Single‐Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm^?2) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single‐molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus “wobble”) of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve nanodomains and enzyme‐induced compositional heterogeneity within membranes, where NR within liquid‐ordered vs. liquid‐disordered domains shows a ≈4° difference in polar angle and a ≈0.3π sr difference in wobble angle. As a new type of imaging spectroscopy, SMOLM exposes the organizational and functional dynamics of lipid‐lipid, lipid‐protein, and lipid‐dye interactions with single‐molecule, nanoscale resolution.     

Switchable Solvatochromic Probes for Live‐Cell Super‐resolution Imaging of Plasma Membrane Organization

Visualization of the nanoscale organization of cell membranes remains challenging because of the lack of appropriate fluorescent probes. Herein, we introduce a new design concept for super‐resolution microscopy probes that combines specific membrane targeting, on/off switching, and environment sensing functions. A functionalization strategy for solvatochromic dye Nile Red that improves its photostability is presented. The dye is grafted to a newly developed membrane‐targeting moiety composed of a sulfonate group and an alkyl chain of varied lengths. While the long‐chain probe with strong membrane binding, NR12A, is suitable for conventional microscopy, the short‐chain probe NR4A, owing to the reversible binding, enables first nanoscale cartography of the lipid order exclusively at the surface of live cells. The latter probe reveals the presence of nanoscopic protrusions and invaginations of lower lipid order in plasma membranes, suggesting a subtle connection between membrane morphology and lipid organization.     

Super-resolution microscopy of lipid bilayer phases

Sub-diffraction optical imaging with nanometer resolution of lipid phase-separated regions is reported. Merocyanine 540, a probe whose fluorescence is sensitive to the lipid phase, is combined with super-resolution imaging to distinguish the liquid- and gel-phase nanoscale domains of lipid bilayers supported on glass. The monomer-dimer equilibrium of MC540 in membranes is deemed responsible for the population difference of single-molecule fluorescence bursts in the different phase regions. The extension of this method to other binary or ternary lipid models or natural systems provides a promising new super-resolution strategy.     

Nanoscale organization of the pathogen receptor DC-SIGN mapped by single-molecule high-resolution fluorescence microscopy.

DC-SIGN, a C-type lectin exclusively expressed on dendritic cells (DCs), plays an important role in pathogen recognition by binding with high affinity to a large variety of microorganisms. Recent experimental evidence points to a direct relation between the function of DC-SIGN as a viral receptor and its spatial arrangement on the plasma membrane. We have investigated the nanoscale organization of fluorescently labeled DC-SIGN on intact isolated DCs by means of near-field scanning optical microscopy (NSOM) combined with single-molecule detection. Fluorescence spots of different intensity and size have been directly visualized by optical means with a spatial resolution of less than 100 nm. Intensity- and size-distribution histograms of the DC-SIGN fluorescent spots confirm that approximately 80 % of the receptors are organized in nanosized domains randomly distributed on the cell membrane. Intensity-size correlation analysis revealed remarkable heterogeneity in the molecular packing density of the domains. Furthermore, we have mapped the intermolecular organization within a dense cluster by means of sequential NSOM imaging combined with discrete single-molecule photobleaching. In this way we have determined the spatial coordinates of 13 different individual dyes, with a localization accuracy of 6 nm. Our experimental observations are all consistent with an arrangement of DC-SIGN designed to maximize its chances of binding to a wide range of microorganisms. Our data also illustrate the potential of NSOM as an ultrasensitive, high-resolution technique to probe nanometer-scale organization of molecules on the cell membrane.     

Heterogeneous molecular distribution in supported multicomponent lipid bilayers

Membrane domains contribute important structural and functional attributes to biological membranes. We describe the heterogeneous nanoscale distribution of lipid molecules within microscale membrane domains in multicomponent lipid bilayers composed of dipalmitoylphosphatidylcholine (DPPC), dilauroylphosphatidylcholine (DLPC), and cholesterol (chol). The lipids were labeled with the fluorescent lipid analogues Bodipy-PC and DiI-C20:0 to identify the distribution of individual membrane components. We used a near-field scanning optical microscope (NSOM) at room temperature to identify the nanoscale structures in the membrane. Simultaneous multicolor NSOM imaging at the emission maxima of the fluorescent analogues revealed a patchy distribution of Bodipy-PC and DiI-C20:0 indicative of phase separations in the bilayer. In a cholesterol-free system (DPPC/DLPC = 1:1), NSOM images proved that the two phosphatidylcholine molecules can coexist in domains at the micrometer level but form nanoscopic patches within the domains; DPPC occurs at the edge of the domains, whereas DLPC is present throughout the domains. In the presence of cholesterol (DPPC/DLPC = 7:3, chol = 18.9%), the two lipid molecules were more miscible but incomplete phase separations also occurred. The average domain sizes were 140-200 nm, well below the resolution capabilities of diffraction-limited light microscopy techniques; the domains were unresolvable by confocal microscopy. Our high-resolution NSOM studies of membrane domain behavior provide a better understanding of complex membrane phase phenomena in multicomponent biological membranes.     

Molecular organization of the antifungal and anticancer drug 2-(2,4-dihydroxyphenylo)-5,6-dichlorobenzothiazole (dHBBT) in solution and in lipid membranes studied by means of electronic absorption spectroscopy

2-(2,4-Dihydroxyphenylo)-5,6-dichlorobenzthiazole (dHBBT) is a new drug from the group of chemical compounds characterized by documented antifungal, antibacterial, cytostatic as well as antitumour activity. Despite general knowledge regarding pharmacological importance of dHBBT its interaction to biomembranes has not been investigated. In this work, we present the electronic absorption spectroscopic study on molecular organization of dHBBT in organic solvents and on its localization and molecular organization within model lipid membranes formed with dipalmitoylphosphatidylcholine (DPPC). The spectroscopic measurements are interpreted within the framework of the exciton splitting theory. It is concluded that complex absorption spectrum of dHBBT both in the organic solvents and incorporated to DPPC represents superposition of two spectral forms: representing monomers and hypsochromically shifted spectrum representing molecular dimers. Analysis of the temperature dependencies of the absorption spectra of dHBBT incorporated to DPPC liposomes suggests localization of the drug in the polar head-group region of the membrane or in the region of the polar-nonpolar interface. Linear dichroism measurements of dHBBT incorporated to DPPC multibilayers reveal roughly vertical orientation of the drug molecules with respect to the plane of the membrane. A model is presented of molecular organization of dHBBT in lipid membranes. Potential effects of dHBBT on membrane physical properties is briefly discussed.     

Single-molecule fluorescence imaging of nanocatalytic processes

This tutorial review covers recent developments in using single-molecule fluorescence microscopy to study nanoscale catalysis. The single-molecule approach enables following catalytic and electrocatalytic reactions on nanocatalysts, including metal nanoparticles and carbon nanotubes, at single-reaction temporal resolution and nanometer spatial precision. Real-time, in situ, multiplexed measurements are readily achievable under ambient solution conditions. These studies provide unprecedented insights into catalytic mechanism, reactivity, selectivity, and dynamics in spite of the inhomogeneity and temporal variations of catalyst structures. Prospects, generality, and limitations of the single-molecule fluorescence approach for studying nanocatalysis are also discussed.     

Lateral Diffusion of Lipids and Diffusion of Water through Lipid Bilayers in the Presence of (1,1-Dimethyl-3-Oxobutyl)Phosphonates

The influence of some amphiphilic (diethyl, dipropyl, and dibutyl) esters of (1,1-dimethyl-3-oxobutyl)phosphonic acid with the regularly changing number of CH₂ groups in the hydrocarbon (hydrophobic) moiety on the lateral diffusion of dioleoyl phosphatidylcholine lipid and transmembrane diffusion of water in the oriented multibilayer system was studied by ¹H pulsed field gradient NMR at phosphonate concentrations up to 30 mol %. The shape of the ³¹P NMR spectra and the dependence of the shape of the ¹H NMR spectra on the bilayer orientation suggest that the presence of phosphonates does not affect the phase state of the system. The lamellar liquid crystalline phase remains unchanged, and phosphonate molecules become incorporated into the bilayer and have the same orientation as phospholipid molecules. The presence of phosphonates in the lipid bilayer increases the coefficients of lipid lateral diffusion and water diffusion through bilayers. This effect depends monotonically on the number of CH₂ groups in the phosphonate molecule. The most probable place for the incorporation of amphiphilic phosphonate molecules is the hydrophilic/hydrophobic interphase region of the bilayer. The molecules incorporated into the interphase disorder the bilayer and increase lateral diffusion of lipids and bilayer permeability compared with the ester-free bilayer. When the number of CH₂ groups in the ester molecule increases from diethyl to dibutyl phosphonate, the arrangement of lipid hydrocarbon tails becomes more ordered. This decreases the lipid lateral diffusion coefficient and bilayer permeability to water molecules.     

The probe rules in single particle tracking

Single particle tracking (SPT) enables light microscopy at a sub-diffraction limited spatial resolution by a combination of imaging at low molecular labeling densities and computational image processing. SPT and related single molecule imaging techniques have found a rapidly expanded use within the life sciences. This expanded use is due to an increased demand and requisite for developing a comprehensive understanding of the spatial dynamics of bio-molecular interactions at a spatial scale that is equivalent to the size of the molecules themselves, as well as by the emergence of new imaging techniques and probes that have made historically very demanding and specialized bio-imaging techniques more easily accessible and achievable. SPT has in particular found extensive use for analyzing the molecular organization of biological membranes. From these and other studies using complementary techniques it has been determined that the organization of native plasma membranes is heterogeneous over a very large range of spatial and temporal scales. The observed heterogeneities in the organization have the practical consequence that the SPT results in investigations of native plasma membranes are time dependent. Furthermore, because the accessible time dynamics, and also the spatial resolution, in an SPT experiment is mainly dependent on the luminous brightness and photostability of the particular SPT probe that is used, available SPT results are ultimately dependent on the SPT probes. The focus of this review is on the impact that the SPT probe has on the experimental results in SPT.     

Substrate-supported lipid nanotube arrays

This Communication describes the self-assembly of phospholipids into lipid nanotubes inside nanoporous anodic aluminum oxide substrate. Orientations of the lipid molecules in such lipid nanoscale structures were verified by high-resolution spin labeling EPR at 95 GHz. The static order parameter of lipids in such nanotube arrays was determined from low-temperature EPR spectra and was found to be exceptionally high, Sstatic approximately 0.9. We propose that substrate-supported lipid nanotube arrays have potential for building robust biochips and biosensors in which rigid nanoporous substrates protect the bilayer surface from contamination. The total bilayer surface in the lipid nanotube arrays is much greater than that in the planar substrate-supported membranes. The lipid nanotube arrays seem to be suitable for developing patterned lipid deposition and could be potentially used for patterning of membrane-associated molecules.     

A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution

The ability to monitor DNA polymerase activity with single-nucleotide resolution has been the cornerstone of a number of advanced single-molecule DNA sequencing concepts. Toward this goal, we report the first observation of the base-by-base DNA polymerase activity with single-base resolution at the single-molecule level. We describe the design and characterization of a supramolecular nanopore device capable of detecting up to nine consecutive DNA polymerase-catalyzed single-nucleotide primer extensions with high sensitivity and spatial resolution (相似文献   

Nanoscale Chemical Imaging of Reversible Photoisomerization of an Azobenzene‐Thiol Self‐Assembled Monolayer by Tip‐Enhanced Raman Spectroscopy

An understanding of the photoisomerization mechanism of molecules bound to a metal surface at the molecular scale is required for designing photoswitches at surfaces. It has remained a challenge to correlate the surface structure and isomerization of photoswitches at ambient conditions. Herein, the photoisomerization of a self‐assembled monolayer of azobenzene‐thiol molecules on a Au surface was investigated using scanning tunneling microscopy and tip‐enhanced Raman spectroscopy. The unique signature of the cis isomer at 1525 cm^?1 observed in tip‐enhanced Raman spectra was clearly distinct from the trans isomer. Furthermore, tip‐enhanced Raman images of azobenzene thiols after ultraviolet and blue light irradiation are shown with nanoscale spatial resolution, demonstrating a reversible conformational change. Interestingly, the cis isomers of azobenzene‐thiol molecules were preferentially observed at Au grain edges, which is confirmed by density functional theory.     

Quantitative Single-Molecule Electrochemiluminescence Bioassay

A single-molecule electrochemiluminescence bioassay is developed here which allows imaging and direct quantification of single biomolecules. Imaging single biomolecules is realized by localizing the electrochemiluminescence events of the labeled molecules. Such an imaging system allows mapping the spatial distribution of biomolecules with electrochemiluminescence and contains quantitative single-molecule insights. We further quantify biomolecules by spatiotemporally merging the repeated reactions at one molecule site and then counting the clustered molecules. The proposed single-molecule electrochemiluminescence bioassay is used to detect carcinoembryonic antigen, showing a limit of detection of 67 attomole concentration which is 10 000 times better than conventional electrochemiluminescence bioassays. This spatial resolution and sensitivity enable single-molecule electrochemiluminescence bioassay a new toolbox for both specific bioimaging and ultrasensitive quantitative analysis.     

Centerband‐only analysis of rotor‐unsynchronized spin echo for measurement of lipid 31P chemical shift anisotropy

Structural diversity and molecular flexibility of phospholipids are essential for biological membranes to play key roles in numerous cellular processes. Uncovering the behavior of individual lipids in membrane dynamics is crucial for understanding the molecular mechanisms underlying biological functions of cell membranes. In this paper, we introduce a simple method to investigate dynamics of lipid molecules in multi‐component systems by measuring the ³¹P chemical shift anisotropy (CSA) under magic angle spinning (MAS) conditions. For achieving both signal separation and CSA determination, we utilized a centerband‐only analysis of rotor‐unsynchronized spin echo (COARSE). This analysis is based on the curve fitting of periodic modulation of centerband intensity along the interpulse delay time in rotor‐unsynchronized spin‐echo experiments. The utility of COARSE was examined by using phospholipid vesicles, a three‐component lipid raft model system, and archaeal purple membranes. We found that the apparent advantages of this method are high resolution and high sensitivity given by the moderate MAS speed and the one‐dimensional acquisition with short spin‐echo delays. COARSE provides an alternative method for CSA measurement that is effective in the investigation of lipid polymorphologies. Copyright © 2015 John Wiley & Sons, Ltd.     

Effect of acidity on the formation of solvent-free lipid bilayers

Glasses with hydrophobized surface are used to form “dry” bilayer lipid membranes (BLM). The contact angle on the silaned glass plates reaches 125°. Partitions of this kind, as opposed to polymer films, make a system more resistant to heat oscillations and mechanical perturbations generated when studying membranes properties. The specific capacitance of BLM (0.86 ± 0.04 μF cm^?2) testifies to the solvent absence in the bilayer. The dramatic drop of the capacitance (area) of the dry membranes with increasing pH is caused by a greater adsorption of lipid molecules on the hydrophobic substrate, which is probably due to changing conformation of their polar “head.”     

Application of pulsed field gradient NMR with high gradient strength for studies of self-diffusion in lipid membranes on the nanoscale

This work demonstrates the feasibility of noninvasive studies of lipid self-diffusion in model lipid membranes on the nanoscale using proton pulsed field gradient (PFG) NMR spectroscopy with high (up to 35 T/m) gradient amplitudes. Application of high gradients affords for the use of sufficiently small diffusion times under the conditions when the width of the gradient pulses is much smaller than the diffusion time. As a result, PFG NMR studies of partially restricted or anomalous diffusion in lipid bilayers become possible over length scales as small as 100 nm. This length scale is important because it is comparable to the size of membrane domains, or lipid rafts, which are believed to exist in biomembranes. In this work, high-gradient PFG NMR has been applied to study lipid self-diffusion in three-component planar-supported multibilayers (1,2-dioleoyl- sn-glycerol-3-phosphocholine/sphingomyelin/cholesterol). The degree of lipid orientation in the bilayers was determined with (31)P NMR. A special insert was designed to mechanically align the multibilayer stack at the magic angle with respect to the direction of the constant magnetic field to address the detrimental effects of proton dipole-dipole interactions on the NMR signal. This insert is an alternative to the conventional method of magic angle orientation of lipid membranes, the goniometer probe, which is not compatible with commercial high-gradient coils because of the lack of space in the magnet bore. Macroscopic orientation of the multibilayer stacks using the insert was confirmed with (1)H NMR spectroscopic studies and the comparison of results obtained from identical experiments using a goniometer probe for orientation. Diffusion studies were carried out at three different constant magnetic field strengths ( B 0) over a range of temperatures and diffusion times. The measured diffusivities were found to be in agreement with the data obtained previously by techniques that are limited to much larger length scales of diffusion observation than high-gradient PFG NMR.     

Single-crystal 55Mn NMR spectra of two Mn12 single-molecule magnets

The initial application is reported of single-crystal 55Mn NMR spectroscopy, and associated orientation dependence studies, to single-molecule magnets (SMMs). The studies were performed on two members of the Mn12 family of SMMs, [Mn12O12(O2CMe)16(H2O)4].2MeCO2H.4H2O (Mn12-Ac) and [Mn12O12(O2CCH2Br)16(H2O)4].4CH)Cl) (Mn12-BrAc). Single-crystal spectra give a dramatic improvement in the spectral resolution over oriented powder spectra, allowing the clear observation of quadrupolar splittings, the determination of quadrupole coupling parameters (e2qQ), and an assessment of the symmetry-lowering perturbation of the core of Mn12-Ac by hydrogen-bonding interactions with lattice solvate molecules of crystallization. The results emphasize the utility of single-crystal NMR studies to probe the cores of these magnetic molecules.     

Diffusion of lipid-like single-molecule fluorophores in the cell membrane

The dicyanomethylenedihydrofuran (DCDHF) class of single-molecule fluorophores contains an amine donor and a dicyanomethylenedihydrofuran acceptor linked by a conjugated unit (benzene, naphthalene, or styrene). Molecules in this class have a number of useful properties in addition to those usually required for single-molecule studies (such as high fluorescence quantum yield and photostability), including second-order optical nonlinearity, large ground-state dipole moment, and sensitivity to local environment. Moreover, most DCDHF molecules have amphiphilic structures, with a polar dicyanomethylenedihydrofuran headgroup and nonpolar hydrocarbon tails on the amine or furan ring, and can be used as fluorescent lipid analogues for live cell imaging. Here we demonstrate that individual molecules of several different DCDHF lipid analogues can be observed diffusing in the plasma membrane of Chinese hamster ovary cells. The photophysical and diffusive behaviors of the DCDHF lipid analogues in membranes are described and are found to be competitive with the well-known lipid probe N-(6-tetramethylrhodaminethiocarbamoyl)-1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine.     

A spectroscopic ellipsometry study of PET membranes from IR to Vis-FUV

A detailed study of Spectroscopic Ellipsometry (SE) spectra of uniaxially stressed, 12μm thick poly(ethylene terephthalate) (PET) membranes were realized in both IR (900-3500 cm⁻¹) and Vis-FUV (1.5 to 6.5 eV) spectral regions and in various orientation angles ∅︁ between the plane of incidence and the machine direction (MD) of the PET membranes. In the IR spectra, the three main modes of the ester group at ∼1126, 1256 and 1721 cm⁻¹ are observed. The first two of these peaks show identical polarization dependence, with preferential orientation ∅︁≈0° (i.e. the plane of reflection parallel to the MD), while the peak at ∼1721 cm⁻¹ is excited in the perpendicular direction, ∅︁≈90°. In the Vis-FUV SE spectra, the dependence of the characteristic electronic absorption bands on the orientation angle ∅︁ is studied. Besides the well known benzene band centered at ∼5 eV, a doublet of less intense peaks appear just above the absorption edge between 4.1 and 4.3 eV with the most striking characteristic that they show polarization selection rules opposing to that of the benzene band. The above characteristics of the electronic Vis-FUV spectra of PET are discussed in a manner comparative to the corresponding IR spectra. The discussion becomes in the context of determining the molecular orientation of PET using a non-destructive technique such as SE.     

Observing a model ion channel gating action in model cell membranes in real time in situ: membrane potential change induced alamethicin orientation change

Ion channels play crucial roles in transport and regulatory functions of living cells. Understanding the gating mechanisms of these channels is important to understanding and treating diseases that have been linked to ion channels. One potential model peptide for studying the mechanism of ion channel gating is alamethicin, which adopts a split α/3(10)-helix structure and responds to changes in electric potential. In this study, sum frequency generation vibrational spectroscopy (SFG-VS), supplemented by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), has been applied to characterize interactions between alamethicin (a model for larger channel proteins) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayers in the presence of an electric potential across the membrane. The membrane potential difference was controlled by changing the pH of the solution in contact with the bilayer and was measured using fluorescence spectroscopy. The orientation angle of alamethicin in POPC lipid bilayers was then determined at different pH values using polarized SFG amide I spectra. Assuming that all molecules adopt the same orientation (a δ distribution), at pH = 6.7 the α-helix at the N-terminus and the 3(10)-helix at the C-terminus tilt at about 72° (θ(1)) and 50° (θ(2)) versus the surface normal, respectively. When pH increases to 11.9, θ(1) and θ(2) decrease to 56.5° and 45°, respectively. The δ distribution assumption was verified using a combination of SFG and ATR-FTIR measurements, which showed a quite narrow distribution in the angle of θ(1) for both pH conditions. This indicates that all alamethicin molecules at the surface adopt a nearly identical orientation in POPC lipid bilayers. The localized pH change in proximity to the bilayer modulates the membrane potential and thus induces a decrease in both the tilt and the bend angles of the two helices in alamethicin. This is the first reported application of SFG to the study of model ion channel gating mechanisms in model cell membranes.