Efficient Long-Range, Directional Energy Transfer through DNA-Templated Dye Aggregates

Multi-Step and Switchable Energy Transfer in Photoluminescent Organosilicone Capsules

Light-harvesting is of vital importance for many events, such as photosynthesis. To efficiently gather and transfer solar energy, delicate antenna is needed, which has been achieved by algae and plants. However, construction of efficient light-harvesting systems using multiple, artificial building blocks is still challenging. Here, blue-emitting organosilicone capsules containing carbon dots (denoted as CDs-Si) in ethanol are prepared, which can effectively transfer energy to green-emitting (silicone-functionalized bodipy, Si-BODIPY) or red-emitting (rhodamine b, RhB) dyes. In ternary system, sequential Förster resonance energy transfer from CDs-Si to Si-BODIPY and further to RhB is realized, which is accompanied with a less pronounced, parallel FRET directly from CDs-Si to RhB. The overall efficiency of energy transfer reaches ≈86%. By introducing a photoswitch (1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)-3,3,4,4,5,5-hexafluoro-1-cyclopentene, DAE) to the system, the emission becomes switchable under alternative illumination with UV and visible light, leading to the formation of smart artificial light-harvesting systems.

Ultrafast Super-Resolution Imaging Exploiting Spontaneous Blinking of Static Excimer Aggregates

Single-molecule localization methods have been popularly exploited to obtain super-resolved images of biological structures. However, the low blinking frequency of randomly switching emission states of individual fluorophores greatly limits the imaging speed of single-molecule localization microscopy (SMLM). Here we present an ultrafast SMLM technique exploiting spontaneous fluorescence blinking of cyanine dye aggregates confined to DNA framework nanostructures. The DNA template guides the formation of static excimer aggregates as a "light-harvesting nanoantenna", whereas intermolecular excitation energy transfer (EET) between static excimers causes collective ultrafast fluorescence blinking of fluorophore aggregates. This DNA framework-based strategy enables the imaging of DNA nanostructures with 12.5-fold improvement in speed compared to conventional SMLM. Further, we demonstrate the use of this strategy to track the movement of super-resolved DNA nanostructures for over 20 min in a microfluidic system. Thus, this ultrafast SMLM holds great potential for revealing the dynamic processes of biomacromolecules in living cells.

Sculpting photoproducts with DNA origami

Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.

DNA Framework-Engineered Assembly of Cyanine Dyes for Structural Identification of Nucleic Acids

DNA nanostructures serve as precise templates for organizing organic dyes, enabling the creation of programmable artificial photonic systems with efficient light-harvesting and energy transfer capabilities. However, regulating the organization of organic dyes on DNA frameworks remains a great challenge. In this study, we investigated the factors influencing the self-assembly behavior of cyanine dye K21 on DNA frameworks. We observed that K21 exhibited diverse assembly modes, including monomers, H-aggregates, J-aggregates, and excimers, when combined with DNA frameworks. By manipulating conditions such as the ion concentration, dye concentration, and structure of DNA frameworks, we successfully achieved precise control over the assembly modes of K21. Leveraging K21's microenvironment-sensitive fluorescence properties on DNA nanostructures, we successfully discriminated between the chirality and topology structures of physiologically relevant G-quadruplexes. This study provides valuable insights into the factors influencing the dynamic assembly behavior of organic dyes on DNA framework nanostructures, offering new perspectives for constructing functional supramolecular aggregates and identifying DNA secondary structures.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

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.

Logic Control of Directional Long-Range Resonance Energy Transfer On 2D DNA Nanosheet

By arranging fluorophores in a directional way on a 2D DNA nanosheet that transfers energy from the initial donor to the acceptor through homogeneous Förster resonance energy transfer (homo-FRET), it is found that the photonic wires (PWs) based on cascade long-range resonance energy transfer (LrRET) up to 15.6 nm can be effectively achieved through the rational selection of the fluorophores and the adjustment of their position with different distance. Then, logic control of directional energy transfer is achieved with the blocking of the energy transfer pathway, making two tumor-associated microRNA (miRNA) inputs produce an obvious output with the association of tumor diagnosis only when they present simultaneously. This research provides a new thought for development of PWs on 2D DNA nanosheets and a smart application of LrRET-based DNA AND logic control of intracellular miRNA imaging and tumor cells recognition.

Engineering Exciton Dynamics with Synthetic DNA Scaffolds

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.

Molecular-Doped Protein-Based Elastomers as a Versatile Platform for Energy-Transfer Studies and Emissive Down-Converting Polymers for Light-Emitting Applications

Much effort is being employed for designing "green" environmental emissive materials that are capable of color-tuning, i.e., down-converting the emission, and white-light generation (WLG). Here, we introduce a protein-based elastomer that can noncovalently bind a variety of chromophores while preventing their aggregation. Such binding capabilities are unique to the albumin-based materials that we use here in a process we refer to as "molecular doping". In the first part of this study, we explore the energy transfer across five different chromophores within the protein matrix, where the closely packed chromophore organization enables high energy-transfer efficiencies among them. In the second part, we show the easy control of blue, green, and red chromophores within the biopolymer, resulting in tunable emission properties of the film and WLG. The highly affordable chosen protein and the straightforward molecular doping strategy make our protein elastomers an attractive choice for an emissive material, as either a scaffold for investigating energy transfer in proteins or possible integration in light-emitting applications.

In Situ Self-Assembly of Fluorogenic RNA Nanozipper Enables Real-Time Imaging of Single Viral mRNA Translation

Real-time visualization of individual viral mRNA translation activities in live cells is essential to obtain critical details of viral mRNA dynamics and to detect its transient responses to environmental stress. Fluorogenic RNA aptamers are powerful tools for real-time imaging of mRNA in live cells, but monitoring the translation activity of individual mRNAs remains a challenge due to their intrinsic photophysical properties. Here, we develop a genetically encoded turn-on 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI)-binding RNA nanozipper with superior brightness and high photostability by in situ self-assembly of multiple nanozippers along single mRNAs. The nanozipper enables real-time imaging of the mobility and dynamic translation of individual viral mRNAs in live cells, providing information on the spatial dynamics and translational elongation rate of viral mRNAs.

Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures

DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.

Contrasting luminescence in heparin and DNA-templated co-assemblies of dimeric cyanostilbenes: efficient energy transfer in heparin-based co-assemblies

Dimeric cationic cyanostilbenes with peripheral alkyl chains demonstrated aggregation in aqueous media depending on the length of the hydrophobic segment and produced luminescent spherical nano-assemblies in the case of long alkyl chain derivatives. In the presence of heparin, a bio-polyanion that is routinely used as an anticoagulant, the self-assembled structures obtained from the amphiphilic dimers showed the formation of higher-order structures whereas the non-assembling dimers exhibited heparin-induced supramolecular structure formation. In both cases, a significant enhancement in the emission was observed. This led to the detection of heparin in aqueous buffer, serum and plasma with a "turn-on" fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA. However, the response towards DNA was opposite to that observed in the case of heparin i.e., "turn-off'' fluorescence response. Notably, depending on the length of the alkyl segment, divergent DNA binding modes of these derivatives were observed. Due to their enhanced luminescence, the heparin-based co-assemblies were further explored as artificial light-harvesting systems exhibiting an efficient energy transfer process to embedded acceptor dyes with a high antenna effect.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

Effect of Substituent Location on the Relationship between the Transition Dipole Moments, Difference Static Dipole, and Hydrophobicity in Squaraine Dyes for Quantum Information Devices

Aggregates of organic dyes that exhibit excitonic coupling have a wide array of applications, including medical imaging, organic photovoltaics, and quantum information devices. The optical properties of a dye monomer, as a basis of dye aggregate, can be modified to strengthen excitonic coupling. Squaraine (SQ) dyes are attractive for those applications due to their strong absorbance peak in the visible range. While the effects of substituent types on the optical properties of SQ dyes have been previously examined, the effects of various substituent locations have not yet been investigated. In this study, density functional theory (DFT) and time-dependent density functional theory (TD-DFT) were used to investigate the relationships between SQ substituent location and several key properties of the performance of dye aggregate systems, namely, difference static dipole (Δd), transition dipole moment (μ), hydrophobicity, and the angle (θ) between Δd and μ. We found that attaching substituents along the long axis of the dye could increase μ while placement off the long axis was shown to increase Δd and reduce θ. The reduction in θ is largely due to a change in the direction of Δd as the direction of μ is not significantly affected by substituent position. Hydrophobicity decreases when electron-donating substituents are located close to the nitrogen of the indolenine ring. These results provide insight into the structure-property relationships of SQ dyes and guide the design of dye monomers for aggregate systems with desired properties and performance.

Two-Dimensional Excitonic Networks Directed by DNA Templates as an Efficient Model Light-Harvesting and Energy Transfer System

Photosynthetic organisms organize discrete light-harvesting complexes into large-scale networks to facilitate efficient light collection and utilization. Inspired by nature, herein, synthetic DNA templates were used to direct the formation of dye aggregates with a cyanine dye, K21, into discrete branched photonic complexes, and two-dimensional (2D) excitonic networks. The DNA templates ranged from four-arm DNA tiles, ≈10 nm in each arm, to 2D wireframe DNA origami nanostructures with different geometries and varying dimensions up to 100×100 nm. These DNA-templated dye aggregates presented strongly coupled spectral features and delocalized exciton characteristics, enabling efficient photon collection and energy transfer. Compared to the discrete branched photonic systems templated on individual DNA tiles, the interconnected excitonic networks showed approximately a 2-fold increase in energy transfer efficiency. This bottom-up assembly strategy paves the way to create 2D excitonic systems with complex geometries and engineered energy pathways.

Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures

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.

A bioinspired sequential energy transfer system constructed via supramolecular copolymerization

Sequential energy transfer is ubiquitous in natural light harvesting systems to make full use of solar energy. Although various artificial systems have been developed with the biomimetic sequential energy transfer character, most of them exhibit the overall energy transfer efficiency lower than 70% due to the disordered organization of donor/acceptor chromophores. Herein a sequential energy transfer system is constructed via supramolecular copolymerization of σ-platinated (hetero)acenes, by taking inspiration from the natural light harvesting of green photosynthetic bacteria. The absorption and emission transitions of the three designed σ-platinated (hetero)acenes range from visible to NIR region through structural variation. Structural similarity of these monomers faciliates supramolecular copolymerization in apolar media via the nucleation-elongation mechanism. The resulting supramolecular copolymers display long diffusion length of excitation energy (> 200 donor units) and high exciton migration rates (~10¹⁴L mol⁻¹ s⁻¹), leading to an overall sequential energy transfer efficiency of 87.4% for the ternary copolymers. The superior properties originate from the dense packing of σ-platinated (hetero)acene monomers in supramolecular copolymers, mimicking the aggregation mode of bacteriochlorophyll pigments in green photosynthetic bacteria. Overall, directional supramolecular copolymerization of donor/acceptor chromophores with high energy transfer efficiency would provide new avenues toward artificial photosynthesis applications.

Sequential energy transfer is ubiquitous in natural light harvesting systems, but most artificial mimics have unsatisfactory energy transfer efficiency. Here, authors synthesize a sequential energy transfer system with overall efficiency of 87.4% via supramolecular copolymerization mimicking the aggregation mode of bacteriochlorophyll pigments in green photosynthetic bacteria.

Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine

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.

DNA-Templated Modulation in the Photophysical Properties of a Fluorescent Molecular Rotor Auramine O by Varying the DNA Composition

This work delineates an integrative approach combining spectroscopic and computational studies to decipher the association-induced fluorescence properties of a fluorescent molecular rotor, viz., auramine O (AuO), after interacting with 20-mer duplex DNA having diverse well-matched base pairs. While exploring the scarcely explored sequence-dependent interaction mechanism of AuO and DNA, we observed that DNA could act as a conducive scaffold to the formation of AuO dimer through noncovalent interactions at lower molecular density. The photophysical properties of AuO depend on the nucleotide compositions as described from sequence-dependent shifting in the emission and absorption maxima. Furthermore, we explored such DNA base pair-dependent fluorescence spectral characteristics of AuO toward discriminating the thermodynamically most stable single nucleotide mismatch in a 20-mer sequence. Our results are interesting and could be useful in developing analogues with further enhanced emission properties toward mismatched DNA sequences.

Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling

A boron dipyrromethene (BODIPY) derivative bearing a cis-proline residue at the meso-position crystallizes in the form of platelets with strong (i.e., Φ_F = 0.34) red fluorescence, but the absorption and emission spectra differ markedly from those for dilute solutions. A key building block for the crystal is a pseudo-dimer where hydrogen bonding aligns the proline groups and separates the terminal chromophores by ca. 25 Å. Comparison with a covalently linked bichromophore suggests that one-dimensional (1D) excitonic coupling between the terminals is too small to perturb the optical properties. However, accretion of the pseudo-dimer forms narrow channels possessing a high density of chromophores. The resultant absorption spectrum exhibits strong excitonic splitting, which can be explained quantitatively using the extended dipole approach and allowing for coupling between ca. 30 BODIPY units. Fluorescence, which decays with a lifetime of 2.2 ns, is assigned to a delocalized and (slightly) super-radiant BODIPY dimer situated at the interface and populated via electronic energy transfer from the interior.

Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds

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.

Deoxyribonucleic Acid Encoded and Size-Defined π-Stacking of Perylene Diimides

Natural photosystems use protein scaffolds to control intermolecular interactions that enable exciton flow, charge generation, and long-range charge separation. In contrast, there is limited structural control in current organic electronic devices such as OLEDs and solar cells. We report here the DNA-encoded assembly of π-conjugated perylene diimides (PDIs) with deterministic control over the number of electronically coupled molecules. The PDIs are integrated within DNA chains using phosphoramidite coupling chemistry, allowing selection of the DNA sequence to either side, and specification of intermolecular DNA hybridization. In this way, we have developed a "toolbox" for construction of any stacking sequence of these semiconducting molecules. We have discovered that we need to use a full hierarchy of interactions: DNA guides the semiconductors into specified close proximity, hydrophobic-hydrophilic differentiation drives aggregation of the semiconductor moieties, and local geometry and electrostatic interactions define intermolecular positioning. As a result, the PDIs pack to give substantial intermolecular π wave function overlap, leading to an evolution of singlet excited states from localized excitons in the PDI monomer to excimers with wave functions delocalized over all five PDIs in the pentamer. This is accompanied by a change in the dominant triplet forming mechanism from localized spin-orbit charge transfer mediated intersystem crossing for the monomer toward a delocalized excimer process for the pentamer. Our modular DNA-based assembly reveals real opportunities for the rapid development of bespoke semiconductor architectures with molecule-by-molecule precision.

Understanding Self-Assembled Pseudoisocyanine Dye Aggregates in DNA Nanostructures and Their Exciton Relay Transfer Capabilities

Progress has been made using B-form DNA duplex strands to template chromophores in ordered molecular aggregates known as J-aggregates. These aggregates can exhibit strong electronic coupling, extended coherent lifetimes, and long-range exciton delocalization under appropriate conditions. Certain cyanine dyes such as pseudoisocyanine (PIC) dye have shown a proclivity to form aggregates in specific DNA sequences. In particular, DX-tiles containing nonalternating poly(dA)-poly(dT) dinucleotide tracks (AT-tracks), which template noncovalent PIC dye aggregates, have been demonstrated to exhibit interesting emergent photonic properties. These DNA-based aggregates are referred to as J-bits for their similarity to J-aggregates. Here, we assemble multifluorophore DX-tile scaffolds which template J-bits into both contiguous and noncontiguous linear arrays. Our goal is to understand the relay capability of noncontiguous J-bit arrays and probe the effects that orientation and position have on the energy transfer between them. We find that linearly contiguous J-bits can relay excitons from an initial AlexaFluor 405 donor to a terminal AlexaFluor 647 acceptor across a distance of up to 16.3 nm. We observed a maximum increase in energy transfer of 41% in the shortest scaffold and an 11% increase in energy transfer across the maximum distance. However, in nonlinear arrays, exciton transfer is not detectable, even when off-axis J-bit-to-J-bit transfer distances were <2 nm. These results, in conjunction with the previous work on PIC-DNA systems, suggest that PIC-DNA-based systems may currently be limited to simple 1-D designs, which prevent isolating J-bits for enhanced energy-transfer characteristics until further understanding and improvements to the system can be made.

Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles

In certain conditions, dye-conjugated icosahedral virus shells exhibit suppression of concentration quenching. The recently observed radiation brightening at high fluorophore densities has been attributed to coherent emission, i.e., to a cooperative process occurring within a subset of the virus-supported fluorophores. Until now, the distribution of fluorophores among potential conjugation sites and the nature of the active subset remained unknown. With the help of mass spectrometry and molecular dynamics simulations, we found which conjugation sites in the brome mosaic virus capsid are accessible to fluorophores. Reactive external surface lysines but also those at the lumenal interface where the coat protein N-termini are located showed virtually unrestricted access to dyes. The third type of labeled lysines was situated at the intercapsomeric interfaces. Through limited proteolysis of flexible N-termini, it was determined that dyes bound to them are unlikely to be involved in the radiation brightening effect. At the same time, specific labeling of genetically inserted cysteines on the exterior capsid surface alone did not lead to radiation brightening. The results suggest that lysines situated within the more rigid structural part of the coat protein provide the chemical environments conducive to radiation brightening, and we discuss some of the characteristics of these environments.

Nanotube Template-Directed Formation of Strongly Coupled Dye Aggregates with Tunable Exciton Fluorescence Controlled by Switching between J- and H-Type Electronic Coupling

Strongly coupled dye aggregates with tailored exciton properties may find their use in developing artificial light-harvesting and optoelectronic devices. Here, we report the control of tubular pseudoisocyanine (PIC) dye J- and H-aggregate formation with tunable exciton fluorescence using lithocholic acid (LCA) as a template. The LCA-templated PIC J-aggregate nanotubes formed at a higher LCA/PIC molar ratio (≥5:1) exhibit a sharp, red-shifted absorption band (at 555 nm), intense fluorescence (at 565 nm), and shorter lifetime (200 ps), all indicating their strong superradiance properties. In contrast, the H-aggregate nanotubes formed at a lower LCA/PIC molar ratio (2:1) exhibit a significantly blue-shifted absorption band (at 420 nm) and highly red-shifted fluorescence emission (at 600 nm) with enhanced lifetime (4.40 ns). The controlled switching of the optical properties of the PIC dye aggregates achieved by controlling the LCA/PIC molar ratio could serve as an important guideline for the design of organic photo-functional materials.

Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions

Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.

A Single Molecule Polyphenylene-Vinylene Photonic Wire

Nanoscale transport of light through single molecule systems is of fundamental importance for light harvesting, nanophotonic circuits, and for understanding photosynthesis. Studies on organization of molecular entities for directional transfer of excitation energy have focused on energy transfer cascades via multiple small molecule dyes. Here, we investigate a single molecule conjugated polymer as a photonic wire. The phenylene-vinylene-based polymer is functionalized with multiple DNA strands and immobilized on DNA origami by hybridization to a track of single-stranded staples extending from the origami structure. Donor and acceptor fluorophores are placed at specific positions along the polymer which enables energy transfer from donor to polymer, through the polymer, and from polymer to acceptor. The structure is characterized by atomic force microscopy, and the energy transfer is studied by ensemble fluorescence spectroscopy and single molecule TIRF microscopy. It is found that the polymer photonic wire is capable of transferring light over distances of 24 nm. This demonstrates the potential residing in the use of conjugated polymers for nanophotonics.

Enhancing Rechargeable Persistent Luminescence via Organic Dye Sensitization

Owing to their unique afterglow ability, long-wavelength light activatable persistent luminescence (PersL) nanoparticles (PLNPs) have been emerging as an important category of imaging probes. Long-wavelength LED light has been shown to be effective in recharging these nanoparticles. However, finding a simple and effective method to amplify such renewable PersL signals under long-wavelength light is still a key challenge. Herein, we discovered that a dye-sensitization strategy was able to effectively boost the renewable PersL signals of the NIR emitting ZnGa₂ O₄ :Cr³⁺ (ZGC)) under long-wavelength LED light. Moreover, as a proof-of-principle tumorectomy demonstration, this new class of dye sensitized ZGC enabled simultaneous intraoperative anatomic tumor navigation and effective microscopic detection of tumor cells in pathological diagnosis.

Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer

Variation of DNA conformation is important in regulating gene expression and mediating drug-DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label-free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i-motifs, G-quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label-free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells.

Polaritons and excitons: Hamiltonian design for enhanced coherence

The primary questions motivating this report are: Are there ways to increase coherence and delocalization of excitation among many molecules at moderate electronic coupling strength? Coherent delocalization of excitation in disordered molecular systems is studied using numerical calculations. The results are relevant to molecular excitons, polaritons, and make connections to classical phase oscillator synchronization. In particular, it is hypothesized that it is not only the magnitude of electronic coupling relative to the standard deviation of energetic disorder that decides the limits of coherence, but that the structure of the Hamiltonian-connections between sites (or molecules) made by electronic coupling-is a significant design parameter. Inspired by synchronization phenomena in analogous systems of phase oscillators, some properties of graphs that define the structure of different Hamiltonian matrices are explored. The report focuses on eigenvalues and ensemble density matrices of various structured, random matrices. Some reasons for the special delocalization properties and robustness of polaritons in the single-excitation subspace (the star graph) are discussed. The key result of this report is that, for some classes of Hamiltonian matrix structure, coherent delocalization is not easily defeated by energy disorder, even when the electronic coupling is small compared to disorder.

DNA-organized artificial LHCs - testing the limits of chromophore segmentation

DNA-organized multi-chromophoric systems containing phenanthrene and pyrene derivatives exhibit a highly efficient excitation energy transfer from phenanthrene (donor) to pyrene (acceptor). The energy transfer also occurs if the phenanthrene antenna is interrupted by intervening DNA base pairs. Artificial light-harvesting complexes composed of up to five phenanthrene-DNA alternations with fluorescence quantum yields as high as 68% are described.

Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers

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.

Interplay between Förster and Dexter Energy Transfer Rates in Isomeric Donor-Bridge-Acceptor Systems

The ability to direct the flow of excitons enable molecular systems to perform highly advanced functions. Intramolecular energy transfer in donor-bridge-acceptor systems can occur by different mechanisms, and the ability to control the excited state energy pathways depends on the capacity to favor one process over another. Here, we show an anticorrelation between the rates of Förster and Dexter types of energy transfer in two isomeric donor-bridge-acceptor systems. Both dyads display intramolecular Förster triplet-to-singlet and Dexter triplet-to-triplet energy transfers. However, as the bridge-acceptor connection point changes, the rate of one energy transfer process increases at the same time as the other one decreases, allowing us to control the energy flow direction. This work shows how rational design can be used to tune excited state energy pathways in molecular dyads, which is of importance for advanced functions such as multiplicity conversion in future molecular materials.

DNA-Scaffolded Proximity Assembly and Confinement of Multienzyme Reactions

Cellular functions rely on a series of organized and regulated multienzyme cascade reactions. The catalytic efficiencies of these cascades depend on the precise spatial organization of the constituent enzymes, which is optimized to facilitate substrate transport and regulate activities. Mimicry of this organization in a non-living, artificial system would be very useful in a broad range of applications—with impacts on both the scientific community and society at large. Self-assembled DNA nanostructures are promising applications to organize biomolecular components into prescribed, multidimensional patterns. In this review, we focus on recent progress in the field of DNA-scaffolded assembly and confinement of multienzyme reactions. DNA self-assembly is exploited to build spatially organized multienzyme cascades with control over their relative distance, substrate diffusion paths, compartmentalization and activity actuation. The combination of addressable DNA assembly and multienzyme cascades can deliver breakthroughs toward the engineering of novel synthetic and biomimetic reactors.

Control of Energy Transfer Between Pyrene- and Perylene-Nucleosides by the Sequence of DNA-Templated Supramolecular Assemblies

DNA was used as supramolecular scaffold to order chromophores and control their optical properties. Ethynylpyrene as energy donor was attached to 2'-desoxy-2-aminoadenosine that binds selectively to thymidines (T) in the template. Ethynylperylene as acceptor was attached to 2'-desoxyuridine that is complementary to 2'-desoxyadenosine (A). This donor-acceptor pair was assembled along single-stranded DNA templates of different A-T sequences to investigate the sequence control of the energy transfer between the chromophores. The fluorescence intensities increase in the mixed assemblies along the DNA templates from A10T10 over (AATT)5 to (AT)10, although these templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This shows that the sequence selective assembly of the two building blocks along DNA templates is programmable and alters the fluorescence readout. Such sequence-controlled supramolecular chemistry represents the key element for future functional π-systems in materials for light harvesting of solar energy.

DNA-Enabled Chiral Gold Nanoparticle-Chromophore Hybrid Structure with Resonant Plasmon-Exciton Coupling Gives Unusual and Strong Circular Dichroism

Circular dichroism (CD) from hybrid complexes of plasmonic nanostructures and chiral molecules has recently attracted significant interest. However, the hierarchical chiral self-assembly of molecules on surfaces of metal nanostructures has remained challenging. As a result, a deep understanding of plasmon-exciton coupling between surface plasmons and chiral collective molecular excitations has not been achieved. In particular, the critical impact of resonant plasmon-exciton coupling within the hybrid is unclear. Here, we employed DNA-templated strategies to control the chiral self-assembly of achiral chromophores with rationally tuned exciton transitions on gold nanosphere (AuNP) or gold nanorod (AuNR) surfaces. Unlike many previous chiral plasmonic hybrids utilizing chiral biomolecules with CD signals in the UV range, we designed structures with the chiral excitonic resonances at visible wavelengths. The constructed hybrid complexes displayed strong chiroptical activity that depends on the spectral overlap between the chiral collective molecular excitations and the plasmon resonances. We find that when spectral overlap is optimized, the molecular CD signal originating from the chiral self-assemblies of chromophores was strongly enhanced (maximum enhancement of nearly an order of magnitude) and a plasmonic CD signal was induced. Surprisingly, the sign of the molecular CD was reversed despite different self-assembly mechanisms of the Au nanoparticle-chromophore hybrids. Our results provide new insight into plasmonic CD enhancements and will inspire further studies on chiral light-matter interactions in strongly coupled plasmonic-excitonic systems.