Coherent exciton delocalization in dye aggregate systems gives rise to a variety of intriguing optical phenomena, including J- and H-aggregate behavior and Davydov splitting. Systems that exhibit coherent exciton delocalization at room temperature are of interest for the development of artificial light-harvesting devices, colorimetric detection schemes, and quantum computers. Here, we report on a simple dye system templated by DNA that exhibits tunable optical properties. At low salt and DNA concentrations, a DNA duplex with two internally functionalized Cy5 dyes (i.e., dimer) persists and displays predominantly J-aggregate behavior. Increasing the salt and/or DNA concentrations was found to promote coupling between two of the DNA duplexes via branch migration, thus forming a four-armed junction (i.e., tetramer) with H-aggregate behavior. This H-tetramer aggregate exhibits a surprisingly large Davydov splitting in its absorbance spectrum that produces a visible color change of the solution from cyan to violet and gives clear evidence of coherent exciton delocalization.

Exciton delocalization in dye aggregate systems is a phenomenon that is revealed by spectral features, such as Davydov splitting, J- and H-aggregate behavior, and fluorescence suppression. Using DNA as an architectural template to assemble dye aggregates enables specific control of the aggregate size and dye type, proximal and precise positioning of the dyes within the aggregates, and a method for constructing large, modular two- and three-dimensional arrays. Here, we report on dye aggregates, organized via an immobile Holliday junction DNA template, that exhibit large Davydov splitting of the absorbance spectrum (125 nm, 397.5 meV), J- and H-aggregate behavior, and near-complete suppression of the fluorescence emission (∼97.6% suppression). Because of the unique optical properties of the aggregates, we have demonstrated that our dye aggregate system is a viable candidate as a sensitive absorbance and fluorescence optical reporter. DNA-templated aggregates exhibiting exciton delocalization may find application in optical detection and imaging, light-harvesting, photovoltaics, optical information processing, and quantum computing.

Molecular excitons are used in a variety of applications including light harvesting, optoelectronics, and nanoscale computing. Controlled aggregation via covalent attachment of dyes to DNA templates is a promising aggregate assembly technique that enables the design of extended dye networks. However, there are few studies of exciton dynamics in DNA-templated dye aggregates. We report time-resolved excited-state dynamics measurements of two cyanine-based dye aggregates, a J-like dimer and an H-like tetramer, formed through DNA-templating of covalently attached dyes. Time-resolved fluorescence and transient absorption indicate that nonradiative decay, in the form of internal conversion, dominates the aggregate ground state recovery dynamics, with singlet exciton lifetimes on the order of tens of picoseconds for the aggregates versus nanoseconds for the monomer. These results highlight the importance of circumventing nonradiative decay pathways in the future design of DNA-templated dye aggregates.

A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.

Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addition of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function.

The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch’s small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.

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.

Molecular excitons play a central role in natural and artificial light harvesting, organic electronics, and nanoscale computing. The structure and dynamics of molecular excitons, critical to each application, are sensitively governed by molecular packing. Deoxyribonucleic acid (DNA) templating is a powerful approach that enables controlled aggregation via sub-nanometer positioning of molecular dyes. However, finer sub-Angstrom control of dye packing is needed to tailor excitonic properties for specific applications. Here, we show that adding rotaxane rings to squaraine dyes templated with DNA promotes an elusive oblique packing arrangement with highly desirable optical properties. Specifically, dimers of these squaraine:rotaxanes exhibit an absorption spectrum with near-equal intensity excitonically split absorption bands. Theoretical analysis indicates that the transitions are mostly electronic in nature and only have similar intensities over a narrow range of packing angles. Compared with squaraine dimers, squaraine:rotaxane dimers also exhibit extended excited-state lifetimes and less structural heterogeneity. The approach proposed here may be generally useful for optimizing excitonic materials for a variety of applications ranging from solar energy conversion to quantum information science.