Engineering couplings for exciton transport using synthetic DNA scaffolds
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A bottom-up perspective on photodynamics and photoprotection in light-harvesting complexes using anti-Brownian trapping
Single-molecule fluorescence spectroscopy allows direct, real-time observation of dynamic photophysical changes in light harvesting complexes. The Anti-Brownian ELectrokinetic (ABEL) trap is one such single-molecule method with useful advantages. This approach is particularly well-suited to make detailed spectroscopic measurements of pigment-protein complexes in solution phase because it enables extended-duration single-molecule observation by counteracting Brownian motion. This Perspective summarizes recent contributions by the authors and others that have utilized the unique capabilities of the ABEL trap to advance our understanding of phycobiliproteins and the phycobilisome complex, the primary light-harvesting apparatus of cyanobacteria. Monitoring the rich spectroscopic data from these measurements, which include brightness, fluorescence lifetime, polarization, and emission spectra, among other measurable parameters, has provided direct characterization of pigments and energy transfer pathways in the phycobilisome, spanning scales from single pigments and monomeric phycobiliproteins to higher order oligomers and protein-protein interactions of the phycobilisome complex. Importantly, new photophysical states and photodynamics were observed to modulate the flow of energy through the phycobilisome and suggest a previously unknown complexity in phycobilisome light harvesting and energy transport with a possible link to photoadaptive or photoprotective functions in cyanobacteria. Here, beyond deepening our collective understanding of natural light-harvesting systems, these and future discoveries may serve as inspiration for engineering improved artificial light-harvesting technologies.
14 SOLAR ENERGY↗
Potential-Dependent Adhesion Forces between dsDNA and Electroactive Surfaces
A promising approach to regulating the interactions between polyelectrolytes and materials is the use of electroactive surfaces that can change their charge state. However, common electroactive groups are too unstable to be practical for this purpose. Here we have performed a single molecule force spectroscopy study of the interactions between dsDNA and an 1,1'-biferrocenylene (BFD = bis(fulvalene)diiron)-terminated self-assembled monolayer surface that allows us to reversibly change the charge state. We found that the interaction force between DNA and the surface is correlated to the oxidation state of the BFD groups, which is conveniently controlled by the electrochemical potentials. We discovered that the electroactive SAM produces much stronger interaction forces than its nonelectroactive counterpart. A model based on the Grahame equation was able to quantitatively reproduce the experimentally observed relation between the applied potentials and adhesion forces. Our electroactive surface provides a model system for quantitative studies of the interactions between polyelectrolyte and charged surfaces in liquid. Furthermore, these insights may enable new opportunities for actively manipulating the binding, orientations, and conformations of polyelectrolytes for biosensing, nanomotors, and other applications.
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Gating Single Molecules with Counterions
We report atomic-scale gating and visualization of local charge distribution within individual rare-earth-based molecular complexes on a metallic surface. The complexes are formed by a positively charged lanthanum ion coordinated to a (pcam)3 molecule and a negatively charged counterion trapped underneath via electrostatic interactions on a Au(111) surface. Local gating is performed by adding an additional negatively charged counterion to one side of the complex, which results in the redistribution of charges within the complex and a positive shift of the frontier orbitals. This is caused by the internal Stark effect induced by the added counterion. This effect is directly captured using tunneling spectroscopy and spectroscopic mapping at 5 K substrate temperature. The polarizability of the complex is corroborated by density functional theory and analytical calculations based on experimental findings. Furthermore, the influence of charge polarization on nearby complexes is investigated in a cluster purposely assembled using three complexes, which reveals maintaining the charge states as in single complexes. These findings will enable the design of robust charged rare-earth complexes to be tailored for potential solid-state applications.
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LHCSR1 Functions as a Dimmer Switch for Light Harvesting
In oxygenic photosynthesis, high light leads to a set of photoprotective processes, known as nonphotochemical quenching, that are required for fitness. In moss and algae, the pigment−protein complex, light-harvesting stress-related (LHCSR), is crucial for photoprotection. Acidification of the thylakoid lumen under high light triggers the activation of LHCSR and the conversion of the xanthophyll violaxanthin into zeaxanthin, which is found within LHCSR. These interrelated molecular components combine to turn on a safety valve that dissipates excess energy as heat. Previous studies of detergent-solubilized LHCSR1 found that pH and zeaxanthin regulate distinct quenching sites via the protein conformation. However, protein function in the native membrane environment can be significantly different. In this work, we applied single-molecule fluorescence spectroscopy to LHCSR1 in membrane nanodiscs. The membrane environment enhanced total quenching, regardless of pH or zeaxanthin-binding. pH-dependent quenching was still observed whereas zeaxanthin-dependent quenching was suppressed. Conformational changes also increased in the membrane, establishing that the local environment can change the nature of the equilibrium between light harvesting and photoprotection.
Hoffmann, Madeline P. [Massachusetts Inst. of Tech↗
Substituent Effects in Mechanochemical Allowed and Forbidden Cyclobutene Ring-Opening Reactions
Woodward and Hoffman once jested that a very powerful Maxwell demon could seize a molecule of cyclobutene at its methylene groups and tear it open in a disrotatory fashion to obtain butadiene (Woodward, R. B.; Hoffmann, R. The Conservation of Orbital Symmetry. Angew. Chem., Int. Ed. 1969, 8, 781–853). Nearly 40 years later, that demon was discovered, and the field of covalent polymer mechanochemistry was born. In the decade since our demon was befriended, many fundamental investigations have been undertaken to build up our understanding of force-modified pathways for electrocyclic ring-opening reactions. In this work, we seek to extend that fundamental understanding by exploring substituent effects in allowed and forbidden ring-opening reactions of cyclobutene (CBE) and benzocyclobutene (BCB) using a combination of single-molecule force spectroscopy (SMFS) and computation. We show that, while the forbidden ring-opening of cis-BCB occurs at a lower force than the allowed ring-opening of trans-BCB on the time scale of the SMFS experiment, the opposite is true for cis- and trans-CBE. Such a reactivity flip is explained through computational analysis and discussion of the so-called allowed/forbidden gap.
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Single-Molecule Detection of the Encounter and Productive Electron Transfer Complexes of a Photosynthetic Reaction Center
Small, diffusible redox proteins play an essential role in electron transfer (ET) in respiration and photosynthesis, sustaining life on Earth by shuttling electrons between membrane-bound complexes via finely tuned and reversible interactions. Ensemble kinetic studies show transient ET complexes form in two distinct stages: an “encounter” complex largely mediated by electrostatic interactions, which subsequently, through subtle reorganization of the binding interface, forms a “productive” ET complex stabilized by additional hydrophobic interactions around the redox-active cofactors. Here, using single-molecule force spectroscopy (SMFS) we dissected the transient ET complexes formed between the photosynthetic reaction center-light harvesting complex 1 (RC-LH1) of Rhodobacter sphaeroides and its native electron donor cytochrome c 2 (cyt c 2 ). Importantly, SMFS resolves the distribution of interaction forces into low (~150 pN) and high (~330 pN) components, with the former more susceptible to salt concentration and to alteration of key charged residues on the RC. Thus, the low force component is suggested to reflect the contribution of electrostatic interactions in forming the initial encounter complex, whereas the high force component reflects the additional stabilization provided by hydrophobic interactions to the productive ET complex. Employing molecular dynamics simulations, we resolve five intermediate states that comprise the encounter, productive ET and leaving complexes, predicting a weak interaction between cyt c 2 and the LH1 ring near the RC-L subunit that could lie along the exit path for oxidized cyt c 2 . The multimodal nature of the interactions of ET complexes captured here may have wider implications for ET in all domains of life.
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X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release
Neurotransmitter:sodium symporters (NSS) are conserved from bacteria to man and serve as targets for drugs, including antidepressants and psychostimulants. Here we report the X-ray structure of the prokaryotic NSS member, LeuT, in a Na+/substrate-bound, inward-facing occluded conformation. To obtain this structure, we were guided by findings from single-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe binding and mutation of the conserved N-terminal Trp8 to Ala both promote an inward-facing state. Compared to the outward-facing occluded conformation, our structure reveals a major tilting of the cytoplasmic end of transmembrane segment (TM) 5, which, together with release of the N-terminus but without coupled movement of TM1, opens a wide cavity towards the second Na + binding site. The structure of this key intermediate in the LeuT transport cycle, in the context of other NSS structures, leads to the proposal of an intracellular release mechanism of substrate and ions in NSS proteins.
Science & Technology - Other Topics↗
Molecular design principles of Lysine-DOPA wet adhesion
The mussel byssus has long been a source of inspiration for the adhesion community. Recently, adhesive synergy between flanking lysine (Lys, K) and 3,4-Dihydroxyphenylalanine (DOPA, Y ) residues in the mussel foot proteins (Mfps) has been highlighted. However, the complex topological relationship of DOPA and Lys as well as the interfacial adhesive roles of other amino acids have been understudied. Herein, we study adhesion of Lys and DOPA-containing peptides to organic and inorganic substrates using single-molecule force spectroscopy (SMFS). We show that a modest increase in peptide length, from K Y to (K Y ) 3 , increases adhesion strength to TiO 2. Surprisingly, further increase in peptide length offers no additional benefit. Additionally, comparison of adhesion of dipeptides containing Lys and either DOPA (K Y ) or phenylalanine (KF) shows that DOPA is stronger and more versatile. We furthermore demonstrate that incorporating a nonadhesive spacer between (K Y ) repeats can mimic the hidden length in the Mfp and act as an effective strategy to dissipate energy.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates
The sequence specificity and programmability of DNA binding and cleavage have enabled widespread applications of CRISPR-Cas12a in genetic engineering. As an RNA-guided CRISPR endonuclease, Cas12a engages a 20-base pair (bp) DNA segment by forming a three-stranded R-loop structure in which the guide RNA hybridizes to the DNA target. Here we use single-molecule torque spectroscopy to investigate the dynamics and mechanics of R-loop formation of two widely used Cas12a orthologs at base-pair resolution. We directly observe kinetic intermediates corresponding to a ~5 bp initial RNA-DNA hybridization and a ~17 bp intermediate preceding R-loop completion, followed by transient DNA unwinding that extends beyond the 20 bp R-loop. The complex multistate landscape of R-loop formation is ortholog-dependent and shaped by target sequence, mismatches, and DNA supercoiling. A four-state kinetic model captures essential features of Cas12a R-loop dynamics and provides a biophysical framework for understanding Cas12a activity and specificity.
59 BASIC BIOLOGICAL SCIENCES↗
Spatially resolved photoluminescence brightening in individual single-walled carbon nanotubes
Single-molecule microscopy was used to image photoluminescence (PL) brightening of individual sodium-dodecyl-sulfate (SDS)-wrapped single-walled carbon nanotubes (SWCNTs) upon the addition of dithiothreitol (DTT). PL enhancement varied for each nanotube (NT), with some brightening by 16% and others by a factor of about 7. Interestingly, NTs that displayed lower initial QY values showed the largest increases in PL enhancement. SDS-SWCNTs longer than the diffraction limit were studied in order to spatially resolve the brightening phenomenon. Quite unexpectedly, a uniform, single-step PL brightening along the NT was consistently observed, suggesting that the PL enhancement is the result of a non-localized process. Furthermore, the even PL brightening seen over SWCNTs that are micrometers long implies that single point defect sites, which are known to be largely responsible for exciton nonradiative decay, play no significant role in the brightening process. Interestingly, affixing the SWCNT strongly to the substrate surface mitigated the PL brightening response, consistent with a hypothesis that surfactant reorganization upon the addition of DTT is responsible for exciton PL brightening.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein
Photosynthetic organisms rely on sophisticated photoprotective mechanisms to prevent oxidative damage under high or fluctuating solar illumination. Cyanobacteria, which have evolved a unique, water-soluble light-harvesting complex—the phycobilisome—achieve photoprotection through a photoactivatable quencher called the Orange Carotenoid Protein (OCP). Phycobilisomes are highly symmetric and modular, formed by hierarchical assembly of conserved subunits into diverse geometries ranging from simple bundles to elaborate fan- or bouquet-like macromolecular architectures. Although OCP is known to provide photoprotection across species of cyanobacteria with different phycobilisome structures, it is not known whether or how these structural variations relate to changes in the photoprotective function of OCP. For example, OCP was recently discovered to bind as a dimer at two specific instances of an abundant structural motif on the tricylindrical phycobilisome of Synechocystis sp. PCC 6803, yet these sites are sterically inaccessible on a more common pentacylindrical phycobilisome ( Anabaena sp. PCC 7120). To understand how structural modularity and binding specificity contribute to conservation of OCP binding sites and function across different phycobilisome architectures, here we compare experimentally measured photophysical states accessible to these prototypical tricylindrical and pentacylindrical phycobilisomes, with and without OCP, at the single-molecule level. Together with Monte Carlo simulations of exciton transfer in OCP-quenched phycobilisomes, our results suggest that OCP binds at distinct and specific sites in each type of phycobilisome, yet provides nearly identical quenching strength to both phycobilisomes. Our findings highlight the utility of modular phycobilisome structures in balancing robust conservation of photoprotective function with adaptability of site-specific binding across species.
59 BASIC BIOLOGICAL SCIENCES↗
Gold Ion Beam Milled Gold Zero-Mode Waveguides
Zero-mode waveguides (ZMWs) are widely used in single molecule fluorescence microscopy for their enhancement of emitted light and the ability to study samples at physiological concentrations. ZMWs are typically produced using photo or electron beam lithography. We report a new method of ZMW production using focused ion beam (FIB) milling with gold ions. We demonstrate that ion-milled gold ZMWs with 200 nm apertures exhibit similar plasmon-enhanced fluorescence seen with ZMWs fabricated with traditional techniques such as electron beam lithography.
36 MATERIALS SCIENCE↗
Atomic Force Microscope Active Optical Probe for Single-Molecule Imaging and Time-Resolved Optical Spectroscopy (DOE SBIR Phase II/IIA Final Report)
Actoprobe LLC reports on the results of its DOE SBIR Phase II/IIA project on the development of Atomic Force Microscope Active Optical Probe for Single-Molecule Imaging and Time-Resolved Optical Spectroscopy. While chemistry science and technology greatly benefit from Atomic Force Microscopy in surface characterization, time-resolved chemical imaging on the single-molecule level lags far behind. Current scanning probe microscopy only obtains information about mechanical but not optical/chemical properties. To address this problem, the Actoprobe LLC research team has proposed a novel class of Atomic Force Microscopy probes, Ultra-Fast Pulsed Active Atomic Force Microscopy Optical Probes (UFP AAOPs), that will allow ultrafast time-resolved optical and chemical imaging at the nanoscale. As envisioned, these unique optical probes will perform the functions of conventional Atomic Force Microscopy probes and, in addition, will simultaneously provide chemical information about molecular scale interactions. This innovation is accomplished by integrating an ultrafast pulsed Quantum Dot laser source into an Atomic Force Microscopy probe. This report describes our progress with the fabrication of an ultrafast micrometer-size semiconductor laser, based on “artificial atoms” - Quantum Dots, integrated with an Atomic Force Microscopy probe. In this Phase II/IIA project, we have demonstrated the feasibility of the UFP AAOP concept by fabricating a first prototype of the UFP AAOP. The excellent performance of the probe has been proven in terms of AFM and optical spatial resolution through rigorous tests. The UFP AAOP provides pulses with less than 4 ps duration and higher than 11 GHz repetition rate, and spatial resolution better than 300 nm at 1240 nm wavelength. Technically, it is possible to reduce the pulse width to less than 1 ps and to improve lateral resolution to ~ 0.5 nm, which implies the potential capability for the probe to characterize chemical compounds with single-molecule resolution. The UFP AAOP fabrication procedure has been developed for wafer-scale production of multiple devices, with the yield of the process estimated to be lower than 1% with the limited fabrication capabilities and equipment available for use in the research project. However, using high-volume production tools and special GaAs processing equipment, the yield can be significantly improved, theoretically to ~ 50%. Finally, economic feasibility and scale-up manufacturing potential were analyzed for UFP AAOP and found to be very promising. In summary, the Actoprobe team has successfully demonstrated the feasibility of the UFP AAOP concept.
36 MATERIALS SCIENCE↗
Exploring the Vibrational Side of Spin-Phonon Coupling in Single-Molecule Magnets via 161 Dy Nuclear Resonance Vibrational Spectroscopy
Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) using the Mossbauer isotope 161 Dy has been employed for the first time to study the vibrational properties of a single-molecule magnet (SMM) incorporating Dy III , namely [Dy(Cy3PO)(2)(H2O)(5)]Br-3•2 (Cy3PO)•2 H2O•2 EtOH. The experimental partial phonon density of states (pDOS), which includes all vibrational modes involving a displacement of the Dy III ion, was reproduced by means of simulations using density functional theory (DFT), enabling the assignment of all intramolecular vibrational modes. This study proves that 161 Dy NRVS is a powerful experimental tool with significant potential to help to clarify the role of phonons in SMMs.
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Theory of Photoluminescence Spectral Line Shapes of Semiconductor Nanocrystals
Single-molecule photoluminescence (PL) spectroscopy of semiconductor nanocrystals (NCs) reveals the nature of exciton–phonon interactions in NCs. Understanding the homogeneous spectral line shapes and their temperature dependence remains an open problem. Here, we develop an atomistic model to describe the PL spectrum of NCs, accounting for excitonic effects, phonon dispersion relations, and exciton–phonon couplings. We validate our model using single-NC measurements on CdSe/CdS NCs from T = 4 to 290 K, and we find that the slightly asymmetric main peak at low temperatures is comprised of a narrow zero-phonon line (ZPL) and acoustic phonon sidebands. Furthermore, we identify the specific phonon modes that give rise to the optical phonon sidebands. At temperatures above 200 K, the spectral line width shows a stronger dependence upon the temperature, which we demonstrate to be correlated with higher order exciton–phonon couplings. We also identify the line width dependence upon reorganization energy, NC core sizes, and shell thicknesses.
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Overcoming photobleaching in imaging of single barium atoms in a solid xenon matrix
Neutrinoless double beta decay is one of the most sensitive probes for new physics beyond the Standard Model of particle physics. One of the isotopes under investigation is 136 Xe, which would double beta decay into 136 Ba. Detecting the single 136 Ba daughter provides a sort of ultimate tool in the discrimination against backgrounds. Previous work demonstrated the ability to perform single atom imaging of Ba atoms in a single-vacancy site of a solid xenon matrix. In this paper, the effort to identify signal from individual barium atoms is extended to Ba atoms in a hexa-vacancy site in the matrix and is achieved despite increased photobleaching in this site. Abrupt fluorescence turn-off of a single Ba atom is also observed. Significant recovery of fluorescence signal lost through photobleaching is demonstrated upon annealing of Ba deposits in the Xe ice. Following annealing, it is observed that Ba atoms in the hexa-vacancy site exhibit antibleaching while Ba atoms in the tetra-vacancy site exhibit bleaching. This may be evidence for a matrix site transfer upon laser excitation. Our findings offer a path of continued research toward tagging of Ba daughters in all significant sites in solid xenon.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Spatially Resolved Mapping of Three-Dimensional Molecular Orientations with ~2 nm Spatial Resolution through Tip-Enhanced Raman Scattering
We record local optical field images of silver nanocubes (75 nm) using tip-enhanced Raman (TER) spectral imaging. The images that we observe are consistent with several recent reports from our group, but here, we demonstrate sub-2 nm spatial resolution in local optical field nanoimaging under ambient laboratory conditions. This is achieved by scanning the substrate (nanocube on Si) relative to a 4-thiobenzonitrile (TBN)-functionalized Ag-coated TER probe. The spatial resolution that we obtain necessitates that only a few molecules govern the recorded optical response; molecular orientation becomes an important consideration in such measurements. We model the orientation through geometry optimization of a TBN molecule chemisorbed onto an Ag79 cluster (sphere with a ~1 nm diameter). Using the computed orientation of the cluster-bound molecule, we then model the optical response using formalism that accounts for the orientation of the molecule relative to vector components of the local optical fields. We find optimal agreement between experiment and theory. In effect, this work reveals the parallels between single-molecule Raman scattering and high-spatial-resolution TER spectroscopy, even when the images themselves cannot be used to visualize a single molecule in real space.
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