1
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Cervantes-Salguero K, Kadrmas M, Ward BM, Lysne D, Wolf A, Piantanida L, Pascual G, Knowlton WB. Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10195-10207. [PMID: 38690801 PMCID: PMC11100016 DOI: 10.1021/acs.langmuir.4c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
With recent advances in DNA-templated dye aggregation for leveraging and engineering molecular excitons, a need exists for minimizing structural heterogeneity. Holliday Junction complexes (HJ) are commonly used to covalently template dye aggregates on their core; however, the global conformation of HJ is detrimentally dynamic. Here, the global conformation of the HJ is selectively tuned by restricting its position and orientation by using a sheet-like DNA origami construct (DOC) physisorbed on glass. The HJ arms are fixed with four different designed interduplex angles (IDAs). Atomic force microscopy confirmed that the HJs are bound to the surface of DOC with tuned IDAs. Dye orientation distributions were determined by combining dipole imaging and super-resolution microscopy. All IDAs led to dye orientations having dispersed distributions along planes perpendicular to the HJ plane, suggesting that stacking occurred between the dye and the neighboring DNA bases. The dye-base stacking interpretation was supported by increasing the size of the core cavity. The narrowest IDA minimizes structural heterogeneity and suggests dye intercalation. A strong correlation is found between the IDA and the orientation of the dye along the HJ plane. These results show that the HJ imposes restrictions on the dye and that the dye-DNA interactions are always present regardless of global conformation. The implications of our results are discussed for the scalability of dye aggregates using DNA self-assembly. Our methodology provides an avenue for the solid-supported single-molecule characterization of molecular assemblies templated on biomolecules─such as DNA and protein templates involved in light-harvesting and catalysis─with tuned conformations and restricted in position and orientation.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Madison Kadrmas
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Brett M. Ward
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Drew Lysne
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Amanda Wolf
- Biomolecular
Sciences Graduate Programs, Boise State
University, Boise, Idaho 83725, United States
| | - Luca Piantanida
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Gissela Pascual
- Micron
School of Materials Science and 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 and Computer Engineering, Boise State University, Boise, Idaho 83725, United States
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2
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Rode AJ, Arpin PC, Turner DB. Theoretical model of femtosecond coherence spectroscopy of vibronic excitons in molecular aggregates. J Chem Phys 2024; 160:164101. [PMID: 38647298 DOI: 10.1063/5.0200570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
When used as pump pulses in transient absorption spectroscopy measurements, femtosecond laser pulses can produce oscillatory signals known as quantum beats. The quantum beats arise from coherent superpositions of the states of the sample and are best studied in the Fourier domain using Femtosecond Coherence Spectroscopy (FCS), which consists of one-dimensional amplitude and phase plots of a specified oscillation frequency as a function of the detection frequency. Prior works have shown ubiquitous amplitude nodes and π phase shifts in FCS from excited-state vibrational wavepackets in monomer samples. However, the FCS arising from vibronic-exciton states in molecular aggregates have not been studied theoretically. Here, we use a model of vibronic-exciton states in molecular dimers based on displaced harmonic oscillators to simulate FCS for dimers in two important cases. Simulations reveal distinct spectral signatures of excited-state vibronic-exciton coherences in molecular dimers that may be used to distinguish them from monomer vibrational coherences. A salient result is that, for certain relative orientations of the transition dipoles, the key resonance condition between the electronic coupling and the frequency of the vibrational mode may yield strong enhancement of the quantum-beat amplitude and, perhaps, also cause a significant decrease of the oscillation frequency to a value far lower than the vibrational frequency. Future studies using these results will lead to new insights into the excited-state coherences generated in photosynthetic pigment-protein complexes.
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Affiliation(s)
- Alexander J Rode
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul C Arpin
- Department of Physics, California State University, Chico, Chico, California 95929, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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3
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Ratto A, Honek JF. Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry. Curr Med Chem 2024; 31:1172-1213. [PMID: 36915986 DOI: 10.2174/0929867330666230313141452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 03/15/2023]
Abstract
The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.
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Affiliation(s)
- Amanda Ratto
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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4
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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5
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Mass OA, Watt DR, Patten LK, Pensack RD, Lee J, Turner DB, Yurke B, Knowlton WB. Exciton delocalization in a fully synthetic DNA-templated bacteriochlorin dimer. Phys Chem Chem Phys 2023; 25:28437-28451. [PMID: 37843877 PMCID: PMC10599410 DOI: 10.1039/d3cp01634j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/23/2023] [Indexed: 10/17/2023]
Abstract
A bacteriochlorophyll a (Bchla) dimer is a basic functional unit in the LH1 and LH2 photosynthetic pigment-protein antenna complexes of purple bacteria, where an ordered, close arrangement of Bchla pigments-secured by noncovalent bonding to a protein template-enables exciton delocalization at room temperature. Stable and tunable synthetic analogs of this key photosynthetic subunit could lead to facile engineering of exciton-based systems such as in artificial photosynthesis, organic optoelectronics, and molecular quantum computing. Here, using a combination of synthesis and theory, we demonstrate that exciton delocalization can be achieved in a dimer of a synthetic bacteriochlorin (BC) featuring stability, high structural modularity, and spectral properties advantageous for exciton-based devices. The BC dimer was covalently templated by DNA, a stable and highly programmable scaffold. To achieve exciton delocalization in the absence of pigment-protein interactions critical for the Bchla dimer, we relied on the strong transition dipole moment in BC enabled by two auxochromes along the Qy transition, and omitting the central metal and isocyclic ring. The spectral properties of the synthetic "free" BC closely resembled those of Bchla in an organic solvent. Applying spectroscopic modeling, the exciton delocalization in the DNA-templated BC dimer was evaluated by extracting the excitonic hopping parameter, J to be 214 cm-1 (26.6 meV). For comparison, the same method applied to the natural protein-templated Bchla dimer yielded J of 286 cm-1 (35.5 meV). The smaller value of J in the BC dimer likely arose from the partial bacteriochlorin intercalation and the difference in medium effect between DNA and protein.
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Affiliation(s)
- Olga A Mass
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Devan R Watt
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Lance K Patten
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, USA.
- Department of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, USA
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6
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Hart SM, Gorman J, Bathe M, Schlau-Cohen GS. Engineering Exciton Dynamics with Synthetic DNA Scaffolds. Acc Chem Res 2023; 56:2051-2061. [PMID: 37345736 DOI: 10.1021/acs.accounts.3c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Excitons are the molecular-scale currency of electronic energy. Control over excitons enables energy to be directed and harnessed for light harvesting, electronics, and sensing. Excitonic circuits achieve such control by arranging electronically active molecules to prescribe desired spatiotemporal dynamics. Photosynthetic solar energy conversion is a canonical example of the power of excitonic circuits, where chromophores are positioned in a protein scaffold to perform efficient light capture, energy transport, and charge separation. Synthetic systems that aim to emulate this functionality include self-assembled aggregates, molecular crystals, and chromophore-modified proteins. While the potential of this approach is clear, these systems lack the structural precision to control excitons or even test the limits of their power. In recent years, DNA origami has emerged as a designer material that exploits biological building blocks to construct nanoscale architectures. The structural precision afforded by DNA origami has enabled the pursuit of naturally inspired organizational principles in a highly precise and scalable manner. In this Account, we describe recent developments in DNA-based platforms that spatially organize chromophores to construct tunable excitonic systems. The high fidelity of DNA base pairing enables the formation of programmable nanoscale architectures, and sequence-specific placement allows for the precise positioning of chromophores within the DNA structure. The integration of a wide range of chromophores across the visible spectrum introduces spectral tunability. These excitonic DNA-chromophore assemblies not only serve as model systems for light harvesting, solar conversion, and sensing but also lay the groundwork for the integration of coupled chromophores into larger-scale nucleic acid architectures.We have used this approach to generate DNA-chromophore assemblies of strongly coupled delocalized excited states through both sequence-specific self-assembly and the covalent attachment of chromophores. These strategies have been leveraged to independently control excitonic coupling and system-bath interaction, which together control energy transfer. We then extended this framework to identify how scaffold configurations can steer the formation of symmetry-breaking charge transfer states, paving the way toward the design of dual light-harvesting and charge separation DNA machinery. In an orthogonal application, we used the programmability of DNA chromophore assemblies to change the optical emission properties of strongly coupled dimers, generating a series of fluorophore-modified constructs with separable emission properties for fluorescence assays. Upcoming advances in the chemical modification of nucleotides, design of large-scale DNA origami, and predictive computational methods will aid in constructing excitonic assemblies for optical and computing applications. Collectively, the development of DNA-chromophore assemblies as a platform for excitonic circuitry offers a pathway to identifying and applying design principles for light harvesting and molecular electronics.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jeffrey Gorman
- Department of Biological Engineering, 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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7
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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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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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Barclay MS, Chowdhury AU, Biaggne A, Huff JS, Wright ND, Davis PH, Li L, Knowlton WB, Yurke B, Pensack RD, Turner DB. Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye. J Chem Phys 2023; 158:035101. [PMID: 36681650 DOI: 10.1063/5.0131795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA-Cy5), double-stranded DNA (dsDNA-Cy5), and Holliday junction DNA (HJ-DNA-Cy5). A line shape analysis of the 2D spectra reveals a strong excitation-emission correlation present in only the dsDNA-Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA-Cy5 complex. These insights will support future studies on DNA's structural heterogeneity.
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Affiliation(s)
- Matthew S Barclay
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Azhad U Chowdhury
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Austin Biaggne
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Jonathan S Huff
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas D Wright
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Paul H Davis
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Lan Li
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - William B Knowlton
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Bernard Yurke
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Ryan D Pensack
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
| | - Daniel B Turner
- Micron School for Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA
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10
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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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11
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Mass OA, Basu S, Patten LK, Terpetschnig EA, Krivoshey AI, Tatarets AL, Pensack RD, Yurke B, Knowlton WB, Lee J. Exciton Chirality Inversion in Dye Dimers Templated by DNA Holliday Junction. J Phys Chem Lett 2022; 13:10688-10696. [PMID: 36355575 PMCID: PMC9706552 DOI: 10.1021/acs.jpclett.2c02721] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
While only one enantiomer of chiral biomolecules performs a biological function, access to both enantiomers (or enantiomorphs) proved to be advantageous for technology. Using dye covalent attachment to a DNA Holliday junction (HJ), we created two pairs of dimers of bis(chloroindolenine)squaraine dye that enabled strongly coupled molecular excitons of opposite chirality in solution. The exciton chirality inversion was achieved by interchanging single covalent linkers of unequal length tethering the dyes of each dimer to the HJ core. Dimers in each pair exhibited profound exciton-coupled circular dichroism (CD) couplets of opposite signs. Dimer geometries, modeled by simultaneous fitting absorption and CD spectra, were related in each pair as nonsuperimposable and nearly exact mirror images. The origin of observed exciton chirality inversion was explained in the view of isomerization of the stacked Holliday junction. This study will open new opportunities for creating excitonic DNA-based materials that rely on programmable system chirality.
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Affiliation(s)
- Olga A. Mass
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Shibani Basu
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Lance K. Patten
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Ewald A. Terpetschnig
- SETA
BioMedicals, LLC, 2014
Silver Court East, Urbana, Illinois 61801, United
States
| | - Alexander I. Krivoshey
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, 60 Nauky Ave., 61072 Kharkiv, Ukraine
| | - Anatoliy L. Tatarets
- SSI
“Institute for Single Crystals” of the National Academy
of Sciences of Ukraine, 60 Nauky Ave., 61072 Kharkiv, Ukraine
| | - Ryan D. Pensack
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron
School of Materials Science & Engineering, Department of Electrical
& Computer Engineering, and Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725, United States
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12
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Hart SM, Banal JL, Castellanos MA, Markova L, Vyborna Y, Gorman J, Häner R, Willard AP, Bathe M, Schlau-Cohen GS. Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds. Chem Sci 2022; 13:13020-13031. [PMID: 36425503 PMCID: PMC9667922 DOI: 10.1039/d2sc02759c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/04/2022] [Indexed: 09/16/2023] Open
Abstract
Strongly-coupled multichromophoric assemblies orchestrate the absorption, transport, and conversion of photonic energy in natural and synthetic systems. Programming these functionalities involves the production of materials in which chromophore placement is precisely controlled. DNA nanomaterials have emerged as a programmable scaffold that introduces the control necessary to select desired excitonic properties. While the ability to control photophysical processes, such as energy transport, has been established, similar control over photochemical processes, such as interchromophore charge transfer, has not been demonstrated in DNA. In particular, charge transfer requires the presence of close-range interchromophoric interactions, which have a particularly steep distance dependence, but are required for eventual energy conversion. Here, we report a DNA-chromophore platform in which long-range excitonic couplings and short-range charge-transfer couplings can be tailored. Using combinatorial screening, we discovered chromophore geometries that enhance or suppress photochemistry. We combined spectroscopic and computational results to establish the presence of symmetry-breaking charge transfer in DNA-scaffolded squaraines, which had not been previously achieved in these chromophores. Our results demonstrate that the geometric control introduced through the DNA can access otherwise inaccessible processes and program the evolution of excitonic states of molecular chromophores, opening up opportunities for designer photoactive materials for light harvesting and computation.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Maria A Castellanos
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Larysa Markova
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Yuliia Vyborna
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
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13
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Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer Aggregates. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196612. [PMID: 36235149 PMCID: PMC9571668 DOI: 10.3390/molecules27196612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
Abstract
Molecular aggregates are of interest to a broad range of fields including light harvesting, organic optoelectronics, and nanoscale computing. In molecular aggregates, nonradiative decay pathways may emerge that were not present in the constituent molecules. Such nonradiative decay pathways may include singlet fission, excimer relaxation, and symmetry-breaking charge transfer. Singlet fission, sometimes referred to as excitation multiplication, is of great interest to the fields of energy conversion and quantum information. For example, endothermic singlet fission, which avoids energy loss, has been observed in covalently bound, linear perylene trimers and tetramers. In this work, the electronic structure and excited-state dynamics of dimers of a perylene derivative templated using DNA were investigated. Specifically, DNA Holliday junctions were used to template the aggregation of two perylene molecules covalently linked to a modified uracil nucleobase through an ethynyl group. The perylenes were templated in the form of monomer, transverse dimer, and adjacent dimer configurations. The electronic structure of the perylene monomers and dimers were characterized via steady-state absorption and fluorescence spectroscopy. Initial insights into their excited-state dynamics were gleaned from relative fluorescence intensity measurements, which indicated that a new nonradiative decay pathway emerges in the dimers. Femtosecond visible transient absorption spectroscopy was subsequently used to elucidate the excited-state dynamics. A new excited-state absorption feature grows in on the tens of picosecond timescale in the dimers, which is attributed to the formation of perylene anions and cations resulting from symmetry-breaking charge transfer. Given the close proximity required for symmetry-breaking charge transfer, the results shed promising light on the prospect of singlet fission in DNA-templated molecular aggregates.
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14
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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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15
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Cervantes-Salguero K, Biaggne A, Youngsman JM, Ward BM, Kim YC, Li L, Hall JA, Knowlton WB, Graugnard E, Kuang W. Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching. Int J Mol Sci 2022; 23:ijms23147690. [PMID: 35887059 PMCID: PMC9323263 DOI: 10.3390/ijms23147690] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 11/18/2022] Open
Abstract
Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Correspondence: (K.C.-S.); (W.K.)
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - John M. Youngsman
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Brett M. Ward
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research Laboratory, Code 6300, Washington, DC 20375, USA;
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - John A. Hall
- Division of Research and Economic Development, Boise State University, Boise, ID 83725, USA;
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
- Correspondence: (K.C.-S.); (W.K.)
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16
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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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17
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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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18
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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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19
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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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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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Wang X, Sha R, Knowlton WB, Seeman NC, Canary JW, Yurke B. Exciton Delocalization in a DNA-Templated Organic Semiconductor Dimer Assembly. ACS NANO 2022; 16:1301-1307. [PMID: 34979076 PMCID: PMC8793135 DOI: 10.1021/acsnano.1c09143] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/29/2021] [Indexed: 06/01/2023]
Abstract
A chiral dimer of an organic semiconductor was assembled from octaniline (octamer of polyaniline) conjugated to DNA. Facile reconfiguration between the monomer and dimer of octaniline-DNA was achieved. The geometry of the dimer and the exciton coupling between octaniline molecules in the assembly was studied both experimentally and theoretically. The octaniline dimer was readily switched between different electronic states by protonic doping and exhibited a Davydov splitting comparable to those previously reported for DNA-dye systems employing dyes with strong transition dipoles. This approach provides a possible platform for studying the fundamental properties of organic semiconductors with DNA-templated assemblies, which serve as candidates for artificial light-harvesting systems and excitonic devices.
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Affiliation(s)
- Xiao Wang
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - William B. Knowlton
- Micron
School for Materials Science and Engineering and Department of Electrical
& Computer Engineering, Boise State
University, Boise, Idaho 83725, United States
| | - Nadrian C. Seeman
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - James W. Canary
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Bernard Yurke
- Micron
School for Materials Science and Engineering and Department of Electrical
& Computer Engineering, Boise State
University, Boise, Idaho 83725, United States
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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: 14] [Impact Index Per Article: 4.7] [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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Barcenas G, Biaggne A, Mass OA, Wilson CK, Obukhova OM, Kolosova OS, Tatarets AL, Terpetschnig E, Pensack RD, Lee J, Knowlton WB, Yurke B, Li L. First-principles studies of substituent effects on squaraine dyes. RSC Adv 2021; 11:19029-19040. [PMID: 35478639 PMCID: PMC9033489 DOI: 10.1039/d1ra01377g] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 05/17/2021] [Indexed: 01/21/2023] Open
Abstract
Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used ab initio theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored via conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications. Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.![]()
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Affiliation(s)
- German Barcenas
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Olga A Mass
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Christopher K Wilson
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Olena M Obukhova
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine
| | - Olga S Kolosova
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine
| | - Anatoliy L Tatarets
- SSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine Kharkov 61072 Ukraine.,SETA BioMedicals Urbana IL 61802 USA
| | | | - Ryan D Pensack
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Chemistry and Biochemistry, Boise State University Boise ID 83725 USA
| | - William B Knowlton
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Electrical and Computer Engineering, Boise State University Boise ID 83725 USA
| | - Bernard Yurke
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Department of Electrical and Computer Engineering, Boise State University Boise ID 83725 USA
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University Boise ID 83725 USA .,Center for Advanced Energy Studies Idaho Falls ID 83401 USA
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24
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Welsh TA, Matsarskaia O, Schweins R, Draper ER. Electronic and assembly properties of a water-soluble blue naphthalene diimide. NEW J CHEM 2021. [DOI: 10.1039/d1nj02557k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Herein we report on the synthesis and characterisation of a water soluble deep blue naphthalene diimide, (iPrNH)2NDI–V.
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Affiliation(s)
| | - Olga Matsarskaia
- Institut Laue-Langevin
- Large Scale Structures Group
- F-38042 Grenoble CEDEX 9
- France
| | - Ralf Schweins
- Institut Laue-Langevin
- Large Scale Structures Group
- F-38042 Grenoble CEDEX 9
- France
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