Ultrasensitive measurements of microbial rhodopsin photocycles using photochromic FRET

Microbial rhodopsins are an important class of light-activated transmembrane proteins whose function is typically studied on bulk samples. Herein, we apply photochromic fluorescence resonance energy transfer to investigate the dynamics of these proteins with sensitivity approaching the single-molecule limit. The brightness of a covalently linked organic fluorophore is modulated by changes in the absorption spectrum of the endogenous retinal chromophore that occur as the molecule undergoes a light-activated photocycle. We studied the photocycles of blue-absorbing proteorhodopsin and sensory rhodopsin II (SRII). Clusters of 2-3 molecules of SRII clearly showed a light-induced photocycle. Single molecules of SRII showed a photocycle upon signal averaging over several illumination cycles.

Mapping nanomagnetic fields using a radical pair reaction

We used a fluorescent chemical indicator of magnetic field to visualize the magnetic field around ferromagnetic nanostructures. The indicator was a chain-linked electron donor-acceptor molecule, phenanthrene-(CH2)12-O-(CH2)2-dimethylaniline, that forms spin-correlated radical pairs upon photoexcitation. The magnetic field altered the coherent spin dynamics, yielding an 80% increase in exciplex fluorescence in a 0.1 T magnetic field. The magnetic field distributions were quantified to precision of 1.8×10(-4) T by image analysis and agreed with finite-element nanomagnetic simulations.

Assessing historical fish community composition using surveys, historical collection data, and species distribution models

Accurate establishment of baseline conditions is critical to successful management and habitat restoration. We demonstrate the ability to robustly estimate historical fish community composition and assess the current status of the urbanized Barton Creek watershed in central Texas, U.S.A. Fish species were surveyed in 2008 and the resulting data compared to three sources of fish occurrence information: (i) historical records from a museum specimen database and literature searches; (ii) a nearly identical survey conducted 15 years earlier; and (iii) a modeled historical community constructed with species distribution models (SDMs). This holistic approach, and especially the application of SDMs, allowed us to discover that the fish community in Barton Creek was more diverse than the historical data and survey methods alone indicated. Sixteen native species with high modeled probability of occurrence within the watershed were not found in the 2008 survey, seven of these were not found in either survey or in any of the historical collection records. Our approach allowed us to more rigorously establish the true baseline for the pre-development fish fauna and then to more accurately assess trends and develop hypotheses regarding factors driving current fish community composition to better inform management decisions and future restoration efforts. Smaller, urbanized freshwater systems, like Barton Creek, typically have a relatively poor historical biodiversity inventory coupled with long histories of alteration, and thus there is a propensity for land managers and researchers to apply inaccurate baseline standards. Our methods provide a way around that limitation by using SDMs derived from larger and richer biodiversity databases of a broader geographic scope. Broadly applied, we propose that this technique has potential to overcome limitations of popular bioassessment metrics (e.g., IBI) to become a versatile and robust management tool for determining status of freshwater biotic communities.

The cat that caught the canary: what to do with single-molecule trapping

It has recently become possible to trap individual fluorescent biomolecules in aqueous solution by using real-time tracking and active feedback to suppress Brownian motion. We propose areas of investigation in which anti-Brownian electrokinetic (ABEL) trapping of single molecules is likely to lead to significant new insights into biomolecular dynamics.

Electrical spiking in Escherichia coli probed with a fluorescent voltage-indicating protein

Bacteria have many voltage- and ligand-gated ion channels, and population-level measurements indicate that membrane potential is important for bacterial survival. However, it has not been possible to probe voltage dynamics in an intact bacterium. Here we developed a method to reveal electrical spiking in Escherichia coli. To probe bacterial membrane potential, we engineered a voltage-sensitive fluorescent protein based on green-absorbing proteorhodopsin. Expression of the proteorhodopsin optical proton sensor (PROPS) in E. coli revealed electrical spiking at up to 1 hertz. Spiking was sensitive to chemical and physical perturbations and coincided with rapid efflux of a small-molecule fluorophore, suggesting that bacterial efflux machinery may be electrically regulated.

Enhanced enantioselectivity in excitation of chiral molecules by superchiral light

A molecule or larger body is chiral if it cannot be superimposed on its mirror image (enantiomer). Electromagnetic fields may be chiral, too, with circularly polarized light (CPL) as the paradigmatic example. A recently introduced measure of the local degree of chiral dissymmetry in electromagnetic fields suggested the existence of optical modes more selective than circularly polarized plane waves in preferentially exciting single enantiomers in certain regions of space. By probing induced fluorescence intensity, we demonstrated experimentally an 11-fold enhancement over CPL in discrimination of the enantiomers of a biperylene derivative by precisely sculpted electromagnetic fields. This result, which agrees to within 15% with theoretical predictions, establishes that optical chirality is a fundamental and tunable property of light, with possible applications ranging from plasmonic sensors to absolute asymmetric synthesis.

Optical imaging through scattering media via magnetically modulated fluorescence

A weak (< 1000 G) magnetic field can influence photochemical processes through its effect on electron spin dynamics in a photogenerated radical pair. In a solution of pyrene and dimethylaniline this effect manifests as magnetic field-dependent exciplex fluorescence. Here we describe magnetofluorescence imaging (MFI). A localized magnetic null defines a fluorescence detection volume, which is scanned through a sample to create an image. MFI forms an image without lenses and in the presence of arbitrarily strong optical scattering. The resolution of MFI is in principle not limited by optical diffraction, although the present implementation is far from the diffraction limit.

Convex lens-induced confinement for imaging single molecules

Fluorescence imaging is used to study the dynamics of a wide variety of single molecules in solution or attached to a surface. Two key challenges in this pursuit are (1) to image immobilized single molecules in the presence of a high level of fluorescent background and (2) to image freely diffusing single molecules for long times. Strategies that perform well by one measure often perform poorly by the other. Here, we present a simple modification to a wide-field fluorescence microscope that addresses both challenges and dramatically improves single-molecule imaging. The technique of convex lens-induced confinement (CLIC) restricts molecules to a wedge-shaped gap of nanoscale depth, formed between a plano-convex lens and a planar coverslip. The shallow depth of the imaging volume leads to 20-fold greater rejection of background fluorescence than is achieved with total internal reflection fluorescence (TIRF) imaging. Elimination of out-of-plane diffusion leads to an approximately 10,000-fold longer diffusion-limited observation time per molecule than is achieved with confocal fluorescence correlation spectroscopy. The CLIC system also provides a new means to determine molecular size. The CLIC system does not require any nanofabrication, nor any custom optics, electronics, or computer control.

Optical chirality and its interaction with matter

We introduce a measure of the local density of chirality of the electromagnetic field. This optical chirality determines the asymmetry in the rates of excitation between a small chiral molecule and its mirror image, and applies to molecules in electromagnetic fields with arbitrary spatial dependence. A continuity equation for optical chirality in the presence of material currents describes the flow of chirality, in a manner analogous to the Poynting theorem for electromagnetic energy. "Superchiral" solutions to Maxwell's equations show larger chiral asymmetry, in some regions of space, than is found in circularly polarized plane waves.

Anti-Brownian traps for studies on single molecules

Until recently, Brownian motion was seen as an immutable feature of small particles in room-temperature liquids. Molecules, viruses, organelles, and small cells jiggle incessantly due to countless collisions with thermally agitated molecules of solvent. Einstein showed in 1905 that this motion is intimately linked to the tendency of every system to relax toward thermal equilibrium. In recent years, we and others have realized that Brownian motion is not as inescapable as one might think. By tracking the motion of a small particle and applying correction forces to the particle or to the measurement apparatus, one can largely suppress the Brownian motion of particles as small as a few nanometers in diameter, in aqueous solution at room temperature. This new ability to stabilize single molecules has led to a host of studies on topics ranging from the conformational dynamics of DNA to the optical properties of metal nanoparticles. In this review, we outline the physical principles behind suppression of Brownian motion. We discuss the relative merits of several systems that have been implemented. We give examples of studies performed with our anti-Brownian Electrokinetic trap (ABEL trap) as well as other anti-Brownian traps, and we discuss prospects for future research.

Surface plasmon resonance enhanced magneto-optics (SuPREMO): Faraday rotation enhancement in gold-coated iron oxide nanocrystals

We report enhanced optical Faraday rotation in gold-coated maghemite (gamma-Fe(2)O(3)) nanoparticles. The Faraday rotation spectrum measured from 480-690 nm shows a peak at about 530 nm, not present in either uncoated maghemite nanoparticles or solid gold nanoparticles. This peak corresponds to an intrinsic electronic transition in the maghemite nanoparticles and is consistent with a near-field enhancement of Faraday rotation resulting from the spectral overlap of the surface plasmon resonance in the gold with the electronic transition in maghemite. This demonstration of surface plasmon resonance-enhanced magneto-optics (SuPREMO) in a composite magnetic/plasmonic nanosystem may enable design of nanostructures for remote sensing and imaging of magnetic fields and for miniaturized magneto-optical devices.

Hardware-based anti-Brownian electrokinetic trap (ABEL trap) for single molecules: Control loop simulations and application to ATP binding stoichiometry in multi-subunit enzymes

The hardware-based Anti-Brownian ELectrokinetic trap (ABEL trap) features a feedback latency as short as 25 µs, suitable for trapping single protein molecules in aqueous solution. The performance of the feedback control loop is analyzed to extract estimates of the position variance for various controller designs. Preliminary data are presented in which the trap is applied to the problem of determining the distribution of numbers of ATP bound for single chaperonin multi-subunit enzymes.

Controlling Brownian motion of single protein molecules and single fluorophores in aqueous buffer

We present an Anti-Brownian Electrokinetic trap (ABEL trap) capable of trapping individual fluorescently labeled protein molecules in aqueous buffer. The ABEL trap operates by tracking the Brownian motion of a single fluorescent particle in solution, and applying a time-dependent electric field designed to induce an electrokinetic drift that cancels the Brownian motion. The trapping strength of the ABEL trap is limited by the latency of the feedback loop. In previous versions of the trap, this latency was set by the finite frame rate of the camera used for video-tracking. In the present system, the motion of the particle is tracked entirely in hardware (without a camera or image-processing software) using a rapidly rotating laser focus and lock-in detection. The feedback latency is set by the finite rate of arrival of photons. We demonstrate trapping of individual molecules of the protein GroEL in buffer, and we show confinement of single fluorophores of the dye Cy3 in water.

Principal-components analysis of shape fluctuations of single DNA molecules

Thermal fluctuations agitate molecules in solution over a broad range of times and distances. By passively watching the shape fluctuations of a thermally driven biomolecule, one can infer properties of the underlying interactions that determine the motion. We applied this concept to single molecules of fluorescently labeled lambda-DNA, a key model system for polymer physics. In contrast to most other single-molecule DNA experiments, we examined the unstretched, equilibrium state of DNA by using an anti-Brownian electrokinetic trap to confine the center of mass of the DNA without perturbing its internal dynamics. We analyze the long-wavelength conformational normal modes, calculate their spring constants, and measure linear and nonlinear couplings between modes. The modes show strong signs of nonlinear hydrodynamics, a feature of the underlying equations of polymer dynamics that has not previously been reported and is neglected in the widely used Rouse and Zimm approximations.

Internal mechanical response of a polymer in solution

We observed single molecules of fluorescently labeled double-stranded (ds) lambda DNA held in an anti-Brownian electrokinetic trap. From the measured density fluctuations we extract the density-density response function of the molecule over times >4.5 ms and distances >250 nm, i.e., how a perturbation in density in one part of the molecule propagates through the rest of the molecule. We find a nonmonotonic radial dependence of the relaxation time. In contrast with earlier measurements on freely diffusing dsDNA, we observe clear signs of internal hydrodynamic interactions.

Suppressing Brownian motion of individual biomolecules in solution

Single biomolecules in free solution have long been of interest for detailed study by optical methods, but Brownian motion prevents the observation of one single molecule for extended periods. We have used an anti-Brownian electrokinetic (ABEL) trap to trap individual protein molecules in free solution, under ambient conditions, without requiring any attachment to beads or surfaces. We also demonstrate trapping and manipulation of single virus particles, lipid vesicles, and fluorescent semiconductor nanocrystals.