Smaller Gold Nanoparticles Release DNA More Efficiently During fs Laser Pulsed Optical Heating

This work investigates the effect of plasmonic gold nanoparticle (AuNP) size on the rate of thermal release of single-stranded oligonucleotides under femtosecond (fs)-pulsed laser irradiation sources. Contrary to the theoretical predictions that larger AuNPs (50-60 nm diameter) would produce the most solution heating and fastest DNA release, it is found that smaller AuNP diameters (25 nm) lead to faster dsDNA denaturation rates. Controlling for the pulse energy fluence, AuNP concentration, DNA loading density, and the distance from the AuNP surface finds the same result. These results imply that the solution temperature increases around the AuNP during fs laser pulse optical heating may not be the only significant influence on dsDNA denaturation, suggesting that direct energy transfer from the AuNP to the DNA (phonon-phonon coupling), which is increased as AuNPs decrease in size, may play a significant role.

Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors

Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing to drug delivery. In this study, we demonstrate that coacervates provide a simple and biocompatible medium to improve nucleic acid biosensors through the sequestration of both the biosensor and target strands within the coacervate, thereby increasing their local concentration. Using the well-established polyarginine (R9) - ATP coacervate system and an energy transfer-based DNA molecular beacon we observed three key improvements: i) a greater than 20-fold reduction of the limit of detection within coacervates when compared to control buffer solutions; ii) an increase in the kinetics, equilibrium was reached more than 4-times faster in coacervates; and iii) enhancement in the dye fluorescent quantum yields within the coacervates, resulting in greater signal-to-noise. The observed benefits translate into coacervates greatly improving bioassay functionality.

Investigating the dissipation of heat and quantum information from DNA-scaffolded chromophore networks

Scaffolded molecular networks are important building blocks in biological pigment-protein complexes, and DNA nanotechnology allows analogous systems to be designed and synthesized. System-environment interactions in these systems are responsible for important processes, such as the dissipation of heat and quantum information. This study investigates the role of nanoscale molecular parameters in tuning these vibronic system-environment dynamics. Here, genetic algorithm methods are used to obtain nanoscale parameters for a DNA-scaffolded chromophore network based on comparisons between its calculated and measured optical spectra. These parameters include the positions, orientations, and energy level characteristics within the network. This information is then used to compute the dynamics, including the vibronic population dynamics and system-environment heat currents, using the hierarchical equations of motion. The dissipation of quantum information is identified by the system's transient change in entropy, which is proportional to the heat currents according to the second law of thermodynamics. These results indicate that the dissipation of quantum information is highly dependent on the particular nanoscale characteristics of the molecular network, which is a necessary first step before gleaning the systematic optimization rules. Subsequently, the I-concurrence dynamics are calculated to understand the evolution of the vibronic system's quantum entanglement, which are found to be long-lived compared to these system-bath dissipation processes.

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.

Towards control of excitonic coupling in DNA-templated Cy5 aggregates: the principal role of chemical substituent hydrophobicity and steric interactions

Understanding and controlling exciton coupling in dye aggregates has become a greater focus as potential applications such as coherent exciton devices, nanophotonics, and biosensing have been proposed. DNA nanostructure templates allow for a powerful modular approach. Using DNA Holliday junction (HJ) templates variations of dye combinations and precision dye positions can be rapidly assayed, as well as creating aggregates of dyes that could not be prepared (either due to excess or lack of solubility) through alternative means. Indodicarbocyanines (Cy5) have been studied in coupled systems due to their large transition dipole moment, which contributes to strong coupling. Cy5-R dyes were recently prepared by chemically modifying the 5,5'-substituents of indole rings, resulting in varying dye hydrophobicity/hydrophilicity, steric considerations, and electron-donating/withdrawing character. We utilized Cy5-R dyes to examine the formation and properties of 30 unique DNA templated homodimers. We find that in our system the sterics of Cy5-R dyes play the determining factor in orientation and coupling strength of dimers, with coupling strengths ranging from 50-138 meV. The hydrophobic properties of the Cy5-R modify the percentage of dimers formed, and have a secondary role in determining the packing characteristics of the dimers when sterics are equivalent. Similar to other reports, we find that positioning of the Cy5-R within the HJ template can favor particular dimer interactions, specifically oblique or H-type dimers.

Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms

Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.

Structural and optical variation of pseudoisocyanine aggregates nucleated on DNA substrates

Coherently coupled pseudoisocyanine (PIC) dye aggregates have demonstrated the ability to delocalize electronic excitations and ultimately migrate excitons with much higher efficiency than similar designs where excitations are isolated to individual chromophores. Here, we report initial evidence of a new type of PIC aggregate, formed through heterogeneous nucleation on DNA oligonucleotides, displaying photophysical properties that differ significantly from previously reported aggregates. This new aggregate, which we call the super aggregate (SA) due to the need for elevated dye excess to form it, is clearly differentiated from previously reported aggregates by spectroscopic and biophysical characterization. In emission spectra, the SA exhibits peak narrowing and, in some cases, significant quantum yield variation, indicative of stronger coupling in cyanine dyes. The SA was further characterized with circular dichroism and atomic force microscopy observing unique features depending on the DNA substrate. Then by integrating an AlexaFluor^TM647 (AF) dye as an energy transfer acceptor into the system, we observed mixed energy transfer characteristics using the different DNA. For example, SA formed with a rigid DNA double crossover tile (DX-tile) substrate resulted in AF emission sensitization. While SA formed with more flexible non-DX-tile DNA (i.e. duplex and single strand DNA) resulted in AF emission quenching. These combined characterizations strongly imply that DNA-based PIC aggregate properties can be controlled through simple modifications to the DNA substrate's sequence and geometry. Ultimately, we aim to inform rational design principles for future device prototyping. For example, one key conclusion of the study is that the high absorbance cross-section and efficient energy transfer observed with rigid substrates made for better photonic antennae, compared to flexible DNA substrates.

Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates-aggregates of chemically distinct dyes-rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm^-1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.

Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis

Cyanine dyes represent a family of organic fluorophores with widespread utility in biological-based applications ranging from real-time PCR probes to protein labeling. One burgeoning use currently being explored with indodicarbocyanine (Cy5) in particular is that of accessing exciton delocalization in designer DNA dye aggregate structures for potential development of light-harvesting devices and room-temperature quantum computers. Tuning the hydrophilicity/hydrophobicity of Cy5 dyes in such DNA structures should influence the strength of their excitonic coupling; however, the requisite commercial Cy5 derivatives available for direct incorporation into DNA are nonexistent. Here, we prepare a series of Cy5 derivatives that possess different 5,5'-substituents and detail their incorporation into a set of DNA sequences. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5'-substituents, including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups were chosen so as to vary the inherent electron-donating/withdrawing character while also tuning their resulting absorption and emission properties. Following the synthesis of parent dyes, one of their pendant alkyl chains was functionalized with a monomethoxytrityl protective group with the remaining hydroxyl-terminated N-propyl linker permitting rapid, same-day phosphoramidite conversion and direct internal DNA incorporation into nascent oligonucleotides with moderate to good yields using a 1 μmole scale automated DNA synthesis. Labeled sequences were cleaved from the controlled pore glass matrix, purified by HPLC, and their photophysical properties were characterized. The DNA-labeled Cy5 derivatives displayed spectroscopic properties that paralleled the parent dyes, with either no change or an increase in fluorescence quantum yield depending upon sequence.

Tuning between Quenching and Energy Transfer in DNA-Templated Heterodimer Aggregates

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.

Mechanistic Understanding of DNA Denaturation in Nanoscale Thermal Gradients Created by Femtosecond Excitation of Gold Nanoparticles

There is significant interest in developing photothermal systems that can precisely control the structure and function of biomolecules through local temperature modulation. One specific application is the denaturation of double-stranded (ds) DNA through femtosecond (fs) laser pulse optical heating of gold nanoparticles (AuNPs); however, the mechanism of DNA melting in these systems is not fully understood. Here, we utilize 55 nm AuNPs with surface-tethered dsDNA, which are locally heated using fs laser pulses to induce DNA melting. By varying the dsDNA distance from the AuNP surface and the laser pulse energy fluence, this system is used to study how the nanosecond duration temperature increase and the steep temperature gradient around the AuNP affect dsDNA dehybridization. Through modifying the distance between the dsDNA and AuNP surface by 3.8 nm in total and the pulse energy fluence from 7.1 to 14.1 J/m², the dehybridization rates ranged from 0.002 to 0.05 DNA per pulse, and the total amount of DNA released into solution was controlled over a range of 26-93% in only 100 s of irradiation. By shifting the dsDNA position as little as ∼1.1 nm, the average dsDNA dehybridization rate is altered up to 30 ± 2%, providing a high level of control over DNA melting and release. By comparing the theoretical temperature around the dsDNA to the experimentally derived temperature, we find that maximum or peak temperatures have a greater influence on the dehybridization rate when the dsDNA is closer to the AuNP surface and when lower laser pulse fluences are used. Furthermore, molecular dynamics simulations mimicking the photothermal heat pulse around a AuNP provide mechanistic insight into the stochastic nature of dehybridization and demonstrate increased base pair separation near the AuNP surface during laser pulse heating when compared to steady-state heating. Understanding how biological materials respond to the short-lived and non-uniform temperature increases innate to fs laser pulse optical heating of AuNPs is critical to improving the functionality and precision of this technique so that it may be implemented into more complex biological systems.

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.

Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes

Structural DNA nanotechnology is a promising approach to create chromophore networks with modular structures and Hamiltonians to control the material's functions. The functional behaviors of these systems depend on the interactions of the chromophores' vibronic states, as well as interactions with their environment. To optimize their functions, it is necessary to characterize the chromophore network's structural and energetic properties, including the electronic delocalization in some cases. In this study, parameters of interest are deduced in DNA-scaffolded Cyanine 3 and Cyanine 5 dimers. The methods include steady-state optical measurements, physical modeling, and a genetic algorithm approach. The parameters include the chromophore network's vibronic Hamiltonian, molecular positions, transition dipole orientations, and environmentally induced energy broadening. Additionally, the study uses temperature-dependent optical measurements to characterize the spectral broadening further. These combined results reveal the quantum mechanical delocalization, which is important for functions like coherent energy transport and quantum information applications.

Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks

Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r⁴ energy transfer distance (r) dependency versus the 1/r⁶ dependency seen for a single donor-acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.

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.

Power of Aerogel Platforms to Explore Mesoscale Transport in Catalysis

We describe the opportunity to deploy aerogels-an ultraporous nanoarchitecture with co-continuous networks of meso/macropores and covalently bonded nanoparticulates-as a platform to address the nature of the electronic, ionic, and mass transport that underlies catalytic activity. As a test case, we fabricated Au||TiO₂ junctions in composite guest-host aerogels in which ∼5 nm Au nanoparticles are incorporated either directly into the anatase TiO₂ network (Au "in" TiO₂, Au_IN-TiO₂ aerogel) or deposited onto preformed TiO₂ aerogel (Au "on" TiO₂, Au_ON/TiO₂ aerogel). The metal-meets-oxide nanoscale interphase as visualized by electron tomography feature extended three-dimensional (3D) interfaces, but Au_IN-TiO₂ aerogels impose a greater degree of Au contact with TiO₂ particles than does the Au_ON/TiO₂ form. Both aerogel variants enable transport of electrons over micrometer-scale distances across the TiO₂ network to Au||TiO₂ junctions, as evidenced by electron paramagnetic resonance (EPR) and ultrafast visible pump-IR probe time-resolved absorption spectroscopy. The siting of gold nanoparticles in the TiO₂ network more effectively disperses trapped electrons. Density functional theory (DFT) calculations find that increased physical contact between Au and TiO₂, induced by oxygen vacancies, produces increased hybridization of midgap states and quenches unpaired trapped electrons. We assign the apparent differences in electron-transport capabilities to a combination of the relatively better-wired Au||TiO₂ junctions in Au_IN-TiO₂ aerogels, which have a greater capacity to dilute accumulated charge over a larger interfacial surface area, with an enhanced ability to discharge the accumulated electrons via catalytic reduction of adsorbed O₂ to O^2- at the interface. Solid-state ¹H nuclear magnetic resonance experiments show that proton spin-lattice relaxation times and possibly proton diffusion are strongly coupled to Au||TiO₂ interfacial design, likely through spin coupling of protons to unpaired electrons trapped at the TiO₂ network. Taken together, our results show that Au||TiO₂ interfacial design strongly impacts charge carrier (electron and proton) transport over mesoscale distances in catalytic aerogel architectures.

Femtosecond Laser Pulse Excitation of DNA-Labeled Gold Nanoparticles: Establishing a Quantitative Local Nanothermometer for Biological Applications

Femtosecond (fs) laser pulsed excitation of plasmonic nanoparticle (NP)-biomolecule conjugates is a promising method to locally heat biological materials. Studies have demonstrated that fs pulses of light can modulate the activity of DNA or proteins when attached to plasmonic NPs; however, the precision over subsequent biological function remains largely undetermined. Specifically, the temperature the localized biomolecules "experience" remains unknown. We used 55 nm gold nanoparticles (AuNPs) displaying double-stranded (ds) DNA to examine how, for dsDNA with different melting temperatures, the laser pulse energy fluence and bulk solution temperature affect the rate of local DNA denaturation. A universal "template" single-stranded DNA was attached to the AuNP surface, and three dye-labeled probe strands, distinct in length and melting temperature, were hybridized to it creating three individual dsDNA-AuNP bioconjugates. The dye-labeled probe strands were used to quantify the rate and amount of DNA release after a given number of light pulses, which was then correlated to the dsDNA denaturation temperature, resulting in a quantitative nanothermometer. The localized DNA denaturation rate could be modulated by more than threefold over the biologically relevant range of 8-53 °C by varying pulse energy fluence, DNA melting temperature, and surrounding bath temperature. With a modified dissociation equation tailored for this system, a "sensed" temperature parameter was extracted and compared to simulated AuNP temperature profiles. Determining actual biological responses in such systems can allow researchers to design precision nanoscale photothermal heating sources.

DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer

Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm⁻¹ and 1545 cm⁻¹ for the 0-bp dimer and 1100 cm⁻¹ for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications.

Dyes coupled to DNA display distance-dependent vibronic couplings that prolongs quantum coherences detected with 2D spectroscopy.

Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency

DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.

Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds

We examine the effect of electronic coupling on the optical properties of Cy3 dimers attached to DNA duplexes as a function of base pair (bp) separation using steady-state and time-resolved spectroscopy. For close Cy3-Cy3 separations, 0 and 1 bp between dyes, intermediate to strong electronic coupling is revealed by modulation of the absorption and fluorescence properties including spectral band shape, peak wavelength, and excited-state lifetime. Using a vibronic exciton model, we estimate coupling strengths of 150 and 266 cm^-1 for the 1 and 0 bp separations, respectively, which are comparable to those found in natural light-harvesting complexes. For the strongest electronic coupling (0 bp separation), we observe that the absorption band shape is strongly affected by the base pairs that surround the dyes, where more strongly hydrogen-bonded G-C pairs produce a red-shifted absorption spectrum consistent with a J-type dimer. This effect is studied theoretically using molecular dynamics simulation, which predicts an in-line dye configuration that is consistent with the experimental J-type spectrum. When the Cy3 dimers are in a standard aqueous buffer, the presence of relatively strong electronic coupling is accompanied by decreased fluorescence lifetime, suggesting that it promotes nonradiative relaxation in cyanine dyes. However, we show that the use of a viscous solvent can suppress this nonradiative recombination and thereby restore the dimer fluorescent emission. Ultrafast transient absorption measurements of Cy3 dimers in both standard aqueous buffer and viscous glycerol buffer suggest that sufficiently strong electronic coupling increases the probability of excited-state relaxation through a dark state that is related to Cy3 torsional motion.

Transient Optical and Terahertz Spectroscopy of Nanoscale Films of RuO2

Solution-deposited nanoscale films of RuO₂ ("nanoskins") are effective transparent conductors once calcined to 200 °C. Upon heating the nanoskins to higher temperature the nanoskins show increased transmission at 550 nm. Electronic microscopy and X-ray diffraction show that the changes in the optical spectrum are accompanied by the formation of rutile RuO₂ nanoparticles. The mechanism for the spectral evolution is clearly observed with ultrafast optical measurements. Following excitation at 400 nm, nanoskins calcined at higher temperatures show increased transmission above 650 nm, consistent with the photobleaching of a surface-plasmon resonance (SPR) band. Calculations based on the optical constants of RuO₂ substantiate the presence of SPR absorption. Sheet resistance and transient terahertz photoconductivity measurements establish that the nanoskins electrically de-wire into separated particles. The plasmonic behavior of the nanoskins has implications their use in a range of optical and electrochemical applications.

Bridging Lanthanide to Quantum Dot Energy Transfer with a Short-Lifetime Organic Dye

Semiconductor nanocrystals or quantum dots (QDs) should act as excellent Förster resonance energy transfer (FRET) acceptors due to their large absorption cross section, tunable emission, and high quantum yields. Engaging this type of FRET can be complicated due to direct excitation of the QD acceptor along with its longer excited-state lifetime. Many cases of QDs acting as energy transfer acceptors are within time-gated FRET from long-lifetime lanthanides, which allow the QDs to decay before observing FRET. Efficient QD sensitization requires the lanthanide to be in close proximity to the QD. To overcome the lifetime mismatch issues and limited transfer range, we utilized a Cy3 dye to bridge the energy transfer from an extremely long lived terbium emitter to the QD. We demonstrated that short-lifetime dyes can be used as energy transfer relays between extended lifetime components and in this way increased the distance of terbium-QD FRET to ∼14 nm.

Evaluating Dye-Labeled DNA Dendrimers for Potential Applications in Molecular Biosensing

DNA nanostructures provide a reliable and predictable scaffold for precisely positioning fluorescent dyes to form energy transfer cascades. Furthermore, these structures and their attendant dye networks can be dynamically manipulated by biochemical inputs, with the changes reflected in the spectral response. However, the complexity of DNA structures that have undergone such types of manipulation for direct biosensing applications is quite limited. Here, we investigate four different modification strategies to effect such dynamic manipulations using a DNA dendrimer scaffold as a testbed, and with applications to biosensing in mind. The dendrimer has a 2:1 branching ratio that organizes the dyes into a FRET-based antenna in which excitonic energy generated on multiple initial Cy3 dyes displayed at the periphery is then transferred inward through Cy3.5 and/or Cy5 relay dyes to a Cy5.5 final acceptor at the focus. Advantages of this design included good transfer efficiency, large spectral separation between the initial donor and final acceptor emissions for signal transduction, and an inherent tolerance to defects. Of the approaches to structural rearrangement, the first two mechanisms we consider employed either toehold-mediated strand displacement or strand replacement and their impact was mainly via direct transfer efficiency, while the other two were more global in their effect using either a belting mechanism or an 8-arm star nanostructure to compress the nanostructure and thereby modulate its spectral response through an enhancement in parallelism. The performance of these mechanisms, their ability to reset, and how they might be utilized in biosensing applications are discussed.

Probing Charge Transfer and Hot Carrier Dynamics in Organic Solar Cells with Terahertz Spectroscopy

Time-resolved terahertz spectroscopy (TRTS) was used to explore charge generation, transfer, and the role of hot carriers in organic solar cell materials. Two model molecular photovoltaic systems were investigated: with zinc phthalocyanine (ZnPc) or alpha-sexathiophene (α-6T) as the electron donors and buckminsterfullerene (C₆₀) as the electron acceptor. TRTS provides charge carrier conductivity dynamics comprised of changes in both population and mobility. By using time-resolved optical spectroscopy in conjunction with TRTS, these two contributions can be disentangled. The sub-picosecond photo-induced conductivity decay dynamics of C₆₀ were revealed to be caused by auto-ionization: the intrinsic process by which charge is generated in molecular solids. In donor-acceptor blends, the long-lived photo-induced conductivity is used for weight fraction optimization of the constituents. In nanoscale multilayer films, the photo-induced conductivity identifies optimal layer thicknesses. In films of ZnPc/C₆₀, electron transfer from ZnPc yields hot charges that localize and become less mobile as they thermalize. Excitation of high-lying Franck Condon states in C₆₀ followed by hole-transfer to ZnPc similarly produces hot charge carriers that self-localize; charge transfer clearly precedes carrier cooling. This picture is contrasted to charge transfer in α-6T/C₆₀, where hole transfer takes place from a thermalized state and produces equilibrium carriers that do not show characteristic signs of cooling and self-localization. These results illustrate the value of terahertz spectroscopic methods for probing charge transfer reactions.

Expanding molecular logic capabilities in DNA-scaffolded multiFRET triads

Dynamic rearrangement of DNA nanostructures provides a straightforward yet powerful mechanism for sequence-specific sensing and potential signaling of such interactions.

Complex Förster energy transfer interactions between semiconductor quantum dots and a redox-active osmium assembly

The ability of luminescent semiconductor quantum dots (QDs) to engage in diverse energy transfer processes with organic dyes, light-harvesting proteins, metal complexes, and redox-active labels continues to stimulate interest in developing them for biosensing and light-harvesting applications. Within biosensing configurations, changes in the rate of energy transfer between the QD and the proximal donor, or acceptor, based upon some external (biological) event form the principle basis for signal transduction. However, designing QD sensors to function optimally is predicated on a full understanding of all relevant energy transfer mechanisms. In this report, we examine energy transfer between a range of CdSe-ZnS core-shell QDs and a redox-active osmium(II) polypyridyl complex. To facilitate this, the Os complex was synthesized as a reactive isothiocyanate and used to label a hexahistidine-terminated peptide. The Os-labeled peptide was ratiometrically self-assembled to the QDs via metal affinity coordination, bringing the Os complex into close proximity of the nanocrystal surface. QDs displaying different emission maxima were assembled with increasing ratios of Os-peptide complex and subjected to detailed steady-state, ultrafast transient absorption, and luminescence lifetime decay analyses. Although the possibility exists for charge transfer quenching interactions, we find that the QD donors engage in relatively efficient Förster resonance energy transfer with the Os complex acceptor despite relatively low overall spectral overlap. These results are in contrast to other similar QD donor-redox-active acceptor systems with similar separation distances, but displaying far higher spectral overlap, where charge transfer processes were reported to be the dominant QD quenching mechanism.

THz detection of small molecule vapors in the atmospheric transmission windows

Using a low power beam of ultrashort THz pulses that propagate in the ambient laboratory environment we have measured the rotational signatures of small molecule vapors at frequencies within the atmospheric transmission windows. We investigate two types of apparatus. In the first type the THz beam propagates along a 6.7 meter round trip path that is external to the spectrometer, and which contains a long sample tube (5.4 meter round trip path) that holds the analyte vapor. The environment of the tube is controlled to simulate dry or humid conditions. In the second apparatus the THz beam propagates over a much longer 170 meter round trip path with analyte vapor contained in a relatively short 1.2 meter round trip path sample chamber. We describe the rotational signatures for each apparatus in the presence of the strong interference from water vapor absorption. For the shorter path long-tube apparatus we find that the peak detection sensitivity is sufficient to resolve a 1% absorption feature. For the more challenging 170 meter path apparatus we find that the peak detection sensitivity is sufficient to resolve a 3-5% absorption feature. The experiments presented here represent a first step towards using ultrashort THz pulses for coherent broad band detection of small molecule gases and vapors under ambient conditions.

Photoexcitation dynamics in films of C60 and Zn phthalocyanine with a layered nanostructure

We elucidate photoexcitation dynamics in C(60) and zinc phthalocyanine (ZnPc) from picoseconds to milliseconds by transient absorption and time-resolved terahertz spectroscopy. Autoionization of C(60) is a precursor to photocarrier generation. Decay of the terahertz signal is due to decreasing photocarrier mobility over the first 20 ps and thereafter reflects recombination dynamics. Singlet diffusion rates in C(60) are determined by modeling the rise of ground state bleaching of ZnPc absorption following C(60) excitation. Recombination dynamics transform from bimolecular to monomolecular as the layer thickness is reduced, revealing a metastable exciplex at the C(60)/ZnPc interface with a lifetime of 150 μs.

Enhanced multiple exciton generation in quasi-one-dimensional semiconductors

The creation of a single electron-hole pair (i.e., exciton) per incident photon is a fundamental limitation for current optoelectronic devices including photodetectors and photovoltaic cells. The prospect of multiple exciton generation per incident photon is of great interest to fundamental science and the improvement of solar cell technology. Multiple exciton generation is known to occur in semiconductor nanostructures with increased efficiency and reduced threshold energy compared to their bulk counterparts. Here we report a significant enhancement of multiple exciton generation in PbSe quasi-one-dimensional semiconductors (nanorods) over zero-dimensional nanostructures (nanocrystals), characterized by a 2-fold increase in efficiency and reduction of the threshold energy to (2.23 ± 0.03)E(g), which approaches the theoretical limit of 2E(g). Photovoltaic cells based on PbSe nanorods are capable of improved power conversion efficiencies, in particular when operated in conjunction with solar concentrators.

Temperature dependent characterization of terahertz vibrations of explosives and related threat materials

Waveguide terahertz time-domain spectroscopy (THz-TDS) is used to characterize the temperature dependent vibrational properties of three threat-related materials: 4-amino-dinitrotoluene (4A-DNT), pentaerythritol tetranitrate (PETN), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). These materials are characterized as thin polycrystalline layers deposited in the 50 micron gap of a metal parallel plate waveguide. For each material waveguide THz-TDS at least partially resolves the underlying vibrational spectrum and reveals new features that have not been observed in previous free space measurements of these materials. Strong experimental evidence for a phase transformation is observed for 4A-DNT as the polycrystalline layer on the waveguide surface is cooled to near 200 K. For PETN a highly resolved spectrum containing eleven vibrational lines is observed at 11 K with full-width at half maximum linewidths ranging from 7 GHz to 40 GHz. Based on comparison to measurements in the literature, our PETN measurement suggests that it is possible to produce narrow linewidths from a polycrystalline layer that approach those from a single crystal. Finally, for HMX, a highly resolved vibrational spectrum is measured that is assigned to the metastable gamma polymorph.

Fabrication of terahertz metamaterials by laser printing

A laser printing technique was used to fabricate split-ring resonators (SRRs) on Si substrates for terahertz (THz) metamaterials and their resonance behavior evaluated by THz time-domain spectroscopy. The laser-printed Ag SRRs exhibited sharp edge definition and excellent thickness uniformity, which resulted in an electromagnetic response similar to that from identical Au SRR structures prepared by conventional photolithography. These results demonstrate that laser printing is a practical alternative to conventional photolithography for fabricating metamaterial structures at terahertz frequencies, since it allows their design to be easily modified and optimized.

Quantum-dot/dopamine bioconjugates function as redox coupled assemblies for in vitro and intracellular pH sensing

The use of semiconductor quantum dots (QDs) for bioimaging and sensing has progressively matured over the past decade. QDs are highly sensitive to charge-transfer processes, which can alter their optical properties. Here, we demonstrate that QD-dopamine-peptide bioconjugates can function as charge-transfer coupled pH sensors. Dopamine is normally characterized by two intrinsic redox properties: a Nernstian dependence of formal potential on pH and oxidation of hydroquinone to quinone by O(2) at basic pH. We show that the latter quinone can function as an electron acceptor quenching QD photoluminescence in a manner that depends directly on pH. We characterize the pH-dependent QD quenching using both electrochemistry and spectroscopy. QD-dopamine conjugates were also used as pH sensors that measured changes in cytoplasmic pH as cells underwent drug-induced alkalosis. A detailed mechanism describing the QD quenching processes that is consistent with dopamine's inherent redox chemistry is presented.

Resonance Energy Transfer Between Luminescent Quantum Dots and Diverse Fluorescent Protein Acceptors

We characterized the resonance energy transfer interactions for conjugates consisting of QD donors self-assembled with three distinct fluorescent protein acceptors: two monomeric fluorescent proteins, the dsRed derivative mCherry or yellow fluorescent protein and the multi-chromophore b-phycoerythrin light harvesting complex. Using steady-state and time-resolved fluorescence, we showed that nonradiative transfer of excitation energy in these conjugates can be described within the Förster dipole-dipole formalism, with transfer efficiencies that vary with the degree of spectral overlap, donor-acceptor separation distance and the number of acceptors per QD. Comparison between the quenching data and simulation of the conjugate structures indicated that while energy transfer to monomeric proteins was identical to what was measured for QD-dye pairs, interactions with b-phycoerythrin were more complex. For the latter, the overall transfer efficiency results from the cumulative contribution of individual channels between the central QD and the chromophores distributed throughout the protein structure. Due to the biocompatible nature of fluorescent proteins, these QD-assemblies may have great potential for use in intracellular imaging and sensing.

7 GHz resolution waveguide THz spectroscopy of explosives related solids showing new features

The vibrational modes of the explosive related solids 2,4- and 2,6-DNT have been measured with waveguide THz time-domain spectroscopy (THz-TDS) to unprecedented precision. Dramatic sharpening of spectral features upon cooling beyond 80 K to 12 K is observed, illustrating the high quality and alignment of the polycrystalline thin films. Many of the observed features have linewidths below 15 GHz. These linewidths are approximately 8 times narrower than for the corresponding measurements via conventional THz-TDS with cooled pellets. For the 2,4- DNT, the line narrowing resolved 19 absorption features compared to only 7 features with the corresponding pellet measurement.

Photophysical properties of dioxolane-substituted pentacene derivatives dispersed in tris(quinolin-8-olato)aluminum(III)

Two novel dioxolane-substituted pentacene derivatives, namely, 6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]pentacene (TP-5) and 2,2,10,10-tetraethyl-6,14-bis-(triisopropylsilylethynyl)-1,3,9,11-tetraoxa-dicyclopenta[b,m]pentacene (EtTP-5), have been synthesized and spectroscopically characterized. Here, we examine the steady-state and time-resolved photoluminescence (PL) of solid-state composite films containing these pentacene derivatives dispersed in tris(quinolin-8-olato)aluminum(III) (Alq(3)). The films show narrow red emission and high absolute photoluminescence quantum yields (phi(PL) = 59% and 76% for films containing approximately 0.25 mol % TP-5 and EtTP-5, respectively). The Förster transfer radius for both guest-host systems is estimated to be approximately 33 A. The TP-5/Alq(3) thin films show a marked decrease in phi(PL) with increasing guest molecule concentrations, accompanied by dramatic changes in the PL spectra, suggesting that intermolecular interactions between pentacene molecules result in the formation of weakly radiative aggregates. In contrast, a lesser degree of fluorescence quenching is observed for EtTP-5/Alq(3) films. The measured fluorescence lifetimes of TP-5 and EtTP-5 are similar (approximately 18 ns) at low concentrations but deviate at higher concentrations as aggregation begins to play a role in the TP-5/Alq(3) films. The onset of aggregation in EtTP-5/Alq(3) films occurs at higher guest molecule concentrations (>1.00 mol %). The addition of ethyl groups on the terminal dioxolane rings leads to an increase in the intermolecular spacing in the solid, thereby reducing the tendency for pi-pi molecular stacking and aggregation.

Synthesis and Characterization of Donor−Acceptor Chromophores for Unidirectional Electron Transfer

[reaction: see text] A series of electron-transfer chromophores containing a donor and acceptor linked by an alkyl spacer were synthesized, and their electronic spectra were investigated. By inclusion with amylose, the supramolecularly encapsulated chromophores exhibit enhanced fluorescence quenching with discrete distance dependence and acquire the ability to sustain self-assemblies of a densely packed supramolecular array on a SiOH/Si substrate.

Dynamics of Energy Transfer of a Dioxolane-Substituted Pentacene Dispersed in 4,4-Bis[N-1-naphthyl-N-phenylamino]biphenyl

We examine the steady-state and time-resolved photoluminescence of guest-host films featuring a dioxolane-substituted pentacene derivative (2,2,10,10-tetraethyl-6,14-bis(triisopropylsilylethynyl)-1,3,9,11-tetraoxadicyclopenta[b,m]pentacene, EtTP-5) dispersed in the hole transporting material (4,4-bis[N-1-naphthyl-N-phenylamino]biphenyl, alpha-NPD). The films show bright red emission (lambda(max) = 640 nm) as a result of efficient Förster energy transfer from alpha-NPD host molecules to EtTP-5 guest molecules. High absolute photoluminescence (PL) quantum yield (phi(PL) = 76% +/- 4%) and fluorescence lifetime (tau = 18.6 +/- 0.8 ns) were measured at low concentration (0.28 mol % EtTP-5), with moderate PL quenching observed upon increasing the EtTP-5 concentration. The concentrated films (> or = 1.50 mol % EtTP-5) show less evidence of aggregation than previously seen when EtTP-5 was dispersed in tris(quinolin-8-olato)aluminum(III), making alpha-NPD a superior host for the red-emitting EtTP-5.

One-Dimensional Energy/Electron Transfer through a Helical Channel

We have synthesized A-D-A-type linear chain chromophores based on oligo(phenylene vinylene) as an electron donor (D) and several electron/energy acceptors (A), which are linked by an alkyl spacer with various lengths and are processed for a helical encapsulation with amylose. Photoinduced electron/energy transfers (eT/ET) of the chromophores are investigated in the presence and absence of the helical encapsulation with respect to D-A distance. Fluorescence intensity of the free chromophores is unusually small, not due to the advancement of eT/ET but most likely to self-quenching by aggregation and/or conformational flexibility in solution. By contrast, the helically encapsulated chromophores exhibit highly efficient eT/ET over a long D-A distance and a well-defined distance effect depending on the acceptor strength.

Light harvesting unsymmetrical conjugated dendrimers as photosynthetic mimics

We review the synthesis and photophysical properties of light harvesting phenylacetylene dendrimers with unsymmetrical branching. We describe the steady state and time dependent experiments that are used to characterize energy transfer properties in the conjugated dendrimers. Finally, we describe investigations of the unsymmetrical phenylacetylene dendrimers as potential materials for applications in fluorescence-based sensors, and for non-linear optics.

Excitation Energy Transfer in Tris(8-hydroxyquinolinato)aluminum Doped with a Pentacene Derivative

We investigate the excitation energy transfer in a guest-host molecular system consisting of a pentacene derivative, namely 6,13-bis(2,6-dimethylphenyl)pentacene (DMPP), doped into tris(8-hydroxyquinolinato)aluminum (Alq(3)) using steady-state and time-resolved photoluminescence (PL) spectroscopy. The concentration dependent energy transfer rate and efficiency are calculated and analyzed in terms of the Förster resonance energy transfer model. A relatively long excitation transfer time ( approximately 0.6-3.4 ns depending on the DMPP concentration) and a large transfer radius (31-36 A) are obtained. The Förster radius calculated directly from the Alq(3) PL-DMPP absorption spectral overlap (26 A) is smaller than the transfer radii obtained from the PL studies, which suggests that excitation energy migration within Alq(3) plays an important role in the energy transfer process, effectively elongating the transfer radius and increasing the transfer rate and efficiency.

Photoluminescence Properties of Conjugated Phenylacetylene Monodendrons in Thin Films

We report the absorption, photoluminescence (PL), and time-dependent PL of thin films of conjugated phenylacetylene monodendrons at both room temperature and at cryogenic temperature. We find that the PL properties of the monodendron thin films are significantly different from their fluorescence in dilute solution due to the presence of interactions between monodendrons in the thin film. These interactions lead to aggregate species in the thin films, which result in broader PL spectra and lower PL quantum yields than for monodendrons in dilute solution. Evidence for excimer-like aggregates in the monodendron thin films is found from time-resolved PL spectra.