1
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Hudson RJ, MacDonald TSC, Cole JH, Schmidt TW, Smith TA, McCamey DR. A framework for multiexcitonic logic. Nat Rev Chem 2024:10.1038/s41570-023-00566-y. [PMID: 38273177 DOI: 10.1038/s41570-023-00566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 01/27/2024]
Abstract
Exciton science sits at the intersection of chemical, optical and spin-based implementations of information processing, but using excitons to conduct logical operations remains relatively unexplored. Excitons encoding information could be read optically (photoexcitation-photoemission) or electrically (charge recombination-separation), travel through materials via exciton energy transfer, and interact with one another in stimuli-responsive molecular excitonic devices. Excitonic logic offers the potential to mediate electrical, optical and chemical information. Additionally, high-spin triplet and quintet (multi)excitons offer access to well defined spin states of relevance to magnetic field effects, classical spintronics and spin-based quantum information science. In this Roadmap, we propose a framework for developing excitonic computing based on singlet fission (SF) and triplet-triplet annihilation (TTA). Various molecular components capable of modulating SF/TTA for logical operations are suggested, including molecular photo-switching and multi-colour photoexcitation. We then outline a pathway for constructing excitonic logic devices, considering aspects of circuit assembly, logical operation synchronization, and exciton transport and amplification. Promising future directions and challenges are identified, and the potential for realizing excitonic computing in the near future is discussed.
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Affiliation(s)
- Rohan J Hudson
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Exciton Science
| | - Thomas S C MacDonald
- Australian Research Council Centre of Excellence in Exciton Science
- School of Physics, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jared H Cole
- Australian Research Council Centre of Excellence in Exciton Science
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Timothy W Schmidt
- Australian Research Council Centre of Excellence in Exciton Science
- School of Chemistry, UNSW Sydney, Sydney, New South Wales, Australia
| | - Trevor A Smith
- School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Exciton Science
| | - Dane R McCamey
- Australian Research Council Centre of Excellence in Exciton Science, .
- School of Physics, UNSW Sydney, Sydney, New South Wales, Australia.
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2
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Rolczynski BS, Díaz SA, Goldman ER, Medintz IL, Melinger JS. Investigating the dissipation of heat and quantum information from DNA-scaffolded chromophore networks. J Chem Phys 2024; 160:034105. [PMID: 38230810 DOI: 10.1063/5.0181034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024] Open
Abstract
Scaffolded molecular networks are important building blocks in biological pigment-protein complexes, and DNA nanotechnology allows analogous systems to be designed and synthesized. System-environment interactions in these systems are responsible for important processes, such as the dissipation of heat and quantum information. This study investigates the role of nanoscale molecular parameters in tuning these vibronic system-environment dynamics. Here, genetic algorithm methods are used to obtain nanoscale parameters for a DNA-scaffolded chromophore network based on comparisons between its calculated and measured optical spectra. These parameters include the positions, orientations, and energy level characteristics within the network. This information is then used to compute the dynamics, including the vibronic population dynamics and system-environment heat currents, using the hierarchical equations of motion. The dissipation of quantum information is identified by the system's transient change in entropy, which is proportional to the heat currents according to the second law of thermodynamics. These results indicate that the dissipation of quantum information is highly dependent on the particular nanoscale characteristics of the molecular network, which is a necessary first step before gleaning the systematic optimization rules. Subsequently, the I-concurrence dynamics are calculated to understand the evolution of the vibronic system's quantum entanglement, which are found to be long-lived compared to these system-bath dissipation processes.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, District of Columbia 20375, USA
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3
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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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4
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Tobiason M, Yurke B, Hughes WL. Generation of DNA oligomers with similar chemical kinetics via in-silico optimization. Commun Chem 2023; 6:226. [PMID: 37853171 PMCID: PMC10584830 DOI: 10.1038/s42004-023-01026-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Networks of interacting DNA oligomers are useful for applications such as biomarker detection, targeted drug delivery, information storage, and photonic information processing. However, differences in the chemical kinetics of hybridization reactions, referred to as kinetic dispersion, can be problematic for some applications. Here, it is found that limiting unnecessary stretches of Watson-Crick base pairing, referred to as unnecessary duplexes, can yield exceptionally low kinetic dispersions. Hybridization kinetics can be affected by unnecessary intra-oligomer duplexes containing only 2 base-pairs, and such duplexes explain up to 94% of previously reported kinetic dispersion. As a general design rule, it is recommended that unnecessary intra-oligomer duplexes larger than 2 base-pairs and unnecessary inter-oligomer duplexes larger than 7 base-pairs be avoided. Unnecessary duplexes typically scale exponentially with network size, and nearly all networks contain unnecessary duplexes substantial enough to affect hybridization kinetics. A new method for generating networks which utilizes in-silico optimization to mitigate unnecessary duplexes is proposed and demonstrated to reduce in-vitro kinetic dispersions as much as 96%. The limitations of the new design rule and generation method are evaluated in-silico by creating new oligomers for several designs, including three previously programmed reactions and one previously engineered structure.
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Affiliation(s)
- Michael Tobiason
- Department of Computer Science, Boise State University, Boise, ID, USA.
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID, USA
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID, USA
| | - William L Hughes
- School of Engineering, University of British Columbia Okanagan Campus, Kelowna, BC, Canada.
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5
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Exciton quantum dynamics in the molecular logic gates for quantum computing. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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6
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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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7
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Rolczynski BS, Díaz SA, Kim YC, Mathur D, Klein WP, Medintz IL, Melinger JS. Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms. Phys Chem Chem Phys 2023; 25:3651-3665. [PMID: 36648290 DOI: 10.1039/d2cp04960k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA.
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8
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Wright N, Huff JS, Barclay MS, Wilson CK, Barcenas G, Duncan KM, Ketteridge M, Obukhova OM, Krivoshey AI, Tatarets AL, Terpetschnig EA, Dean JC, Knowlton WB, Yurke B, Li L, Mass OA, Davis PH, Lee J, Turner DB, Pensack RD. Intramolecular Charge Transfer and Ultrafast Nonradiative Decay in DNA-Tethered Asymmetric Nitro- and Dimethylamino-Substituted Squaraines. J Phys Chem A 2023; 127:1141-1157. [PMID: 36705555 PMCID: PMC9923757 DOI: 10.1021/acs.jpca.2c06442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular (dye) aggregates are a materials platform of interest in light harvesting, organic optoelectronics, and nanoscale computing, including quantum information science (QIS). Strong excitonic interactions between dyes are key to their use in QIS; critically, properties of the individual dyes govern the extent of these interactions. In this work, the electronic structure and excited-state dynamics of a series of indolenine-based squaraine dyes incorporating dimethylamino (electron donating) and/or nitro (electron withdrawing) substituents, so-called asymmetric dyes, were characterized. The dyes were covalently tethered to DNA Holliday junctions to suppress aggregation and permit characterization of their monomer photophysics. A combination of density functional theory and steady-state absorption spectroscopy shows that the difference static dipole moment (Δd) successively increases with the addition of these substituents while simultaneously maintaining a large transition dipole moment (μ). Steady-state fluorescence and time-resolved absorption and fluorescence spectroscopies uncover a significant nonradiative decay pathway in the asymmetrically substituted dyes that drastically reduces their excited-state lifetime (τ). This work indicates that Δd can indeed be increased by functionalizing dyes with electron donating and withdrawing substituents and that, in certain classes of dyes such as these asymmetric squaraines, strategies may be needed to ensure long τ, e.g., by rigidifying the π-conjugated network.
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Affiliation(s)
- Nicholas
D. Wright
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Jonathan S. Huff
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Matthew S. Barclay
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - German Barcenas
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Katelyn M. Duncan
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Maia Ketteridge
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Olena M. Obukhova
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Alexander I. Krivoshey
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Anatoliy L. Tatarets
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | | | - Jacob C. Dean
- Department
of Physical Science, Southern Utah University, Cedar City, Utah 84720, United States
| | - William B. Knowlton
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Lan Li
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States,Center
for
Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Olga A. Mass
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States,Center
for
Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Jeunghoon Lee
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Daniel B. Turner
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Ryan D. Pensack
- †Micron
School of Materials Science & Engineering, ⊥Department of Electrical
& Computer Engineering, ○Department of Chemistry & Biochemistry, Boise State University, Boise, Idaho 83725, United States,
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9
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Fernandes R, Chowdhary S, Mikula N, Saleh N, Kanevche K, Berlepsch HV, Hosogi N, Heberle J, Weber M, Böttcher C, Koksch B. Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures. Angew Chem Int Ed Engl 2022; 61:e202208647. [PMID: 36161448 PMCID: PMC9828782 DOI: 10.1002/anie.202208647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/12/2023]
Abstract
Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.
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Affiliation(s)
- Rita Fernandes
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Suvrat Chowdhary
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Natalia Mikula
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Noureldin Saleh
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Katerina Kanevche
- Department of PhysicsExperimental Molecular BiophysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Hans v. Berlepsch
- Research Center for Electron Microscopy and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | | | - Joachim Heberle
- Department of PhysicsExperimental Molecular BiophysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Marcus Weber
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Christoph Böttcher
- Research Center for Electron Microscopy and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Beate Koksch
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
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10
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Huff J, Díaz S, Barclay MS, Chowdhury AU, Chiriboga M, Ellis GA, Mathur D, Patten LK, Roy SK, Sup A, Biaggne A, Rolczynski BS, Cunningham PD, Li L, Lee J, Davis PH, Yurke B, Knowlton WB, Medintz IL, Turner DB, Melinger JS, Pensack RD. Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:17164-17175. [PMID: 36268205 PMCID: PMC9575151 DOI: 10.1021/acs.jpcc.2c04336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/08/2022] [Indexed: 06/01/2023]
Abstract
Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates-aggregates of chemically distinct dyes-rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm-1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.
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Affiliation(s)
- Jonathan
S. Huff
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Sebastián
A. Díaz
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Matthew S. Barclay
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Azhad U. Chowdhury
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew Chiriboga
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
- Volgenau
School of Engineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Gregory A. Ellis
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Simon K. Roy
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Aaron Sup
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Austin Biaggne
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Brian S. Rolczynski
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Paul D. Cunningham
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Lan Li
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Daniel B. Turner
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Joseph S. Melinger
- Center for Bio/Molecular Science
and Engineering Code 6900, Electronics Science and
Technology Division Code 6800, U.S. Naval
Research Laboratory, Washington, District of Columbia 20375, United States
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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11
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Biaggne A, Kim YC, Melinger JS, Knowlton WB, Yurke B, Li L. Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions. RSC Adv 2022; 12:28063-28078. [PMID: 36320263 PMCID: PMC9530999 DOI: 10.1039/d2ra05045e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
Dye aggregates and their excitonic properties are of interest for their applications to organic photovoltaics, non-linear optics, and quantum information systems. DNA scaffolding has been shown to be effective at promoting the aggregation of dyes in a controllable manner. Specifically, isolated DNA Holliday junctions have been used to achieve strongly coupled cyanine dye dimers. However, the structural properties of the dimers and the DNA, as well as the role of Holliday junction isomerization are not fully understood. To study the dynamics of cyanine dimers in DNA, molecular dynamics simulations were carried out for adjacent and transverse dimers attached to Holliday junctions in two different isomers. It was found that dyes attached to adjacent strands in the junction exhibit stronger dye-DNA interactions and larger inter-dye separations compared to transversely attached dimers, as well as end-to-end arrangements. Transverse dimers exhibit lower inter-dye separations and more stacked configurations. Furthermore, differences in Holliday junction isomer are analyzed and compared to dye orientations. For transverse dyes exhibiting the smaller inter-dye separations, excitonic couplings were calculated and shown to be in agreement with experiment. Our results suggested that dye attachment locations on DNA Holliday junctions affect dye-DNA interactions, dye dynamics, and resultant dye orientations which can guide the design of DNA-templated cyanine dimers with desired properties. Molecular dynamics simulations reveal dye attachment and DNA Holliday junction isomer effects on dye dimer orientations and excitonic couplings. These simulations can guide synthesis and experiments of dye-DNA structures for excitonic applications.![]()
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research LaboratoryWashingtonDC20375USA
| | - Joseph. S. Melinger
- Electronics Science and Technology Division, U.S. Naval Research LaboratoryWashingtonDC20375USA
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Department of Electrical and Computer Engineering, Boise State UniversityBoiseID 83725USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Department of Electrical and Computer Engineering, Boise State UniversityBoiseID 83725USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State UniversityBoiseID 83725USA,Center for Advanced Energy StudiesIdaho FallsID 83401USA
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12
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Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction. Molecules 2022; 27:molecules27134006. [PMID: 35807250 PMCID: PMC9268628 DOI: 10.3390/molecules27134006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/18/2022] [Accepted: 06/18/2022] [Indexed: 12/04/2022] Open
Abstract
A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye–dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.
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13
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Algar WR, Krause KD. Developing FRET Networks for Sensing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:17-36. [PMID: 35300526 DOI: 10.1146/annurev-anchem-061020-014925] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Förster resonance energy transfer (FRET) is a widely used fluorescence-based sensing mechanism. To date, most implementations of FRET sensors have relied on a discrete donor-acceptor pair for detection of each analytical target. FRET networks are an emerging concept in which target recognition perturbs a set of interconnected FRET pathways between multiple emitters. Here, we review the energy transfer topologies and scaffold materials for FRET networks, propose a general nomenclature, and qualitatively summarize the dynamics of the competitive, sequential, homoFRET, and heteroFRET pathways that constitute FRET networks. Implementations of FRET networks for sensing are also described, including concentric FRET probes, other single-vector multiplexing, and logic gates and switches. Unresolved questions and future research directions for current systems are discussed, as are potential but currently unexplored applications of FRET networks in sensing.
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Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada;
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada;
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14
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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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15
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Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates. Molecules 2022; 27:molecules27113456. [PMID: 35684394 PMCID: PMC9182218 DOI: 10.3390/molecules27113456] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023] Open
Abstract
Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1cm−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.
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16
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Barclay MS, Wilson CK, Roy SK, Mass OA, Obukhova OM, Svoiakov RP, Tatarets AL, Chowdhury AU, Huff JS, Turner DB, Davis PH, Terpetschnig EA, Yurke B, Knowlton WB, Lee J, Pensack RD. Oblique Packing and Tunable Excitonic Coupling in DNA‐Templated Squaraine Rotaxane Dimer Aggregates. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matthew S. Barclay
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Christopher K. Wilson
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Simon K. Roy
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Olga A. Mass
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Olena M. Obukhova
- SSI Institute for Single Crystals NAS of Ukraine: Naukovo-tehnologicnij kompleks Institut monokristaliv Nacional'na akademia nauk Ukraini Department of Luminescent Materials and Dyes UKRAINE
| | - Rostyslav P. Svoiakov
- SSI Institute for Single Crystals NAS of Ukraine: Naukovo-tehnologicnij kompleks Institut monokristaliv Nacional'na akademia nauk Ukraini Department of Luminescent Materials and Dyes UKRAINE
| | - Anatoliy L. Tatarets
- SSI Institute for Single Crystals NAS of Ukraine: Naukovo-tehnologicnij kompleks Institut monokristaliv Nacional'na akademia nauk Ukraini Department of Luminescent Materials and Dyes UKRAINE
| | - Azhad U. Chowdhury
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Jonathan S. Huff
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Daniel B. Turner
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | - Paul H. Davis
- Boise State University Micron School of Materials Science & Engineering UNITED STATES
| | | | - Bernard Yurke
- Boise State University Micron School of Materials Science & Engineering; Department of Electrical & Computer Engineering UNITED STATES
| | - William B. Knowlton
- Boise State University Micron School of Materials Science & Engineering; Department of Electrical & Computer Engineering UNITED STATES
| | - Jeunghoon Lee
- Boise State University Micron School of Materials Science & Engineering; Department of Chemistry & Biochemistry UNITED STATES
| | - Ryan D. Pensack
- Boise State University Micron School of Materials Science & Engineering 1435 W University Dr 83706 Boise UNITED STATES
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17
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Chowdhury A, Díaz S, Huff JS, Barclay MS, Chiriboga M, Ellis GA, Mathur D, Patten LK, Sup A, Hallstrom N, Cunningham PD, Lee J, Davis PH, Turner DB, Yurke B, Knowlton WB, Medintz IL, Melinger JS, Pensack RD. Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates. J Phys Chem Lett 2022; 13:2782-2791. [PMID: 35319215 PMCID: PMC8978177 DOI: 10.1021/acs.jpclett.2c00017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Molecular excitons, which propagate spatially via electronic energy transfer, are central to numerous applications including light harvesting, organic optoelectronics, and nanoscale computing; they may also benefit applications such as photothermal therapy and photoacoustic imaging through the local generation of heat via rapid excited-state quenching. Here we show how to tune between energy transfer and quenching for heterodimers of the same pair of cyanine dyes by altering their spatial configuration on a DNA template. We assemble "transverse" and "adjacent" heterodimers of Cy5 and Cy5.5 using DNA Holliday junctions. We find that the transverse heterodimers exhibit optical properties consistent with excitonically interacting dyes and fluorescence quenching, while the adjacent heterodimers exhibit optical properties consistent with nonexcitonically interacting dyes and disproportionately large Cy5.5 emission, suggestive of energy transfer between dyes. We use transient absorption spectroscopy to show that quenching in the transverse heterodimer occurs via rapid nonradiative decay to the ground state (∼31 ps) and that in the adjacent heterodimer rapid energy transfer from Cy5 to Cy5.5 (∼420 fs) is followed by Cy5.5 excited-state relaxation (∼700 ps). Accessing such drastically different photophysics, which may be tuned on demand for different target applications, highlights the utility of DNA as a template for dye aggregation.
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Affiliation(s)
- Azhad
U. Chowdhury
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Sebastián
A. Díaz
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Jonathan S. Huff
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew S. Barclay
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew Chiriboga
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
- Volgenau
School of Engineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Gregory A. Ellis
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of
Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Aaron Sup
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Natalya Hallstrom
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul D. Cunningham
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H. Davis
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Daniel B. Turner
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Igor L. Medintz
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S. Melinger
- Center for Bio/Molecular
Science and Engineering Code 6900 and Electronics Science
and Technology Division Code 6800, U.S.
Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Physics, Department of Chemistry
& Biochemistry, and Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
- (R.D.P.) Email
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18
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. A DNA‐Based Two‐Component Excitonic Switch Utilizing High‐Performance Diarylethenes. Angew Chem Int Ed Engl 2022; 61:e202117735. [PMID: 35076154 PMCID: PMC9305942 DOI: 10.1002/anie.202117735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 11/13/2022]
Abstract
Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2′‐deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non‐nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all‐optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double‐methylated 2′‐deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster‐Resonance‐Energy‐Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance‐ and orientation‐dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.
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Affiliation(s)
- Simon M. Büllmann
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Nicolas F. Zorn
- Institute for Physical Chemistry Heidelberg University Im Neuenheimer Feld 253 69120 Heidelberg Germany
| | - Jana Zaumseil
- Institute for Physical Chemistry Heidelberg University Im Neuenheimer Feld 253 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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19
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Hart SM, Wang X, Guo J, Bathe M, Schlau-Cohen GS. Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds. J Phys Chem Lett 2022; 13:1863-1871. [PMID: 35175058 DOI: 10.1021/acs.jpclett.1c03848] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular materials for light harvesting, computing, and fluorescence imaging require nanoscale integration of electronically active subunits. Variation in the optical absorption and emission properties of the subunits has primarily been achieved through modifications to the chemical structure, which is often synthetically challenging. Here, we introduce a facile method for varying optical absorption and emission properties by changing the geometry of a strongly coupled Cy3 dimer on a double-crossover (DX) DNA tile. Leveraging the versatility and programmability of DNA, we tune the length of the complementary strand so that it "pushes" or "pulls" the dimer, inducing dramatic changes in the photophysics including lifetime differences observable at the ensemble and single-molecule level. The separable lifetimes, along with environmental sensitivity also observed in the photophysics, suggest that the Cy3-DX tile constructs could serve as fluorescence probes for multiplexed imaging. More generally, these constructs establish a framework for easily controllable photophysics via geometric changes to coupled chromophores, which could be applied in light-harvesting devices and molecular electronics.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jiajia Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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20
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Mass OA, Wilson CK, Barcenas G, Terpetschnig EA, Obukhova OM, Kolosova OS, Tatarets AL, Li L, Yurke B, Knowlton WB, Pensack RD, Lee J. Influence of Hydrophobicity on Excitonic Coupling in DNA-Templated Indolenine Squaraine Dye Aggregates. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:3475-3488. [PMID: 35242270 PMCID: PMC8883467 DOI: 10.1021/acs.jpcc.1c08981] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/15/2022] [Indexed: 06/01/2023]
Abstract
Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn-Renger-May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm-1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
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Affiliation(s)
- Olga A. Mass
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - German Barcenas
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | | | - Olena M. Obukhova
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Olga S. Kolosova
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Anatoliy L. Tatarets
- State
Scientific Institution “Institute for Single Crystals”
of National Academy of Sciences of Ukraine, Kharkiv 61072, Ukraine
| | - Lan Li
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Center
for Advanced Energy Studies, Idaho
Falls, Idaho 83401, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ryan. D. Pensack
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Chemistry and Biochemistry, Boise State
University, Boise, Idaho 83725, United
States
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21
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. Ein DNA‐basierter exzitonischer Zweikomponenten‐Schalter auf der Grundlage von Hochleistungs‐Diarylethenen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simon M. Büllmann
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
| | - Theresa Kolmar
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
| | - Nicolas F. Zorn
- Physikalisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Jana Zaumseil
- Physikalisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Andres Jäschke
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
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22
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Roy S, Mass OA, Kellis DL, Wilson CK, Hall JA, Yurke B, Knowlton WB. Exciton Delocalization and Scaffold Stability in Bridged Nucleotide-Substituted, DNA Duplex-Templated Cyanine Aggregates. J Phys Chem B 2021; 125:13670-13684. [PMID: 34894675 PMCID: PMC8713290 DOI: 10.1021/acs.jpcb.1c07602] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/04/2021] [Indexed: 11/28/2022]
Abstract
Molecular excitons play a foundational role in chromophore aggregates found in light-harvesting systems and offer potential applications in engineered excitonic systems. Controlled aggregation of chromophores to promote exciton delocalization has been achieved by covalently tethering chromophores to deoxyribonucleic acid (DNA) scaffolds. Although many studies have documented changes in the optical properties of chromophores upon aggregation using DNA scaffolds, more limited work has investigated how structural modifications of DNA via bridged nucleotides and chromophore covalent attachment impact scaffold stability as well as the configuration and optical behavior of attached aggregates. Here we investigated the impact of two types of bridged nucleotides, LNA and BNA, as a structural modification of duplex DNA-templated cyanine (Cy5) aggregates. The bridged nucleotides were incorporated in the domain of one to four Cy5 chromophores attached between adjacent bases of a DNA duplex. We found that bridged nucleotides increase the stability of DNA scaffolds carrying Cy5 aggregates in comparison with natural nucleotides in analogous constructs. Exciton coupling strength and delocalization in Cy5 aggregates were evaluated via steady-state absorption, circular dichroism, and theoretical modeling. Replacing natural nucleotides with bridged nucleotides resulted in a noticeable increase in the coupling strength (≥10 meV) between chromophores and increased H-like stacking behavior (i.e., more face-to-face stacking). Our results suggest that bridged nucleotides may be useful for increasing scaffold stability and coupling between DNA templated chromophores.
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Affiliation(s)
- Simon
K. Roy
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Olga A. Mass
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Donald L. Kellis
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K. Wilson
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - John A. Hall
- Division
of Research and Economic Development, Boise
State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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23
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Rolczynski BS, Díaz SA, Kim YC, Medintz IL, Cunningham PD, Melinger JS. Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes. J Phys Chem A 2021; 125:9632-9644. [PMID: 34709821 DOI: 10.1021/acs.jpca.1c07205] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Structural DNA nanotechnology is a promising approach to create chromophore networks with modular structures and Hamiltonians to control the material's functions. The functional behaviors of these systems depend on the interactions of the chromophores' vibronic states, as well as interactions with their environment. To optimize their functions, it is necessary to characterize the chromophore network's structural and energetic properties, including the electronic delocalization in some cases. In this study, parameters of interest are deduced in DNA-scaffolded Cyanine 3 and Cyanine 5 dimers. The methods include steady-state optical measurements, physical modeling, and a genetic algorithm approach. The parameters include the chromophore network's vibronic Hamiltonian, molecular positions, transition dipole orientations, and environmentally induced energy broadening. Additionally, the study uses temperature-dependent optical measurements to characterize the spectral broadening further. These combined results reveal the quantum mechanical delocalization, which is important for functions like coherent energy transport and quantum information applications.
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Affiliation(s)
- Brian S Rolczynski
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, 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
| | - Young C Kim
- Materials Science and Technology Division, Code 6300, U.S. Naval Research Laboratory, Washington, D.C. 20375, 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
| | - Paul D Cunningham
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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24
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Huff JS, Turner DB, Mass OA, Patten LK, Wilson CK, Roy SK, Barclay MS, Yurke B, Knowlton WB, Davis PH, Pensack RD. Excited-State Lifetimes of DNA-Templated Cyanine Dimer, Trimer, and Tetramer Aggregates: The Role of Exciton Delocalization, Dye Separation, and DNA Heterogeneity. J Phys Chem B 2021; 125:10240-10259. [PMID: 34473494 PMCID: PMC8450906 DOI: 10.1021/acs.jpcb.1c04517] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
DNA-templated molecular
(dye) aggregates are a novel class of materials
that have garnered attention in a broad range of areas including light
harvesting, sensing, and computing. Using DNA to template dye aggregation
is attractive due to the relative ease with which DNA nanostructures
can be assembled in solution, the diverse array of nanostructures
that can be assembled, and the ability to precisely position dyes
to within a few Angstroms of one another. These factors, combined
with the programmability of DNA, raise the prospect of designer materials
custom tailored for specific applications. Although considerable progress
has been made in characterizing the optical properties and associated
electronic structures of these materials, less is known about their
excited-state dynamics. For example, little is known about how the
excited-state lifetime, a parameter essential to many applications,
is influenced by structural factors, such as the number of dyes within
the aggregate and their spatial arrangement. In this work, we use
a combination of transient absorption spectroscopy and global target
analysis to measure excited-state lifetimes in a series of DNA-templated
cyanine dye aggregates. Specifically, we investigate six distinct
dimer, trimer, and tetramer aggregates—based on the ubiquitous
cyanine dye Cy5—templated using both duplex and Holliday junction
DNA nanostructures. We find that these DNA-templated Cy5 aggregates
all exhibit significantly reduced excited-state lifetimes, some by
more than 2 orders of magnitude, and observe considerable variation
among the lifetimes. We attribute the reduced excited-state lifetimes
to enhanced nonradiative decay and proceed to discuss various structural
factors, including exciton delocalization, dye separation, and DNA
heterogeneity, that may contribute to the observed reduction and variability
of excited-state lifetimes. Guided by insights from structural modeling,
we find that the reduced lifetimes and enhanced nonradiative decay
are most strongly correlated with the distance between the dyes. These
results inform potential tradeoffs between dye separation, excitonic
coupling strength, and excited-state lifetime that motivate deeper
mechanistic understanding, potentially via further dye and dye template
design.
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Affiliation(s)
- Jonathan S Huff
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Daniel B Turner
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Olga A Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Lance K Patten
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Christopher K Wilson
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Simon K Roy
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Matthew S Barclay
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States.,Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States.,Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
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25
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Barclay MS, Roy SK, Huff JS, Mass OA, Turner DB, Wilson CK, Kellis DL, Terpetschnig EA, Lee J, Davis PH, Yurke B, Knowlton WB, Pensack RD. Rotaxane rings promote oblique packing and extended lifetimes in DNA-templated molecular dye aggregates. Commun Chem 2021; 4:19. [PMID: 35474961 PMCID: PMC9037907 DOI: 10.1038/s42004-021-00456-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/14/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular excitons play a central role in natural and artificial light harvesting, organic electrònics, and nanoscale computing. The structure and dynamics of molecular excitons, critical to each application, are sensitively governed by molecular packing. Deoxyribonucleic acid (DNA) templating is a powerful approach that enables controlled aggregation via sub-nanometer positioning of molecular dyes. However, finer sub-Angstrom control of dye packing is needed to tailor excitonic properties for specific applications. Here, we show that adding rotaxane rings to squaraine dyes templated with DNA promotes an elusive oblique packing arrangement with highly desirable optical properties. Specifically, dimers of these squaraine:rotaxanes exhibit an absorption spectrum with near-equal intensity excitonically split absorption bands. Theoretical analysis indicates that the transitions are mostly electronic in nature and only have similar intensities over a narrow range of packing angles. Compared with squaraine dimers, squaraine:rotaxane dimers also exhibit extended excited-state lifetimes and less structural heterogeneity. The approach proposed here may be generally useful for optimizing excitonic materials for a variety of applications ranging from solar energy conversion to quantum information science.
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Affiliation(s)
- Matthew S. Barclay
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | - Simon K. Roy
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | - Jonathan S. Huff
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | - Olga A. Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | - Daniel B. Turner
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | - Christopher K. Wilson
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | - Donald L. Kellis
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
| | | | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
- Department of Chemistry & Biochemistry, Boise State University, Boise, ID 83725 USA
| | - Paul H. Davis
- 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
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID 83725 USA
| | - William B. Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID 83725 USA
| | - Ryan D. Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725 USA
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26
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Biaggne A, Knowlton WB, Yurke B, Lee J, Li L. Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations. Molecules 2021; 26:molecules26030524. [PMID: 33498306 PMCID: PMC7863957 DOI: 10.3390/molecules26030524] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of withdrawing substituents (W-W pairs) exhibiting the most negative solvation energies, suggesting dyes with W-W pairs are more soluble than others. With respect to pristine Cy5, the transition dipole moment was relatively unaffected upon substitution while numerous W-W pairs and pairs of donating and withdrawing substituents (D-W pairs) enhanced the static dipole difference. The increase in static dipole difference was correlated with an increase in the magnitude of the sum of the Hammett constants of the substituents on the dye. The results of this study provide insight into how specific substituents affect Cy5 monomers and which pairs can be used to engineer dyes with desired properties.
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Affiliation(s)
- Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- 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; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (W.B.K.); (B.Y.); (J.L.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
- Correspondence:
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27
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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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28
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Cunningham PD, Díaz SA, Yurke B, Medintz IL, Melinger JS. Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers. J Phys Chem B 2020; 124:8042-8049. [PMID: 32706583 DOI: 10.1021/acs.jpcb.0c06732] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.
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Affiliation(s)
- Paul D Cunningham
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Sebastián A Díaz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Bernard Yurke
- Boise State University, Boise, Idaho 83725, United States
| | - Igor L Medintz
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S Melinger
- U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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29
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Liu J, Guillemeney L, Abécassis B, Coolen L. Long Range Energy Transfer in Self-Assembled Stacks of Semiconducting Nanoplatelets. NANO LETTERS 2020; 20:3465-3470. [PMID: 32315197 DOI: 10.1021/acs.nanolett.0c00376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fluorescent emitters like ions, dye molecules, or semiconductor nanoparticles are widely used in optoelectronic devices, usually within densely packed layers. Their luminescence properties can then be very different from when they are isolated, because of short-range interparticle interactions such as Förster resonant energy transfer (FRET). Understanding these interactions is crucial to mitigate FRET-related losses and could also lead to new energy transfer strategies. Exciton migration by FRET hopping between consecutive neighbor fluorophores has been evidenced in various systems but was generally limited to distances of tens of nanometers and involved only a few emitters. Here, we image self-assembled linear chains of CdSe nanoplatelets (colloidal quantum wells) and demonstrate exciton migration over 500 nm distances, corresponding to FRET hopping over 90 platelets. By comparing a diffusion-equation model to our experimental data, we measure a (1.5 ps)-1 FRET rate, much faster than all decay mechanisms, so that strong FRET-mediated collective photophysical effects can be expected.
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Affiliation(s)
- Jiawen Liu
- Sorbonne Université, CNRS, Institut de NanoSciences de Paris, INSP, F-75005 Paris, France
| | - Lilian Guillemeney
- Université de Lyon, CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, F-69007 Lyon, France
| | - Benjamin Abécassis
- Université de Lyon, CNRS, École Normale Supérieure de Lyon, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, F-69007 Lyon, France
| | - Laurent Coolen
- Sorbonne Université, CNRS, Institut de NanoSciences de Paris, INSP, F-75005 Paris, France
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30
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Zhang Y, Reinhardt A, Wang P, Song J, Ke Y. Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand. Angew Chem Int Ed Engl 2020; 59:8594-8600. [PMID: 32043698 DOI: 10.1002/anie.201915063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/13/2020] [Indexed: 01/13/2023]
Abstract
Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a "seed" strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4-7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100082, China
| | - Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jie Song
- Department of Instrument Science and Engineering, School of Electronic Information and electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA, 30322, USA
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31
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Zhang Y, Reinhardt A, Wang P, Song J, Ke Y. Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering College of Materials Science and Engineering Beijing University of Chemical Technology Beijing 100082 China
| | - Aleks Reinhardt
- Department of Chemistry University of Cambridge Cambridge CB2 1EW UK
| | - Pengfei Wang
- Institute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Jie Song
- Department of Instrument Science and Engineering School of Electronic Information and electrical Engineering Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Emory University School of Medicine Atlanta GA 30322 USA
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32
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Huff JS, Davis PH, Christy A, Kellis DL, Kandadai N, Toa ZSD, Scholes GD, Yurke B, Knowlton WB, Pensack RD. DNA-Templated Aggregates of Strongly Coupled Cyanine Dyes: Nonradiative Decay Governs Exciton Lifetimes. J Phys Chem Lett 2019; 10:2386-2392. [PMID: 31010285 DOI: 10.1021/acs.jpclett.9b00404] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. We report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.
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Affiliation(s)
| | | | | | | | | | - Zi S D Toa
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Gregory D Scholes
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
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33
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Zhu P, Fu W, Wei S, Liu X, Wang C, Lu Y, Shang Y, Wu X, Wu Y, Zhu S. A high-throughput and ultrasensitive identification methodology for unauthorized GMP component based on suspension array and logical calculator. Sci Rep 2019; 9:7311. [PMID: 31086245 PMCID: PMC6513989 DOI: 10.1038/s41598-019-43863-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/24/2019] [Indexed: 01/08/2023] Open
Abstract
To solve the problem of the unauthorized GMP components within import and export goods, the LI-US (Logic Identification of unauthorized GMP content by Universal-primer Suspension-array) system, which takes advantage of suspension array and logic calculator, was developed in the present study. Seventeen signal input channels have been optimized and validated in our research to ensure the multiplex practicality of the LI-US system. Three LI-US logic gates, including a YES gate, an OR gate and an AND gate, were designed as different detection strategies for GMP identification. The feasibility and specificity of the LI-US system were validated in the present study. Combining the optimization and evaluation of the signal input procedure, the sensitivity of this LI-US system reached 0.05% of the GMP mass concentration. The practicability evaluation of LI-US demonstrated its application within different substrates and varieties. In conclusion, the LI-US system was developed with extremely high specificity, sensitivity and practicability among different substrates and varieties, which could meet the demands of unauthorized GMP contents for both import and export goods.
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Affiliation(s)
- Pengyu Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Wei Fu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Shuang Wei
- Guangdong Entry-Exit Inspection and Quarantine Bureau, Guangdong, 510000, China
| | - Xiao Liu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Chenguang Wang
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Yun Lu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Ying Shang
- Yunnan Insititute of Food Safety, Kunmming University of Science and technology, Yunnan, 650500, China
| | - Xiyang Wu
- Department of Food Science and Engineering, Jinan University, Guangzhou, 510000, China
| | - Yuping Wu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China.
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China.
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34
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Kellis DL, Sarter C, Cannon BL, Davis PH, Graugnard E, Lee J, Pensack RD, Kolmar T, Jäschke A, Yurke B, Knowlton WB. An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases. ACS NANO 2019; 13:2986-2994. [PMID: 30758934 DOI: 10.1021/acsnano.8b07504] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch's small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.
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Affiliation(s)
- Donald L Kellis
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Christopher Sarter
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , 69120 Heidelberg , Germany
| | - Brittany L Cannon
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
- Department of Chemistry & Biochemistry , Boise State University , Boise , Idaho 83725 , United States
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , 69120 Heidelberg , Germany
| | - Bernard Yurke
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , United States
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35
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Augenstein Y, Vetter A, Lahijani BV, Herzig HP, Rockstuhl C, Kim MS. Inverse photonic design of functional elements that focus Bloch surface waves. LIGHT, SCIENCE & APPLICATIONS 2018; 7:104. [PMID: 30564310 PMCID: PMC6289961 DOI: 10.1038/s41377-018-0106-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 11/24/2018] [Indexed: 05/03/2023]
Abstract
Bloch surface waves (BSWs) are sustained at the interface of a suitably designed one-dimensional (1D) dielectric photonic crystal and an ambient material. The elements that control the propagation of BSWs are defined by a spatially structured device layer on top of the 1D photonic crystal that locally changes the effective index of the BSW. An example of such an element is a focusing device that squeezes an incident BSW into a tiny space. However, the ability to focus BSWs is limited since the index contrast achievable with the device layer is usually only on the order of Δn≈0.1 for practical reasons. Conventional elements, e.g., discs or triangles, which rely on a photonic nanojet to focus BSWs, operate insufficiently at such a low index contrast. To solve this problem, we utilize an inverse photonic design strategy to attain functional elements that focus BSWs efficiently into spatial domains slightly smaller than half the wavelength. Selected examples of such functional elements are fabricated. Their ability to focus BSWs is experimentally verified by measuring the field distributions with a scanning near-field optical microscope. Our focusing elements are promising ingredients for a future generation of integrated photonic devices that rely on BSWs, e.g., to carry information, or lab-on-chip devices for specific sensing applications.
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Affiliation(s)
- Yannick Augenstein
- Institute of Theoretical Solid State Physics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Andreas Vetter
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- SUSS MicroOptics SA, Rogues-Terres 61, Hauterive, 2068 Switzerland
| | - Babak Vosoughi Lahijani
- Optics & Photonics Technology Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Hans Peter Herzig
- Optics & Photonics Technology Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Carsten Rockstuhl
- Institute of Theoretical Solid State Physics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Myun-Sik Kim
- Optics & Photonics Technology Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
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36
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Sawaya NPD, Rappoport D, Tabor DP, Aspuru-Guzik A. Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling. ACS NANO 2018; 12:6410-6420. [PMID: 29920202 DOI: 10.1021/acsnano.8b00584] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Regulating energy transfer pathways through materials is a central goal of nanotechnology, as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. Here we introduce a proposal for a molecular exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. Our proposal relies on excitation migration via the second excited singlet (S2) state of the gate molecule. It exhibits the following features, only a subset of which are present in previous exciton switching schemes: picosecond time scale actuation, amplification/gain behavior, and a lack of molecular rearrangement. We demonstrate that the device can be used to produce universal binary logic or amplification of an exciton current, providing an excitonic platform with several potential uses, including signal processing for microscopy and spectroscopy methods that implement tunable exciton flux.
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Affiliation(s)
- Nicolas P D Sawaya
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
- Intel Laboratories , Santa Clara , California 95054 , United States
| | - Dmitrij Rappoport
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Daniel P Tabor
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
- Senior Fellow, Canadian Institute for Advanced Research, Bioinspired Solar Energy Program , Toronto , ON M5G 1Z8 , Canada
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37
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Peveler WJ, Algar WR. More Than a Light Switch: Engineering Unconventional Fluorescent Configurations for Biological Sensing. ACS Chem Biol 2018; 13:1752-1766. [PMID: 29461796 DOI: 10.1021/acschembio.7b01022] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence is a powerful and sensitive tool in biological detection, used widely for cellular imaging and in vitro molecular diagnostics. Over time, three prominent conventions have emerged in the design of fluorescent biosensors: a sensor is ideally specific for its target, only one fluorescence signal turns on or off in response to the target, and each target requires its own sensor and signal combination. These are conventions but not requirements, and sensors that break with one or more of these conventions can offer new capabilities and advantages. Here, we review "unconventional" fluorescent sensor configurations based on fluorescent dyes, proteins, and nanomaterials such as quantum dots and metal nanoclusters. These configurations include multifluorophore Förster resonance energy transfer (FRET) networks, temporal multiplexing, photonic logic, and cross-reactive arrays or "noses". The more complex but carefully engineered biorecognition and fluorescence signaling modalities in unconventional designs are richer in information, afford greater multiplexing capacity, and are potentially better suited to the analysis of complex biological samples, interactions, processes, and diseases. We conclude with a short perspective on the future of unconventional fluorescent sensors and encourage researchers to imagine sensing beyond the metaphorical light bulb and light switch combination.
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Affiliation(s)
- William J. Peveler
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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38
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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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39
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Pilo-Pais M, Acuna GP, Tinnefeld P, Liedl T. Sculpting Light by Arranging Optical Components with DNA Nanostructures. MRS BULLETIN 2017; 42:936-942. [PMID: 31168224 PMCID: PMC6546597 DOI: 10.1557/mrs.2017.278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA nanotechnology has developed into a state where the design and assembly of complex nanoscale structures has become fast, reliable, cost-effective, and accessible to non-experts. Nanometer-precise positioning of organic (dyes, biomolecules, etc.) and inorganic (metal nanoparticles, colloidal quantum dots, etc.) components on DNA nanostructures is straightforward and modular. In this perspective article, we identify the opportunities and challenges that DNA-assembled devices and materials are facing for optical antennas, metamaterials, and sensing applications. With the abilities of arranging hybrid materials in defined geometries, plasmonic effects will, for example, amplify molecular recognition transduction so that single-molecule events will be measureable with simple devices. On the larger scale, DNA nanotechnology has the potential of breaking the symmetry of common self-assembled functional materials creating pre-defined optical properties such as refractive index tuning, Bragg reflection and topological insulation.
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Affiliation(s)
- Mauricio Pilo-Pais
- Faculty of Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Guillermo P Acuna
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig University of Technology, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Department for Chemistry and Center for Nanoscience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience, Ludwig-Maximilians-Universität München, 80539, München, Germany
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40
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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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41
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Abstract
Self-assembled nucleic acids perform biological, chemical, and mechanical work at the nanoscale. DNA-based molecular machines have been designed here to perform work by reacting with cancer-specific miRNA mimics and then regulating gene expression in vitro by tuning RNA polymerase activity. Because RNA production is topologically restrained, the machines demonstrate chromatin analogous gene expression (CAGE). With modular and tunable design features, CAGE has potential for molecular biology, synthetic biology, and personalized medicine applications.
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Affiliation(s)
| | - William L. Hughes
- Micron School of Materials Science & Engineering
- College of Innovation + Design, Boise State University, Boise, Idaho 83725, United States
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42
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Massey M, Medintz IL, Ancona MG, Algar WR. Time-Gated FRET and DNA-Based Photonic Molecular Logic Gates: AND, OR, NAND, and NOR. ACS Sens 2017; 2:1205-1214. [PMID: 28787151 DOI: 10.1021/acssensors.7b00355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular logic devices (MLDs) constructed from DNA are promising for applications in bioanalysis, computing, and other applications requiring Boolean logic. These MLDs accept oligonucleotide inputs and generate fluorescence output through changes in structure. Although fluorescent dyes are most common in MLD designs, nontraditional luminescent materials with unique optical properties can potentially enhance MLD capabilities. In this context, luminescent lanthanide complexes (LLCs) have been largely overlooked. Here, we demonstrate a set of high-contrast DNA photonic logic gates based on toehold-mediated strand displacement and time-gated FRET. The gates include NAND, NOR, OR, and AND designs that accept two unlabeled target oligonucleotide sequences as inputs. Bright "true" output states utilize time-gated, FRET-sensitized emission from an Alexa Fluor 546 (A546) dye acceptor paired with a luminescent terbium cryptate (Tb) donor. Dark "false" output states are generated through either displacement of the A546, or through competitive and sequential quenching of the Tb or A546 by a dark quencher. Time-gated FRET and the long luminescence lifetime and spectrally narrow emission lines of the Tb donor enable 4-10-fold contrast between Boolean outputs, ≤10% signal variation for a common output, multicolor implementation of two logic gates in parallel, and effective performance in buffer and serum. These metrics exceed those reported for many other logic gate designs with only fluorescent dyes and with other non-LLC materials. Preliminary three-input AND and NAND gates are also demonstrated. The powerful combination of an LLC FRET donor with DNA-based logic gates is anticipated to have many future applications in bioanalysis.
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Affiliation(s)
- Melissa Massey
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | | | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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43
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Zadegan RM, Lindau EG, Klein WP, Green C, Graugnard E, Yurke B, Kuang W, Hughes WL. Twisting of DNA Origami from Intercalators. Sci Rep 2017; 7:7382. [PMID: 28785065 PMCID: PMC5547094 DOI: 10.1038/s41598-017-07796-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/10/2017] [Indexed: 02/07/2023] Open
Abstract
DNA nanostructures represent the confluence of materials science, computer science, biology, and engineering. As functional assemblies, they are capable of performing mechanical and chemical work. In this study, we demonstrate global twisting of DNA nanorails made from two DNA origami six-helix bundles. Twisting was controlled using ethidium bromide or SYBR Green I as model intercalators. Our findings demonstrate that DNA nanorails: (i) twist when subjected to intercalators and the amount of twisting is concentration dependent, and (ii) twisting saturates at elevated concentrations. This study provides insight into how complex DNA structures undergo conformational changes when exposed to intercalators and may be of relevance when exploring how intercalating drugs interact with condensed biological structures such as chromatin and chromosomes, as well as chromatin analogous gene expression devices.
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Affiliation(s)
- Reza M Zadegan
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Elias G Lindau
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - William P Klein
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Christopher Green
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Bernard Yurke
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - Wan Kuang
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho, 83725, United States
| | - William L Hughes
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho, 83725, United States.
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44
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Fresch B, Remacle F, Levine RD. Implementation of Probabilistic Algorithms by Multi-chromophoric Molecular Networks with Application to Multiple Travelling Pathways. Chemphyschem 2017; 18:1782-1789. [DOI: 10.1002/cphc.201700228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Barbara Fresch
- Department of Chemical Science; University of Padova; Via Marzolo 1 35131 Italy
| | - Françoise Remacle
- Department of Chemistry, B6c; University of Liege; B4000 Liege Belgium
- The Fritz Haber Center for Molecular Dynamics and Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Raphael D. Levine
- The Fritz Haber Center for Molecular Dynamics and Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
- Crump Institute for Molecular Imaging and Department of Molecular and Medical Pharmacology; David Geffen School of Medicine and Department of Chemistry and Biochemistry; University of California, Los Angeles; California 90095 USA
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45
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LaBoda CD, Lebeck AR, Dwyer CL. An Optically Modulated Self-Assembled Resonance Energy Transfer Pass Gate. NANO LETTERS 2017; 17:3775-3781. [PMID: 28488874 DOI: 10.1021/acs.nanolett.7b01112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We demonstrate an optically controlled molecular-scale pass gate that uses the photoinduced dark states of fluorescent molecules to modulate the flow of excitons. The device consists of four fluorophores spatially arranged on a self-assembled DNA nanostructure. Together, they form a resonance energy transfer (RET) network resembling a standard transistor with a source, channel, drain, and gate. When the gate fluorophore is directly excited, the device is toggled on. Excitons flow freely from the source to the drain, producing strong output fluorescence. Without this excitation, exciton flow through the device is hindered by absorbing paths along the way, resulting in weak output fluorescence. In this Letter, we describe the design and fabrication of the pass gate. We perform a steady-state analysis revealing that the on/off fluorescence ratio for this particular implementation is ∼8.7. To demonstrate dynamic modulation of the pass gate, we toggle the gate excitation on and off and measure the corresponding change in output fluorescence. We characterize the rise and fall times of these transitions, showing that they are faster and/or more easily achieved than other methods of RET network modulation. The pass gate is the first dynamic RET-based logic gate exclusively modulated by dark states and serves as a proof-of-concept device for building more complex RET systems in the future.
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Affiliation(s)
- Craig D LaBoda
- Department of Electrical and Computer Engineering and ‡Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Alvin R Lebeck
- Department of Electrical and Computer Engineering and ‡Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Chris L Dwyer
- Department of Electrical and Computer Engineering and ‡Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
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46
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Zhang Z, Wu Y, Yu F, Niu C, Du Z, Chen Y, Du J. Rapid and annealing-free self-assembly of DNA building blocks for 3D hydrogel chaperoned by cationic comb-type copolymers. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2017; 28:1511-1524. [PMID: 28514924 DOI: 10.1080/09205063.2017.1332706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The construction and self-assembly of DNA building blocks are the foundation of bottom-up development of three-dimensional DNA nanostructures or hydrogels. However, most self-assembly from DNA components is impeded by the mishybridized intermediates or the thermodynamic instability. To enable rapid production of complicated DNA objects with high yields no need for annealing process, herein different DNA building blocks (Y-shaped, L- and L'-shaped units) were assembled in presence of a cationic comb-type copolymer, poly (L-lysine)-graft-dextran (PLL-g-Dex), under physiological conditions. The results demonstrated that PLL-g-Dex not only significantly promoted the self-assembly of DNA blocks with high efficiency, but also stabilized the assembled multi-level structures especially for promoting the complicated 3D DNA hydrogel formation. This study develops a novel strategy for rapid and high-yield production of DNA hydrogel even derived from instable building blocks at relatively low DNA concentrations, which would endow DNA nanotechnology for more practical applications.
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Affiliation(s)
- Zheng Zhang
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
| | - Yuyang Wu
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
| | - Feng Yu
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
| | - Chaoqun Niu
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
| | - Zhi Du
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
| | - Yong Chen
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
| | - Jie Du
- a State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Provincial Key Laboratory of Research on Utilization of Si-Zr-Ti Resources , Hainan University , Haikou , P.R. China
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47
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Brown CW, Buckhout-White S, Díaz SA, Melinger JS, Ancona MG, Goldman ER, Medintz IL. Evaluating Dye-Labeled DNA Dendrimers for Potential Applications in Molecular Biosensing. ACS Sens 2017; 2:401-410. [PMID: 28723206 DOI: 10.1021/acssensors.6b00778] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA nanostructures provide a reliable and predictable scaffold for precisely positioning fluorescent dyes to form energy transfer cascades. Furthermore, these structures and their attendant dye networks can be dynamically manipulated by biochemical inputs, with the changes reflected in the spectral response. However, the complexity of DNA structures that have undergone such types of manipulation for direct biosensing applications is quite limited. Here, we investigate four different modification strategies to effect such dynamic manipulations using a DNA dendrimer scaffold as a testbed, and with applications to biosensing in mind. The dendrimer has a 2:1 branching ratio that organizes the dyes into a FRET-based antenna in which excitonic energy generated on multiple initial Cy3 dyes displayed at the periphery is then transferred inward through Cy3.5 and/or Cy5 relay dyes to a Cy5.5 final acceptor at the focus. Advantages of this design included good transfer efficiency, large spectral separation between the initial donor and final acceptor emissions for signal transduction, and an inherent tolerance to defects. Of the approaches to structural rearrangement, the first two mechanisms we consider employed either toehold-mediated strand displacement or strand replacement and their impact was mainly via direct transfer efficiency, while the other two were more global in their effect using either a belting mechanism or an 8-arm star nanostructure to compress the nanostructure and thereby modulate its spectral response through an enhancement in parallelism. The performance of these mechanisms, their ability to reset, and how they might be utilized in biosensing applications are discussed.
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Affiliation(s)
- Carl W. Brown
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | | | - Sebastián A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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48
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Wayment-Steele HK, Frenkel D, Reinhardt A. Investigating the role of boundary bricks in DNA brick self-assembly. SOFT MATTER 2017; 13:1670-1680. [PMID: 28165104 DOI: 10.1039/c6sm02719a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the standard DNA brick set-up, distinct 32-nucleotide strands of single-stranded DNA are each designed to bind specifically to four other such molecules. Experimentally, it has been demonstrated that the overall yield is increased if certain bricks which occur on the outer faces of target structures are merged with adjacent bricks. However, it is not well understood by what mechanism such 'boundary bricks' increase the yield, as they likely influence both the nucleation process and the final stability of the target structure. Here, we use Monte Carlo simulations with a patchy particle model of DNA bricks to investigate the role of boundary bricks in the self-assembly of complex multicomponent target structures. We demonstrate that boundary bricks lower the free-energy barrier to nucleation and that boundary bricks on edges stabilize the final structure. However, boundary bricks are also more prone to aggregation, as they can stabilize partially assembled intermediates. We explore some design strategies that permit us to benefit from the stabilizing role of boundary bricks whilst minimizing their ability to hinder assembly; in particular, we show that maximizing the total number of boundary bricks is not an optimal strategy.
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Affiliation(s)
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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49
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Olson X, Kotani S, Padilla JE, Hallstrom N, Goltry S, Lee J, Yurke B, Hughes WL, Graugnard E. Availability: A Metric for Nucleic Acid Strand Displacement Systems. ACS Synth Biol 2017; 6:84-93. [PMID: 26875531 PMCID: PMC5259754 DOI: 10.1021/acssynbio.5b00231] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 12/20/2022]
Abstract
DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.
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Affiliation(s)
- Xiaoping Olson
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Shohei Kotani
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Jennifer E. Padilla
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Natalya Hallstrom
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Sara Goltry
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - William L. Hughes
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron
School of Materials Science & Engineering, Department of Chemistry & Biochemistry, and Department of Electrical
& Computer Engineering, Boise State
University, 1910 University
Drive, Boise, Idaho 83725, United States
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50
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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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