Reversible Nucleic Acid Storage in Deconstructable Glassy Polymer Networks.

The rapid decline in DNA sequencing costs has fueled the demand for nucleic acid collection to unravel genomic information, develop treatments for genetic diseases, and track emerging biological threats. Current approaches to maintaining these nucleic acid collections hinge on continuous electricity for maintaining low-temperature and intricate cold-chain logistics. Inspired by the millennia-long preservation of fossilized biological specimens in calcified minerals or glassy amber, we present Thermoset-REinforced Xeropreservation (T-REX): a method for storing DNA in deconstructable glassy polymer networks. Key to T-REX is the development of polyplexes for nucleic acid encapsulation, streamlining the transfer of DNA from aqueous to organic phases, replete with initiators, monomers, cross-linkers, and thionolactone-based cleavable comonomers required to form the polymer networks. This process successfully encapsulates DNA that spans different length scales, from tens of bases to gigabases, in a matter of hours compared to days with traditional silica-based encapsulation. Further, T-REX permits the extraction of DNA using comparatively benign reagents, unlike the hazardous hydrofluoric acid required for recovery from silica. T-REX provides a path toward low-cost, time-efficient, and long-term nucleic acid preservation for synthetic biology, genomics, and digital information storage, potentially overcoming traditional low-temperature storage challenges.

Random access DNA memory using Boolean search in an archival file storage system.

DNA is an ultrahigh-density storage medium that could meet exponentially growing worldwide demand for archival data storage if DNA synthesis costs declined sufficiently and if random access of files within exabyte-to-yottabyte-scale DNA data pools were feasible. Here, we demonstrate a path to overcome the second barrier by encapsulating data-encoding DNA file sequences within impervious silica capsules that are surface labelled with single-stranded DNA barcodes. Barcodes are chosen to represent file metadata, enabling selection of sets of files with Boolean logic directly, without use of amplification. We demonstrate random access of image files from a prototypical 2-kilobyte image database using fluorescence sorting with selection sensitivity of one in 106 files, which thereby enables one in 106N selection capability using N optical channels. Our strategy thereby offers a scalable concept for random access of archival files in large-scale molecular datasets.

Programmed coherent coupling in a synthetic DNA-based excitonic circuit.

Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.

Emissive Molecular Aggregates and Energy Migration in Luminescent Solar Concentrators.

Luminescent solar concentrators (LSCs) are light harvesting devices that are ideally suited to light collection in the urban environment where direct sunlight is often not available. LSCs consist of highly luminescent compounds embedded or coated on a transparent substrate that absorb diffuse or direct solar radiation over a large area. The resulting luminescence is trapped in the waveguide by total internal reflection to the thin edges of the substrate where the concentrated light can be used to improve the performance of photovoltaic devices. The concept of LSCs has been around for several decades, and yet the efficiencies of current devices are still below expectations for commercial viability. There are two primary challenges when designing new chromophores for LSC applications. Reabsorption of dye emission by chromophores within the waveguide is a significant loss mechanism attenuating the light output of LSCs. Concentration quenching, particularly in organic dye systems, restricts the quantity of chromophores that can be incorporated in the waveguide thus limiting the light absorbed by the LSC. Frequently, a compromise between increased light harvesting of the incident light and decreasing emission quantum yield is required for most organic chromophore-based systems due to concentration quenching. The low Stokes shift of common organic dyes used in current LSCs also imposes another optimization problem. Increasing light absorption of LSCs based on organic dyes to achieve efficient light harvesting also enhances reabsorption. Ideally, a design strategy to simultaneously optimize light harvesting, concentration quenching, and reabsorption of LSC chromophores is clearly needed to address the significant losses in LSCs. Over the past few years, research in our group has targeted novel dye structures that address these primary challenges. There is a common perception that dye aggregates are to be avoided in LSCs. It became apparent in our studies that aggregates of chromophores exhibiting aggregation-induced emission (AIE) behavior are attractive candidates for LSC applications. Strategic application of AIE chromophores has led to the development of the first organic-based transparent solar concentrator that harvests UV light as well as the demonstration of reabsorption reduction by taking advantage of energy migration processes between chromophores. Further developments led us to the application of perylene diimides using an energy migration/energy transfer approach. To prevent concentration quenching, a molecularly insulated perylene diimide with bulky substituents attached to the imide positions was designed and synthesized. By combining the insulated perylene diimide with a commercial perylene dye as an energy donor-acceptor emitter pair, detrimental luminescence reabsorption was reduced while achieving a high chromophore concentration for efficient light absorption. This Account reviews and reinspects some of our recent work and the improvements in the field of LSCs.

Molecular model of J-aggregated pseudoisocyanine fibers.

Aggregated cyanines form ordered supramolecular structures with the potential to transport energy efficiently over long distances, a hallmark of photosynthetic light-harvesting complexes. In concentrated aqueous solution, pseudoisocyanine (PIC) spontaneously forms fibers with a chiral J-band red-shifted 1600 cm-1 from the monomeric 0-0 transition. A cryogenic transmission electron microscopy analysis of these fibers show an average fiber width of 2.89 nm, although the molecular-level structure of the aggregate is currently unknown. To determine a molecular model for these PIC fibers, the calculated spectra and dynamics using a Frenkel exciton model are compared to experiment. A chiral aggregate model in which the PIC monomers are neither parallel nor orthogonal to the long axis of the fiber is shown to replicate the experimental spectra most closely. This model can be physically realized by the sequential binding of PIC dimers and monomers to the ends of the fiber. These insights into the molecular aggregation model for aqueous PIC can also be applied to other similar cyanine-based supramolecular complexes with the potential for long-range energy transport, a key building block for the rational design of novel excitonic systems.

High performance p-type molecular electron donors for OPV applications via alkylthiophene catenation chromophore extension.

The synthesis of key 4-alkyl-substituted 5-(trimethylsilyl)thiophene-2-boronic acid pinacol esters 3 allowed a simplified alkylthiophene catenation process to access bis-, ter-, quater-, and quinquethiophene π-bridges for the synthesis of acceptor-π-bridge-donor- π-bridge-acceptor (A-π-D-π-A) electron donor molecules. Based on the known benzodithiophene-terthiophene-rhodanine (BTR) material, the BXR series of materials, BMR (X = M, monothiophene), BBR (X = B, bithiophene), known BTR (X = T, terthiophene), BQR (X = Q, quaterthiophene), and BPR (X = P(penta), quinquethiophene) were synthesised to examine the influence of chromophore extension on the device performance and stability for OPV applications. The BTxR (x = 4, butyl, and x = 8, octyl) series of materials were synthesised by varying the oligothiophene π-bridge alkyl substituent to examine structure-property relationships in OPV device performance. The devices assembled using electron donors with an extended chromophore (BQR and BPR) are shown to be more thermally stable than the BTR containing devices, with un-optimized efficiencies up to 9.0% PCE. BQR has been incorporated as a secondary donor in ternary blend devices with PTB7-Th resulting in high-performance OPV devices with up to 10.7% PCE.

Organic Photovoltaic Materials--Design, Synthesis and Scale-Up.

This account describes the work of our group in the area of organic photovoltaics in the past six years. The emphasis is on our experiences in the development of the organic materials, their characterization, scale-up and application in devices. We share our insight into the relationship between synthetic methods, molecular properties, bulk material properties and device performance.

Efficient light harvesting of a luminescent solar concentrator using excitation energy transfer from an aggregation-induced emitter.

The compromise between light absorption and reabsorption losses limits the potential light conversion efficiency of luminescent solar concentrators (LSCs). Current approaches do not fully address both issues. By using the excitation energy transfer (EET) strategy with a donor chromophore that exhibits aggregation-induced emission (AIE) behaviour, it is shown that both transmission and reabsorption losses can be minimized in a LSC device achieving high light collection and concentration efficiencies. The light harvesting performance of the LSC developed has been characterized using fluorescence quantum yield measurements and Monte Carlo ray tracing simulations. Comparative incident photon conversion efficiency and short-circuit current data based on the LSC coupled to a silicon solar cell provide additional evidence for improved performance.

Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language.

The surge in nucleic acid analytics requires scalable storage and retrieval systems akin to electronic databases used to organize digital data. Such a system could transform disease diagnosis, ecological preservation, and molecular surveillance of biothreats. Current storage systems use individual containers for nucleic acid samples, requiring single-sample retrieval that falls short compared with digital databases that allow complex and combinatorial data retrieval on aggregated data. Here, we leverage protective microcapsules with combinatorial DNA labeling that enables arbitrary retrieval on pooled biosamples analogous to Structured Query Languages. Ninety-six encapsulated pooled mock SARS-CoV-2 genomic samples barcoded with patient metadata are used to demonstrate queries with simultaneous matches to sample collection date ranges, locations, and patient health statuses, illustrating how such flexible queries can be used to yield immunological or epidemiological insights. The approach applies to any biosample database labeled with orthogonal barcodes, enabling complex post-hoc analysis, for example, to study global biothreat epidemiology.

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.

Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami.

Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.

Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds.

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.

Scalable Nucleic Acid Storage and Retrieval Using Barcoded Microcapsules.

Rapid advances in nucleic acid sequencing and synthesis technologies have spurred a major need to collect, store, and sequence the DNA and RNA from viral, bacterial, and mammalian sources and organisms. However, current approaches to storing nucleic acids rely on a low-temperature environment and require robotics for access, posing challenges for scalable and low-cost nucleic acid storage. Here, we present an alternative method for storing nucleic acids, termed Preservation and Access of Nucleic aciDs using barcOded micRocApsules (PANDORA). Nucleic acids spanning kilobases to gigabases and from different sources, including animals, bacteria, and viruses, are encapsulated into silica microcapsules to protect them from environmental denaturants at room temperature. Molecular barcodes attached to each microcapsule enable sample pooling and subsequent identification and retrieval using fluorescence-activated sorting. We demonstrate quantitative storage and rapid access to targeted nucleic acids from a pool emulating standard retrieval operations implemented in conventional storage systems, including recovery of 100,000-200,000 samples and Boolean logic selection using four unique barcodes. Quantitative polymerase chain reaction and short-read sequencing of the retrieved samples validated the sorting experiments and the integrity of the released nucleic acids. Our proposed approach offers a scalable long-term, room-temperature storage and retrieval of nucleic acids with high sample fidelity.

Identification of Nonradiative Decay Pathways in Cy3.

Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.

Programming Structured DNA Assemblies to Probe Biophysical Processes.

Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.

Photophysics of J-Aggregate-Mediated Energy Transfer on DNA.

Achieving nanoscale spatial and electronic control over the formation of dye aggregates is a major synthetic challenge due to their typically inhomogeneous self-assembly, which limits control over their higher-order organization. To address these challenges, synthetic DNA-templated pseudoisocyanine (PIC) J-aggregates were recently introduced. However, the dependence of the photophysics of the superradiant exciton on the underlying DNA template length and the impact of static disorder on energy transfer through these PIC J-aggregates remain unknown. We examine the delocalization length progression of superradiant PIC excitons by varying the length of poly-A DNA tracts that template PIC J-aggregates. We then investigate the energy-transfer efficiency from PIC J-aggregates with DNA duplex template length, which we found to be limited by static disorder. Utilizing the self-assembled and selective formation of superradiant excitons on DNA provides a platform to determine the function of delocalized excitons in the context of nanoscale energy transport.

Concentrating aggregation-induced fluorescence in planar waveguides: a proof-of-principle.

The photophysical properties of fluorescent dyes are key determinants in the performance of luminescent solar concentrators (LSCs). First-generation dyes--coumarin, perylenes, and rhodamines--used in LSCs suffer from both concentration quenching in the solid-state and small Stokes shifts which limit the current LSC efficiencies to below theoretical limits. Here we show that fluorophores that exhibit aggregation-induced emission (AIE) are promising materials for LSC applications. Experiments and Monte Carlo simulations show that the optical quantum efficiencies of LSCs with AIE fluorophores are at least comparable to those of LSCs with first-generation dyes as the active materials even without the use of any optical accessories to enhance the trapping efficiency of the LSCs. Our results demonstrate that AIE fluorophores can potentially solve some key limiting properties of first-generation LSC dyes.