Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms.

The ε4-allele variant of apolipoprotein E (ApoE4) is the strongest genetic risk factor for Alzheimer's disease, although it only differs from its neutral counterpart ApoE3 by a single amino acid substitution. While ApoE4 influences the formation of plaques and neurofibrillary tangles, the structural determinants of pathogenicity remain undetermined due to limited structural information. Previous studies have led to conflicting models of the C-terminal region positioning with respect to the N-terminal domain across isoforms largely because the data are potentially confounded by the presence of heterogeneous oligomers. Here, we apply a combination of single-molecule spectroscopy and molecular dynamics simulations to construct an atomically detailed model of monomeric ApoE4 and probe the effect of lipid association. Importantly, our approach overcomes previous limitations by allowing us to work at picomolar concentrations where only the monomer is present. Our data reveal that ApoE4 is far more disordered and extended than previously thought and retains significant conformational heterogeneity after binding lipids. Comparing the proximity of the N- and C-terminal domains across the three major isoforms (ApoE4, ApoE3, and ApoE2) suggests that all maintain heterogeneous conformations in their monomeric form, with ApoE2 adopting a slightly more compact ensemble. Overall, these data provide a foundation for understanding how ApoE4 differs from nonpathogenic and protective variants of the protein.

Ultrafast dynamics and ultrasensitive single particle spectroscopy of optically robust core/alloy shell semiconductor quantum dots.

A "one-pot one-step" synthesis method of Core/Alloy Shell (CAS) quantum dots (QDs) offers the scope of large scale synthesis in a less time consuming, more economical, highly reproducible and high-throughput manner in comparison to "multi-pot multi-step" synthesis for Core/Shell (CS) QDs. Rapid initial nucleation, and smooth & uniform shell growth lead to the formation of a compositionally-gradient alloyed hetero-structure with very significantly reduced interfacial trap density in CAS QDs. Thus, interfacial strain gets reduced in a much smoother manner leading to enhanced confinement for the photo-generated charge carriers in CAS QDs. Convincing proof of alloy-shelling for a CAS QD has been provided from HRTEM images at the single particle level. The band gap could be tuned as a function of composition, temperature, reactivity difference of precursors, etc. and a high PLQY and improved photochemical stability could be achieved for a small sized CAS QD. From the ultrafast exciton dynamics in CdSe and InP CAS QDs, it has been shown that (a) the hot exciton thermalization/relaxation happens in <500 fs, (b) hot electron trapping dynamics occurs within a ∼1 ps time scale, (c) band edge exciton trapping occurs within a 10-25 ps timescale and (d) for CdSe CAS QDs the hot hole gets trapped in about 35 ps. From fast PL decay dynamics, it has been shown that the amplitude of the intermediate time constant can be correlated with the PLQY. A model has been provided to understand these ultrafast to fast exciton dynamical processes. At the ultrasensitive single particle level, unlike CS QDs, CdSe CAS QDs have been shown to exhibit (a) constancy of PLmax (i.e. no bluing) and (b) constancy of PL intensity (i.e. no bleaching) of the single CAS QDs for continuous irradiation for one hour under an air atmosphere. Thus, CAS QDs hold the promise of being a superior optical probe in comparison to CS QDs both at the ensemble and at the single particle level, leading to enhanced flexibility of the CAS QDs towards designing and developing next generation application devices.

Membrane potential sensing: Material design and method development for single particle optical electrophysiology.

We review the development of "single" nanoparticle-based inorganic and organic voltage sensors, which can eventually become a viable tool for "non-genetic optogenetics." The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark Effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (∼2% Δλ spectral Stark shift up to ∼30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic facet-selective coating, enabling effective compartmentalization beyond non-specific staining. Self-spiking- and patched-HEK293 cells and cortical neurons, when stained with hybrid nanobiomaterials, show clear photoluminescence intensity changes in response to membrane potential (MP) changes. Organic voltage nanosensors based on polystyrene beads and nanodisk technology utilize Fluorescence (Förster) Resonance Energy Transfer (FRET) to sense local electric fields. Voltage sensing FRET pairs achieve voltage sensitivity up to ∼35% ΔF/F per 120 mV in cultures. Non-invasive MP recording from individual targeted sites (synapses and spines) with nanodisks has been realized. However, both of these QCSE- and FRET-based voltage nanosensors yet need to reach the milestone of recording individual action potentials from individual targeted sites.

Mechanical Tension of Biomembranes Can Be Measured by Super Resolution (STED) Microscopy of Force-Induced Nanotubes.

Membrane tension modulates the morphology of plasma-membrane tubular protrusions in cells but is difficult to measure. Here, we propose to use microscopy imaging to assess the membrane tension. We report direct measurement of membrane nanotube diameters with unprecedented resolution using stimulated emission depletion (STED) microscopy. For this purpose, we integrated an optical tweezers setup in a commercial microscope equipped for STED imaging and established micropipette aspiration of giant vesicles. Membrane nanotubes were pulled from the vesicles at specific membrane tension imposed by the aspiration pipet. Tube diameters calculated from the applied tension using the membrane curvature elasticity model are in excellent agreement with data measured directly with STED. Our approach can be extended to cellular membranes and will then allow us to estimate the mechanical membrane tension within the force-induced nanotubes.

Mechanical-Bending-Induced Fluorescence Enhancement in Plastically Flexible Crystals of a GFP Chromophore Analogue.

Single crystals of optoelectronic materials that respond to external stimuli, such as mechanical, light, or heat, are immensely attractive for next generation smart materials. Here we report single crystals of a green fluorescent protein (GFP) chromophore analogue with irreversible mechanical bending and associated unusual enhancement of the fluorescence, which is attributed to the strained molecular packing in the perturbed region. Soft crystalline materials with such fluorescence intensity modulations occurring in response to mechanical stimuli under ambient pressure conditions will have potential implications for the design of technologically relevant tunable fluorescent materials.

Reply to the 'Comment on ""Where does the fluorescing moiety reside in a carbon dot?"- Investigations based on fluorescence anisotropy decay and resonance energy transfer dynamics"' by H. C. Joshi, Phys. Chem. Chem. Phys., 2019, 21, DOI: 10.1039/c9cp00136k.

The claim that the analysis regarding resonance energy transfer should have been made using different equations than those that we have used is negated based on the following points: (1) we are well aware of the equations the author has provided in his comment. The equation (eqn (3) mentioned below) that the author has written is undoubtedly too simple to describe the complex system delineated in our original paper. This particular equation is perhaps OK for simple dye (donor and acceptor) systems; however, such a simple equation is never enough for nanoparticle/quantum dot systems. (2) Another equation suggested by the author in his comment (eqn (2)) contains a parameter called donor concentration in excited state. We have categorically described in page 6-7 of our original paper why it is difficult to measure the donor concentration accurately even in the ground state. When the donor concentration can't be known accurately it can't be used in the suggested equation. (3) Donor-acceptor distance calculated by eqn (3)/Table 1 provided by the author deviates more than 100% from the distance that is physically feasible. Such kinds of problems are well documented in the literature. (4) One of the papers cited by the author in his comment and many other published papers clearly mention that in the case when all donor molecules/particles do not take part in the resonance energy transfer process or the stoichiometry of a donor-acceptor complex is not known or deviates strongly from 1 : 1, especially in quantum dots or any other nanomaterial system, it is not possible to extract accurate dynamical information related to RET from donor decay. Instead risetime of acceptor yields much more accurate information. Such situations do arise in our system as well.

Asymmetric Ionic Conditions Generate Large Membrane Curvatures.

Biological membranes possess intrinsic asymmetry. This asymmetry is associated not only with leaflet composition in terms of membrane species but also with differences in the cytosolic and periplasmic solutions containing macromolecules and ions. There has been a long quest for understanding the effect of ions on the physical and morphological properties of membranes. Here, we elucidate the changes in the mechanical properties of membranes exposed to asymmetric buffer conditions and the associated curvature generation. As a model system, we used giant unilamellar vesicles (GUVs) with asymmetric salt and sugar solutions on the two sides of the membrane. We aspirated the GUVs into micropipettes and attached small beads to their membranes. An optical tweezer was used to exert a local force on a bead, thereby pulling out a membrane tube from the vesicle. The assay allowed us to measure the spontaneous curvature and the bending rigidity of the bilayer in the presence of different ions and sugar. At low sugar/salt (inside/out) concentrations, the membrane spontaneous curvature generated by NaCl and KCl is close to zero, but negative in the presence of LiCl. In the latter case, the membrane bulges away from the salt solution. At high sugar/salt conditions, the membranes were observed to become more flexible and the spontaneous curvature was enhanced to even more negative values, comparable to those generated by some proteins. Our findings reveal the reshaping role of alkali chlorides on biomembranes.

"Where does the fluorescing moiety reside in a carbon dot?" - Investigations based on fluorescence anisotropy decay and resonance energy transfer dynamics.

It has been shown recently that aggregated dyes are responsible for very high fluorescence in a carbon dot (CD). However, what is the location of the fluorescing moiety in CD? Is it inside the CD or attached to the CD's surface? In order to answer these intriguing questions regarding the location of the fluorescing moiety in a CD, we performed rotational anisotropy decay dynamics and resonance energy transfer (RET) dynamics. Rotational correlation time of ∼120 picoseconds nullifies the fact that the whole CD is fluorescing. Instead, we can say that the fluorescing moiety is either embedded inside the CD or attached to the surface of the CD or linked to the CD through covalent bonds. From the fluorescence anisotropy decay dynamics in solvents of different viscosities, we could show that the fluorescing moiety is not attached to the surface of the CD or for that matter, the fluorescing moiety is not in a rigid environment inside the CD. RET dynamical analysis has shown that the time for RET (from CD to acceptor Rh123) is about 5.4 ns and the RET dynamics are independent of the acceptor concentration. Using RET dynamics, we could prove that the fluorescing moiety is not outside the CD; rather, it is inside the CD, but not in a rigid environment. The geometric distance between the fluorescing moiety of the CD and the acceptor (Rh123) has been obtained to be 4.55 nm. Using Förster formulation, the distance between the fluorescing moiety inside the CD and the acceptor Rh123 has been calculated to be 4.24 nm. Thus, we could not only reveal the exact location of the fluorescing moiety in a CD, but we could also demonstrate that unlike for many other nanomaterials, Förster formulation could explain the experimental observables regarding RET involving CD reasonably well.

Nearly suppressed photoluminescence blinking of small-sized, blue-green-orange-red emitting single CdSe-based core/gradient alloy shell/shell quantum dots: correlation between truncation time and photoluminescence quantum yield.

CdSe-based core/gradient alloy shell/shell semiconductor quantum dots (CGASS QDs) have been shown to be optically quite superior compared to core-shell QDs. However, very little is known about CGASS QDs at the single particle level. Photoluminescence blinking dynamics of four differently emitting (blue (λem = 510), green (λem = 532), orange (λem = 591), and red (λem = 619)) single CGASS QDs having average sizes <∼7 nm have been probed in our home-built total internal reflection fluorescence (TIRF) microscope. All four samples possess an average ON-fraction of 0.70-0.85, which hints towards nearly suppressed PL blinking in these gradiently alloyed systems. Suppression of blinking has been so far achieved with QDs having sizes greater than 10 nm and mostly emitting in the red region (λem > 600 nm). In this manuscript, we report nearly suppressed PL blinking behaviour of CGASS QDs with average sizes <∼7 nm and emitting in the entire range of the visible spectrum, i.e. from blue to green to orange to red. The probability density distribution of both ON- and OFF-event durations for all of these CGASS QDs could be fitted well with a modified inverse truncated power law with an additional exponential model equation. It has been found that unlike most of the literature reports, the power law exponent for OFF-event durations is greater than the power law exponent for ON-event durations for all four samples. This suggests that relatively large ON-event durations are interrupted by comparatively small OFF-event durations. This in turn is indicative of a suppressed non-radiative Auger recombination process for these CGASS systems. However, in these four different samples the ON-event truncation time varies inversely with the OFF-event truncation time, which hints that both the ON- and OFF-event truncation processes are dictated by some common factor. We have employed 2D joint probability distribution analysis to probe the correlation between the event durations and found that residual memory exists in both the ON- and OFF-event durations. Positively correlated successive ON-ON and OFF-OFF event durations and negatively correlated (anti-correlated) ON-OFF event durations perhaps suggest the involvement of more than one type of trapping process within the blinking framework. The timescale corresponding to the additional exponential term has been assigned to hole trapping for ON-event duration statistics. Similarly, for OFF-event duration statistics, this component suggests hole detrapping. We found that the average duration of the exponential process for the ON-event durations is an order of magnitude higher than that of the OFF-event durations. This indicates that the holes are trapped for a significantly long time. When electron trapping is followed by such a hole trapping, long ON-event durations result. We have observed long ON-event durations, as high as 50 s. The competing charge tunnelling model has been used to account for the observed blinking behaviour in these CGASS QDs. Quite interestingly, the PLQY of all of these differently emitting QDs (an ensemble level property) could be correlated with the truncation time (a property at the single particle level). A respective concomitant increase-decrease of ON-OFF event truncation times with increasing PLQY is also indicative of a varying degree of suppression of the Auger recombination processes in these four different CGASS QDs.

Two-Photon Fluorescence Tracking of Colloidal Clusters.

In situ dynamics of colloidal cluster formation from nanoparticles is yet to be addressed. Using two-photon fluorescence (TPF) that has been amply used for single particle tracking, we demonstrate in situ measurement of effective three-dimensional optical trap stiffness of nanoparticles and their aggregates without using any position sensitive detector. Optical trap stiffness is an essential measure of the strength of an optical trap. TPF is a zero-background detection scheme and has excellent signal-to-noise-ratio, which can be easily extended to study the formation of colloidal cluster of nanospheres in the optical trapping regime. TPF tracking can successfully distinguish colloidal cluster from its monomer.

Exploring the physics of efficient optical trapping of dielectric nanoparticles with ultrafast pulsed excitation.

Stable optical trapping of dielectric nanoparticles with low power high-repetition-rate ultrafast pulsed excitation has received considerable attention in recent years. However, the exact role of such excitation has been quite illusive so far since, for dielectric micron-sized particles, the trapping efficiency turns out to be similar to that of continuous-wave excitation and independent of pulse chirping. In order to provide a coherent explanation of this apparently puzzling phenomenon, we justify the superior role of high-repetition-rate pulsed excitation in dielectric nanoparticle trapping which is otherwise not possible with continuous-wave excitation at a similar average power level. We quantitatively estimate the optimal combination of pulse peak power and pulse repetition rate leading to a stable trap and discuss the role of inertial response on the dependence of trapping efficiency on pulse width. In addition, we report gradual trapping of individual quantum dots detected by a stepwise rise in a two-photon fluorescence signal from the trapped quantum dots which conclusively proves individual particle trapping.

Towards optical measurements of membrane potential values in Bacillus subtilis using fluorescence lifetime.

Membrane potential (MP) changes can provide a simple readout of bacterial functional and metabolic state or stress levels. While several optical methods exist for measuring fast changes in MP in excitable cells, there is a dearth of such methods for absolute and precise measurements of steady-state membrane potentials (MPs) in bacterial cells. Conventional electrode-based methods for the measurement of MP are not suitable for calibrating optical methods in small bacterial cells. While optical measurement based on Nernstian indicators have been successfully used, they do not provide absolute or precise quantification of MP or its changes. We present a novel, calibrated MP recording approach to address this gap. Our method is based on (i) a unique VoltageFluor (VF) optical transducer, whose fluorescence lifetime varies as a function of MP via photoinduced electron transfer (PeT) and (ii) a quantitative phasor-FLIM analysis for high-throughput readout. This method allows MP changes to be easily recorded, quantified and visualized. Using our preliminary Bacillus subtilis-specific MP versus VF lifetime calibration, we estimated the MP for unperturbed B. subtilis cells to be -65 mV and that for chemically depolarized cells as -14 mV. Our work paves the way for deeper insights into bacterial electrophysiology and bioelectricity research.

Fluorescence Correlation Spectroscopy and Phase Separation.

A quantitative understanding of the forces controlling the assembly and functioning of biomolecular condensates requires the identification of phase boundaries at which condensates form as well as the determination of tie-lines. Here, we describe in detail how Fluorescence Correlation Spectroscopy (FCS) provides a versatile approach to estimate phase boundaries of single-component and multicomponent solutions as well as insights about the transport properties of the condensate.

Excluded Volume and Weak Interactions in Crowded Solutions Modulate Conformations and RNA Binding of an Intrinsically Disordered Tail.

The cellular milieu is a solution crowded with a significant concentration of different components (proteins, nucleic acids, metabolites, etc.). Such a crowded environment affects protein conformations, dynamics, and interactions. Intrinsically disordered proteins and regions are particularly sensitive to these effects. Here, we investigate the impact on an intrinsically disordered tail that flanks a folded domain, the N-terminal domain, and the RNA-binding domain of the SARS-CoV-2 nucleocapsid protein. We mimic the crowded environment of the cell using polyethylene glycol (PEG) and study its impact on protein conformations using single-molecule Förster resonance energy transfer. We found that high-molecular-weight PEG induces a collapse of the disordered N-terminal tail, whereas low-molecular-weight PEG induces a chain expansion. Our data can be explained by accounting for two opposing contributions: favorable interactions between the protein and crowder molecules and screening of excluded volume interactions. We further characterized the interaction between protein and RNA in the presence of crowding agents. While for all PEG molecules tested, we observed an increase in the binding affinity, the trend is not monotonic as a function of the degree of PEG polymerization. This points to the role of nonspecific protein-PEG interactions on binding in addition to the entropic effects due to crowding. To separate the enthalpic and entropic components of the effects, we investigated the temperature dependence of the association constants in the absence and presence of crowders. Finally, we compared the effects of crowding across mutations in the disordered region and found that the threefold difference in association constants for two naturally occurring variants of the SARS-CoV-2 nucleocapsid protein is reduced to almost identical affinities in the presence of crowders. Overall, our data provide new insights into understanding and modeling the contribution of crowding effects on disordered regions, including the impact of interactions between proteins and crowders and their interplay when binding a ligand.

Excitation-Energy-Dependent Photoluminescence Quantum Yield is Inherent to Optically Robust Core/Alloy-Shell Quantum Dots in a Vast Energy Landscape.

The importance of alloy-shelling in optically robust Core/Alloy-Shell (CAS) QDs has been described from structural and energetic aspects. Unlike fluorescent dyes, both Core/Shell (CS) and CAS QDs exhibit excitation-energy-dependent photoluminescence quantum yield (PLQY). For both CdSe and InP CAS QDs (with metal- and nonmetal-based alloy-shelling, respectively), with increasing excitation energy, (a) the ultrafast rise-time or relaxation-time to the band-edge increases and (b) the magnitude of the normalized bleach signal decreases. Ultrasensitive single-particle spectroscopic investigation results showed that with decreasing excitation energy, (a) the fraction of ON events increases, (b) the ratio of exciton-detrapping rate/trapping rate increases, and (c) the extent of beneficial hole trapping increases. A relative decrease in PLQY with increasing excitation energy is much less pronounced in CAS QDs than in CS QDs. Unless trap states are removed completely especially in the higher-energy landscape, PLQY will remain inherently dependent on excitation energy for QDs in the vast energy landscape. When reporting the PLQY of QDs, the magnitude of the excitation energy must be mentioned.

Super-Resolution Imaging of Highly Curved Membrane Structures in Giant Vesicles Encapsulating Molecular Condensates.

Molecular crowding is an inherent feature of cell interiors. Synthetic cells as provided by giant unilamellar vesicles (GUVs) encapsulating macromolecules (poly(ethylene glycol) and dextran) represent an excellent mimetic system to study membrane transformations associated with molecular crowding and protein condensation. Similarly to cells, such GUVs exhibit highly curved structures like nanotubes. Upon liquid-liquid phase separation their membrane deforms into apparent kinks at the contact line of the interface between the two aqueous phases. These structures, nanotubes, and kinks, have dimensions below optical resolution. Here, these are studied with super-resolution stimulated emission depletion (STED) microscopy facilitated by immobilization in a microfluidic device. The cylindrical nature of the nanotubes based on the superior resolution of STED and automated data analysis is demonstrated. The deduced membrane spontaneous curvature is in excellent agreement with theoretical predictions. Furthermore, the membrane kink-like structure is resolved as a smoothly curved membrane demonstrating the existence of the intrinsic contact angle, which describes the wettability contrast of the encapsulated phases to the membrane. Resolving these highly curved membrane structures with STED imaging provides important insights in the membrane properties and interactions underlying cellular activities.

Two-photon fluorescence diagnostics of femtosecond laser tweezers.

We show how two-photon fluorescence signal can be used as an effective detection scheme for trapping particles of any size in comparison to methods using back-scattered light. Development of such a diagnostic scheme allows us a direct observation of trapping a single nanoparticle, which shows new directions to spectroscopy at the single-molecule level in solution.

Unravelling halide-dependent charge carrier dynamics in CsPb(Br/Cl)3 perovskite nanocrystals.

With an increasing bromide content in CsPb(Br/Cl)3 perovskite nanocrystals (PNCs), the steady state photoluminescence quantum yield value increases from 28% to 50% to 76%. Ultrafast transient absorption analyses reveal that the normalized band edge population increases more than two-fold on excitation at the band edge with increasing bromide content, and the hot exciton trapping time increases from 450 fs to 520 fs to 700 fs with increasing bromide content. Ultrasensitive single particle spectroscopic analyses reveal that the peak of the ON fraction distribution increases from 0.65 to 0.75 to 0.85 with increasing bromide content. More specifically, the percentage of PNCs with the ON fraction >75% increases four fold from 24% to 50% to 98% with increasing bromide content. Moreover, the ratio of the detrapping rate and trapping rate increases more than 25 fold with an increase in bromide content, signifying the excitons remaining in the trap state for a smaller time with increasing bromide content. In order to standardize the measurement and analyses, all these three PNCs have the same size and shape, and all the excitations have been made at the same energy above the band edge for all three PNCs and for both ultrafast transient absorption and ultrasensitive single particle measurements.

Near-Ergodic CsPbBr3 Perovskite Nanocrystal with Minimal Statistical Aging.

Optical robustness, uniformity, ergodicity, statistical aging, etc. dictate the applicability of nanocrystals. Based on a series of multimodal statistical analyses such as the Kolmogorov-Smirnov test, Lévy statistics, etc., we demonstrate that for CsPbBr3 perovskite nanocrystals (PNCs): (a) the extent of heterogeneity in the quality and associated physical processes is minimal; (b) the optical robustness is very high, and (c) indeed, a single PNC can depict optical behavior of its ensemble. In addition, toward prospective applications, an optically robust CsPbBr3 PNC exhibits (i) near-ergodicity and (ii) minimal statistical aging, which are extremely vital and complementary to its high defect tolerance.

Near-Unity Photoluminescence Quantum Yield and Highly Suppressed Blinking in a Toxic-Metal-Free Quantum Dot.

There is no literature report of simultaneously achieving near-unity PLQY (ensemble level) and highly suppressed blinking (ultrasensitive single-particle spectroscopy (SPS) level) in a toxic-metal-free QD. In this Letter we report accomplishing near-unity PLQY (96%) and highly suppressed blinking (>80% ON fraction) in a toxic-metal-free CuInS2/ZnSeS Core/Alloy-Shell (CAS) QD. In addition, (i) gigantic enhancement of PLQY (from 15% (Core) to 96% (CAS QD)), (ii) ultrahigh stability over 1 year without significant reduction of PLQY at the ensemble level, (iii) high magnitude (nearly 3 times) of electron detrapping/trapping rate, and (iv) very long ON duration (∼2 min) without blinking at the SPS level enable this ultrasmall (∼3.3 nm) CAS QD to be quite suitable for single-particle tracking/bioimaging. A model explaining all these excellent optical properties has been provided. This ultrabright CAS QD has been successfully utilized toward fabrication of low-cost microcontroller-based stable and bright yellow and white QD-LEDs.