, DNA origami has emerged as a powerful tool for organizing multiple chromophores with base-pair accuracy and full geometric freedom. Here, we present a programmable antenna array on a DNA origami platform that enables the implementation of rationally designed antenna structures. We systematically analyze the light-harvesting efficiency with respect to number of donors and interdye distances of a ring-like antenna using ensemble and single-molecule fluorescence spectroscopy and detailed Förster modeling. This comprehensive study demonstrates exquisite and reliable structural control over multichromophoric geometries and points to DNA origami as highly versatile platform for testing design concepts in artificial light-harvesting networks.
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Affiliation(s)
- Elisa A. Hemmig
- Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Celestino Creatore
- Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Bettina Wünsch
- Institut
für Physikalische und Theoretische Chemie, TU Braunschweig, 38106 Braunschweig, Germany
| | - Lisa Hecker
- Institut
für Physikalische und Theoretische Chemie, TU Braunschweig, 38106 Braunschweig, Germany
| | - Philip Mair
- Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - M. Andy Parker
- Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Stephen Emmott
- Computational
Science Laboratory, Microsoft Research, Cambridge CB1 2FB, United Kingdom
| | - Philip Tinnefeld
- Institut
für Physikalische und Theoretische Chemie, TU Braunschweig, 38106 Braunschweig, Germany
| | - Ulrich F. Keyser
- Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
- E-mail:
| | - Alex W. Chin
- Cavendish Laboratory, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
- E-mail:
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43
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Wächtler M, Kübel J, Barthelmes K, Winter A, Schmiedel A, Pascher T, Lambert C, Schubert US, Dietzek B. Energy transfer and formation of long-lived 3MLCT states in multimetallic complexes with extended highly conjugated bis-terpyridyl ligands. Phys Chem Chem Phys 2016; 18:2350-60. [DOI: 10.1039/c5cp04447b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Multimetallic complexes with extended conjugated ligands show efficient energy transfer to the lowest excited states and prolonged Fe(ii) 3MLCT lifetimes.
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Affiliation(s)
- Maria Wächtler
- Leibniz Institute of Photonic Technology e.V
- 07745 Jena
- Germany
| | - Joachim Kübel
- Leibniz Institute of Photonic Technology e.V
- 07745 Jena
- Germany
- Institute of Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
| | - Kevin Barthelmes
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - Andreas Winter
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - Alexander Schmiedel
- Institut für Organische Chemie
- Universität Würzburg
- Wilhelm Conrad Röntgen Research Center for Complex Material Systems
- Center for Nanosystems Chemistry
- 97074 Würzburg
| | | | - Christoph Lambert
- Institut für Organische Chemie
- Universität Würzburg
- Wilhelm Conrad Röntgen Research Center for Complex Material Systems
- Center for Nanosystems Chemistry
- 97074 Würzburg
| | - Ulrich S. Schubert
- Laboratory of Organic and Macromolecular Chemistry (IOMC)
- Friedrich Schiller University Jena
- 07743 Jena
- Germany
- Jena Center for Soft Matter (JCSM)
| | - Benjamin Dietzek
- Leibniz Institute of Photonic Technology e.V
- 07745 Jena
- Germany
- Institute of Physical Chemistry and Abbe Center of Photonics
- Friedrich Schiller University Jena
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44
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Mutsamwira S, Ainscough EW, Partridge AC, Derrick PJ, Filichev VV. DNA-Based Assemblies for Photochemical Upconversion. J Phys Chem B 2015; 119:14045-52. [DOI: 10.1021/acs.jpcb.5b07489] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saymore Mutsamwira
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Eric W. Ainscough
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Ashton C. Partridge
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
- Department
of Physics and School of Engineering, The University of Auckland, 20 Symonds Street, Auckland 1010, New Zealand
| | - Peter J. Derrick
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
- Department
of Physics and School of Engineering, The University of Auckland, 20 Symonds Street, Auckland 1010, New Zealand
| | - Vyacheslav V. Filichev
- Institute
of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
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45
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Kryjewski M, Goslinski T, Mielcarek J. Functionality stored in the structures of cyclodextrin–porphyrinoid systems. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.04.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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46
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Use of biomolecular scaffolds for assembling multistep light harvesting and energy transfer devices. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2015. [DOI: 10.1016/j.jphotochemrev.2014.12.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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48
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Assembling programmable FRET-based photonic networks using designer DNA scaffolds. Nat Commun 2014; 5:5615. [PMID: 25504073 PMCID: PMC4275599 DOI: 10.1038/ncomms6615] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022] Open
Abstract
DNA demonstrates a remarkable capacity for creating designer nanostructures and devices. A growing number of these structures utilize Förster resonance energy transfer (FRET) as part of the device's functionality, readout or characterization, and, as device sophistication increases so do the concomitant FRET requirements. Here we create multi-dye FRET cascades and assess how well DNA can marshal organic dyes into nanoantennae that focus excitonic energy. We evaluate 36 increasingly complex designs including linear, bifurcated, Holliday junction, 8-arm star and dendrimers involving up to five different dyes engaging in four-consecutive FRET steps, while systematically varying fluorophore spacing by Förster distance (R0). Decreasing R0 while augmenting cross-sectional collection area with multiple donors significantly increases terminal exciton delivery efficiency within dendrimers compared with the first linear constructs. Förster modelling confirms that best results are obtained when there are multiple interacting FRET pathways rather than independent channels by which excitons travel from initial donor(s) to final acceptor.
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49
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Clavé G, Chatelain G, Filoramo A, Gasparutto D, Saint-Pierre C, Le Cam E, Piétrement O, Guérineau V, Campidelli S. Synthesis of a multibranched porphyrin-oligonucleotide scaffold for the construction of DNA-based nano-architectures. Org Biomol Chem 2014; 12:2778-83. [PMID: 24668242 DOI: 10.1039/c4ob00202d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.
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Affiliation(s)
- Guillaume Clavé
- CEA Saclay, IRAMIS, NIMBE, Laboratoire d'Innovation en Chimie des Surfaces et Nanosciences (LICSEN), F-91191 Gif sur Yvette, France.
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Tamaki T, Nosaka T, Ogawa T. Synthesis of a series of Zinc(II)/freebase porphyrin dimers and trimers with programmable sequences from a common key molecule. J Org Chem 2014; 79:11029-38. [PMID: 25341080 DOI: 10.1021/jo502046d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have developed a new methodology that enables the synthesis of any sequence of metal porphyrin arrays starting from a common key molecule. Using this method, we prepared porphyrin dimers and trimers with varying component unit sequences via consecutive Suzuki coupling reactions using the same key porphyrin compound under the same reaction conditions. The key porphyrin compound was synthesized on a gram scale in one batch, and the coupling reactions afforded the desired oligomers in good yields. Thus, the prepared porphyrin arrays showed unique physical properties depending on the sequence of the central metals. The reaction is potentially applicable for the automated synthesis of porphyrin arrays.
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Affiliation(s)
- Takashi Tamaki
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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