Electrostatic modulation of multiple binding events between loquacious-PD and double-stranded RNA.

Electrostatics can alter the RNA-binding properties of proteins that display structure selectivity without sequence specificity. Loquacious-PD relies on this broad scope response to mediate the interaction of endonucleases with double stranded RNAs. Multimodal spectroscopic probes with in situ perturbations reveal an efficient and stable binding mechanism that disfavors high protein density complexes and is sensitive to local electrostatics.

Dynamic Response of Surface-Bound Peptides to a pH Perturbation Under Controlled Electrostatic Conditions.

The dynamic conformations of a thin peptide film covalently-linked to the surface of a transparent electrode are characterized over the course of a perturbation to their local pH by a photoacid under a controlled electrostatic potential. The local environment at this functionalized electrified interface is probed by the ultrafast fluorescence intensity and transient anisotropy of chromophores sparsely attached to the peptide side chains. A partition of chromophores into two sub-populations is observed, one buried in the peptide layer and another that is solvent exposed, and their relative contributions to the observed fluorescence signal are affected by both pH and voltage stimuli. The photophysical properties of solvent-exposed chromophores reveal that while the average conformation of the peptide mat is dictated by the pH of the surrounding electrolyte, their fluctuations are largely determined by the local electrostatic conditions set by the electrode's surface potential.

Photoactivation Properties of Self-n-Doped Perylene Diimides: Concentration-dependent Radical Anion and Dianion Formation.

Perylene diimides (PDIs) have garnered attention as organic photocatalysts in recent years for their ability to drive challenging synthetic transformations, such as aryl halide reduction and olefin iodoperfluoroalkylation. Previous work in this area employs spectator pendant groups attached to the imide nitrogen positions of PDIs that are only added to impart solubility. In this work, we employ electron-rich ammonium iodide or ammonium hydroxide pendant groups capable of self-n-doping the PDI core to form radical anions (R •- ) and dianions (D ••2- ). We observe R •- formation is favored at low concentrations where aliphatic linkers are able to freely rotate, while D ••2- formation is favored at elevated concentrations likely due to Coulombic stabilization between adjacent chromophores in a similar manner to that of Kasha exciton stabilization. Cyclic voltammetric measurements are consistent with steric encumbrance increasing the Lewis basicity of anions through Coulombic destabilization. However, sterics also inhibit dianion formation by disrupting aggregation. Finally, femtosecond transient absorption measurements reveal that low wavelength excitation (400 nm) preferentially favors the excitation of R •- to the strongly reducing doublet excited state 2[R •- ]*. In contrast, higher wavelength excitation (520 nm) favors the formation of the singlet excited state 1[N]*. These findings highlight the importance of dopant architecture, counterion selection, excitation wavelength, and concentration on R •- and D ••2- formation, which has substantial implications for future photocatalytic applications. We anticipate these findings will enable more efficient systems based on self-n-doped PDIs.

Selectively Altering the Reactivity of Transient Organic Radical Ions via Their Solvation Environment.

Photoexcitation of the charge transfer band of electron donor-acceptor complexes composed of toluene and 1,2,4,5-tetracyanobenzene yields organic radical ion pairs whose ultrafast reactive dynamics are determined by equilibrium solvent properties. A comparative study of ultrafast reaction rates in a series of alkane alcohols identified their dependence on the local polarizability and hydrogen bond donating/accepting character of the solvent. Because of the rapid and efficient equilibration of these radical ion pairs into solvent-separated species, simple modifications to bulk conditions can be used as a means to selectively alter their decay rates. Selectively altering distinct stages in this photochemical cycle via cosolutes or additives is a valuable step toward understanding and controlling the reactivity of organic radical ions in complex environments.

Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA.

Dicer-2 cleaves double-stranded RNA into siRNAs in a terminus-dependent manner as part of D. melanogaster's RNA interference pathway. Using ultrafast fluorescence, we probe the local environment of chromophores at the dsRNA terminus upon binding by Dicer-2 and interrogate the effects of Loquacious-PD, an accessory protein. We find substrate-selective modes of molecular recognition that distinguish between blunt and 3'overhang termini, but whose differences are greatly reduced by Loquacious-PD. These results connect the molecular recognition properties of Dicer-2 to its selective processing of dsRNAs with different termini and to its need for Loquacious-PD to efficiently produce endogenous siRNAs.

Efficient and effective single-step screening of individual samples for SARS-CoV-2 RNA using multi-dimensional pooling and Bayesian inference.

Rapid and widespread implementation of infectious disease surveillance is a critical component in the response to novel health threats. Molecular assays are the preferred method to detect a broad range of viral pathogens with high sensitivity and specificity. The implementation of molecular assay testing in a rapidly evolving public health emergency, such as the ongoing COVID-19 pandemic, can be hindered by resource availability or technical constraints. We present a screening strategy that is easily scaled up to support a sustained large volume of testing over long periods of time. This non-adaptive pooled-sample screening protocol employs Bayesian inference to yield a reportable outcome for each individual sample in a single testing step (no confirmation of positive results required). The proposed method is validated using clinical specimens tested using a real-time reverse transcription polymerase chain reaction test for SARS-CoV-2. This screening protocol has substantial advantages for its implementation, including higher sample throughput, faster time to results, no need to retrieve previously screened samples from storage to undergo retesting, and excellent performance of the algorithm's sensitivity and specificity compared with the individual test's metrics.

Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces.

The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.

Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self-nonself discrimination.

Some RIG-I-like receptors (RLRs) discriminate viral and cellular dsRNA by their termini, and Drosophila melanogaster Dicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3'-overhanging termini. We investigated the transient kinetic mechanism of the dmDcr-2 reaction using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. Indeed, we found that ATP binding to dmDcr-2's helicase domain impacts association and dissociation kinetics of dsRNA in a termini-dependent manner, revealing termini-dependent discrimination of dsRNA on a biologically relevant time scale (seconds). ATP hydrolysis promotes transient unwinding of dsRNA termini followed by slow rewinding, and directional translocation of the enzyme to the cleavage site. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent modulation in conformational fluctuations (nanoseconds) of the helicase and Platform-PAZ domains that is correlated with termini-dependent dsRNA cleavage. Our study offers a kinetic framework for comparison to other Dicers, as well as all members of the RLRs involved in innate immunity.

Multimodal spectroscopic investigation of the conformation and local environment of biomolecules at an electrified interface.

The complex and dynamic interfacial regions between biological samples and electronic components pose many challenges for characterization, including their evolution over multiple temporal and spatial scales. Spectroscopic probes of buried interfaces employing mid-infrared plasmon resonances and time-resolved fluorescence detection in the visible range are used to study the properties of polypeptides adsorbed at the surface of a working electrode. Information from these complementary spectroscopic probes reveals the interplay of solvation, electric fields, and ion concentration on their resulting macromolecular conformations.

Role of Polar Protic Solvents in the Dissociation and Reactivity of Photogenerated Radical Ion Pairs.

The UV photolysis of bimolecular charge transfer complexes is employed to yield reactive radical ions in their solvent-equilibrated electronic ground state. In polar protic media, noncovalent complexes of 1,2,4,5-tetracyanobenzene and toluene undergo efficient, ultrafast dissociation to ion pairs and equilibrate with their solvent environment before the resulting radical ions engage in electron transfer and proton abstraction on subnanosecond time scales. Solvent molecules play a critical role in these reactive pathways and in the dissociation and relaxation processes that precede them. We report a clear separation of time scales for these relaxation and reactive processes, which implies that solvent-solute interactions can be used as a tool for tuning the reaction pathways of equilibrated radical ions in solution.

Efficient Charge Transport in Disordered Conjugated Polymer Microstructures.

A new class of conjugated polymers with high charge mobilities exhibits the apparently conflicting morphological features of increased order at the molecular scale while lacking long-range order and crystallinity. To exploit their unique properties, mechanistic insights for charge transport events taking place from the molecular to the device scale must be uncovered. Thus, a central contributor to the continued progress in conjugated optoelectronic materials will be the development of advanced characterization tools, particularly those targeted to measuring the charge-transfer processes in heterogeneous, anisotropic, and hierarchically structured materials. This feature article describes the morphological properties that make partially ordered polymers an intriguing materials system to explore connections between chemical identity, solid-phase microstructure, and hierarchical charge transport. To this end, recent directions in materials development and new opportunities for characterization are discussed.

Resolving ultrafast exciton migration in organic solids at the nanoscale.

Effectiveness of molecular-based light harvesting relies on transport of excitons to charge-transfer sites. Measuring exciton migration, however, has been challenging because of the mismatch between nanoscale migration lengths and the diffraction limit. Instead of using bulk substrate quenching methods, here we define quenching boundaries all-optically with sub-diffraction resolution, thus characterizing spatiotemporal exciton migration on its native nanometre and picosecond scales. By transforming stimulated emission depletion microscopy into a time-resolved ultrafast approach, we measure a 16-nm migration length in poly(2,5-di(hexyloxy)cyanoterephthalylidene) conjugated polymer films. Combined with Monte Carlo exciton hopping simulations, we show that migration in these films is essentially diffusive because intrinsic chromophore energetic disorder is comparable to chromophore inhomogeneous broadening. Our approach will enable previously unattainable correlation of local material structure to exciton migration character, applicable not only to photovoltaic or display-destined organic semiconductors but also to explaining the quintessential exciton migration exhibited in photosynthesis.

Resolving and Controlling Photoinduced Ultrafast Solvation in the Solid State.

Solid-state solvation (SSS) is a solid-state analogue of solvent-solute interactions in the liquid state. Although it could enable exceptionally fine control over the energetic properties of solid-state devices, its molecular mechanisms have remained largely unexplored. We use ultrafast transient absorption and optical Kerr effect spectroscopies to independently track and correlate both the excited-state dynamics of an organic emitter and the polarization anisotropy relaxation of a small polar dopant embedded in an amorphous polystyrene matrix. The results demonstrate that the dopants are able to rotationally reorient on ultrafast time scales following light-induced changes in the electronic configuration of the emitter, minimizing the system energy. The solid-state dopant-emitter dynamics are intrinsically analogous to liquid-state solvent-solute interactions. In addition, tuning the dopant/polymer pore ratio offers control over solvation dynamics by exploiting molecular-scale confinement of the dopants by the polymer matrix. Our findings will enable refined strategies for tuning optoelectronic material properties using SSS and offer new strategies to investigate mobility and disorder in heterogeneous solid and glassy materials.

Uncovering Single-Molecule Photophysical Heterogeneity of Bright, Thermally Activated Delayed Fluorescence Emitters Dispersed in Glassy Hosts.

Recently developed all-organic emitters used in display applications achieve high brightness by harvesting triplet populations via thermally activated delayed fluorescence. The photophysical properties of these emitters therefore involve new inherent complexities and are strongly affected by interactions with their host material in the solid state. Ensemble measurements occlude the molecular details of how host-guest interactions determine fundamental properties such as the essential balance of singlet oscillator strength and triplet harvesting. Therefore, using time-resolved fluorescence spectroscopy, we interrogate these emitters at the single-molecule level and compare their properties in two distinct glassy polymer hosts. We find that nonbonding interactions with aromatic moieties in the host appear to mediate the molecular configurations of the emitters, but also promote nonradiative quenching pathways. We also find substantial heterogeneity in the time-resolved photoluminescence of these emitters, which is dominated by static disorder in the polymer. Finally, since singlet-triplet cycling underpins the mechanism for increased brightness, we present the first room-temperature measurement of singlet-triplet equilibration dynamics in this family of emitters. Our observations present a molecular-scale interrogation of host-guest interactions in a disordered film, with implications for highly efficient organic light-emitting devices. Combining a single-molecule experimental technique with an emitter that is sensitive to triplet dynamics, yet read out via fluorescence, should also provide a complementary approach to performing fundamental studies of glassy materials over a large dynamic range of time scales.

Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity.

Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.

Percolation, Tie-Molecules, and the Microstructural Determinants of Charge Transport in Semicrystalline Conjugated Polymers.

Semiconducting polymers play an important role in a wide range of optical and electronic material applications. It is widely accepted that the polymer ordering impacts charge transport in such devices. However, the connection between molecular ordering and device performance is difficult to predict due to the current need for a mathematical theory of the physics that dictate charge transport in semiconducting polymers. We present an analytical and computational description of semicrystalline conjugated polymer materials that captures the impact of polymer conformation on charge transport in heterogeneous thin films. We first develop an analytical theory for the statistical behavior of a polymer chain emanating from a crystallite, predicting the average distance to the first kink that would trap a charge. This analysis is used to define the conditions where percolation would lead to efficient transport through a semicrystalline material. We then establish a model that predicts the multiscale charge transport. This model is used to identify the speed limits of charge transport at short and long time scales for varying fraction of crystallinity. This work provides a rational framework to connect molecular organization to device performance.

Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers.

Existing models for the electronic properties of conjugated polymers do not capture the spatial arrangement of the disordered macromolecular chains over which charge transport occurs. Here, we present an analytical and computational description in which the morphology of individual polymer chains is dictated by well-known statistical models and the electronic coupling between units is determined using Marcus theory. The multiscale transport of charges in these materials (high mobility at short length scales, low mobility at long length scales) is naturally described with our framework. Additionally, the dependence of mobility with electric field and temperature is explained in terms of conformational variability and spatial correlation. Our model offers a predictive approach to connecting processing conditions with transport behavior.

A general relationship between disorder, aggregation and charge transport in conjugated polymers.

Conjugated polymer chains have many degrees of conformational freedom and interact weakly with each other, resulting in complex microstructures in the solid state. Understanding charge transport in such systems, which have amorphous and ordered phases exhibiting varying degrees of order, has proved difficult owing to the contribution of electronic processes at various length scales. The growing technological appeal of these semiconductors makes such fundamental knowledge extremely important for materials and process design. We propose a unified model of how charge carriers travel in conjugated polymer films. We show that in high-molecular-weight semiconducting polymers the limiting charge transport step is trapping caused by lattice disorder, and that short-range intermolecular aggregation is sufficient for efficient long-range charge transport. This generalization explains the seemingly contradicting high performance of recently reported, poorly ordered polymers and suggests molecular design strategies to further improve the performance of future generations of organic electronic materials.