Single-molecule Behavior Research Articles

Electron-donating effect dominated 5,6-dimethoxy-2-(2,2,2-trifluoroethyl)-1-indone dysprosium SMM

A series of three β-diketone mononuclear lanthanide complexes, namely, Dy(5,6-DTFI)3(H2O)2·H2O2CH2Cl2 (1), Tb(5,6-DTFI)3(H2O)2·H2O2CH2Cl2 (2) and Ho(5,6-DTFI)3(H2O)2·H2O2CH2Cl2 (3) (5,6-DTFI=5,6-dimethoxy-2-(2,2,2-trifluoroethyl)-1-indone) have been isolated by reactions of 5,6-DTFI and LnCl3·6H2O (Ln=Dy, Tb, Ho). X-ray crystallographic analysis reveals that complexes 1–3 are all eight-coordinated mononuclear structures. Magnetic studies indicate that complex 1 is of single-molecule magnetic behaviors under 0 Oe. Notably, the ligands play essential role on regulating their magnetism. The corresponding structural and magnetic parameters have been discussed in details.

Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels

Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer. Using this practical scale model, transport regimes of ssDNA with respect to the ζ-potential of the channel wall, the ion concentration, and the polymer length were successfully characterized. It was found that the relationship between the radius of gyration of ssDNA and the channel radius is critical to the formation of deformation regimes in a narrow channel. We conclude that a combination of electroosmotic flow velocity gradients and electric fields due to electrically polarized channel surfaces affects the alignment of molecular conformations, such that the ssDNA is stretched/compressed at negative/positive ζ-potentials in comparatively low-concentration solutions. Furthermore, this work suggests the possibility of controlling the center-of-mass position by tuning the salt concentration. These results should be applicable to the design of molecular manipulation techniques based on liquid flows in micro/nanofluidic devices.

Single-molecule force-conductance spectroscopy of hydrogen-bonded complexes

The emerging ability to study physical properties at the single-molecule limit highlights the disparity between what is observable in an ensemble of molecules and the heterogeneous contributions of its constituent parts. A particularly convenient platform for single-molecule studies are molecular junctions where forces and voltages can be applied to individual molecules, giving access to a series of electromechanical observables that can form the basis of highly discriminating multidimensional single-molecule spectroscopies. Here, we computationally examine the ability of force and conductance to inform about molecular recognition events at the single-molecule limit. For this, we consider the force-conductance characteristics of a prototypical class of hydrogen bonded bimolecular complexes sandwiched between gold electrodes. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The simulations combine classical molecular dynamics of the mechanical deformation of the junction with non-equilibrium Green’s function computations of the electronic transport. As shown, in these complexes hydrogen bonds mediate transport either by directly participating as a possible transport pathway or by stabilizing molecular conformations with enhanced conductance properties. Further, we observe that force-conductance correlations can be very sensitive to small changes in the chemical structure of the complexes and provide detailed information about the behavior of single molecules that cannot be gleaned from either measurement alone. In fact, there are regions during the elongation that are only mechanically active, others that are only conductance active, and regions where both force and conductance changes as the complex is mechanically manipulated. The implication is that force and conductance provide complementary information about the evolution of molecules in junctions that can be used to interrogate basic structure-transport relations at the single-molecule limit.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy.

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed.

Time-resolved biophysical approaches to nucleocytoplasmic transport

Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope. These methods are here divided into three major classes, according to the differences in the way they report on the molecular process of nucleocytoplasmic transport. In detail, the first class encompasses those methods based on the perturbation of the fluorescence signal, also known as ensemble-averaging methods, which average the behavior of many molecules (across many pores). The second class comprises those methods based on the localization of single fluorescently-labelled molecules and tracking of their position in space and time, potentially across single pores. Finally, the third class encompasses methods based on the statistical analysis of spontaneous fluorescence fluctuations out of the equilibrium or stationary state of the system. In this case, the behavior of single molecules is probed in presence of many similarly-labelled molecules, without dwelling on any of them. Here these three classes, with their respective pros and cons as well as their main applications to nucleocytoplasmic shuttling will be briefly reviewed and discussed.

Synthesis, structures and magnetic properties of chiral 3d–3d′–4f heterotrimetallic complexes based on [(Tp*)Fe(CN)3]−

A series of chiral cyano- and phenolate-bridged heterotrimetallic compounds have been obtained. The Dy and Tb derivatives exhibit similar single-molecule magnetic behaviors under a 1000 Oe dc field.

Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells.

Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.

Controlling the intracell diffusion behaviour of Ag monomers on Si(111)-(7 × 7) by voltage pulse manipulation

In this paper, we present the controlled modulation of the intracell diffusion energy barrier of silver (Ag) monomers on the Si(111)-(7 × 7) substrate through voltage pulses. After the voltage pulse is performed, the diffusion energy barrier of Ag monomers on Si(111)-(7 × 7) could be locally increased. Such changes consequently enable us to gradually restrict the diffusion area of Ag monomers. It provides a way to control the diffusion behavior of single atoms or molecules by modulating the diffusion energy barrier through indirectly performing voltage pulse on the substrate.

Editorial: Quantitative Biology: Dynamics of Living Systems.

Editorial: Quantitative Biology: Dynamics of Living Systems.

Automated single particle detection and tracking for large microscopy datasets.

Recent advances in optical microscopy have enabled the acquisition of very large datasets from living cells with unprecedented spatial and temporal resolutions. Our ability to process these datasets now plays an essential role in order to understand many biological processes. In this paper, we present an automated particle detection algorithm capable of operating in low signal-to-noise fluorescence microscopy environments and handling large datasets. When combined with our particle linking framework, it can provide hitherto intractable quantitative measurements describing the dynamics of large cohorts of cellular components from organelles to single molecules. We begin with validating the performance of our method on synthetic image data, and then extend the validation to include experiment images with ground truth. Finally, we apply the algorithm to two single-particle-tracking photo-activated localization microscopy biological datasets, acquired from living primary cells with very high temporal rates. Our analysis of the dynamics of very large cohorts of 10 000 s of membrane-associated protein molecules show that they behave as if caged in nanodomains. We show that the robustness and efficiency of our method provides a tool for the examination of single-molecule behaviour with unprecedented spatial detail and high acquisition rates.

Single-Molecule Studies in Live Cells.

Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies.

Changes in single-molecule integrin dynamics linked to local cellular behavior.

Recent advances in light microscopy permit visualization of the behavior of individual molecules within dense macromolecular ensembles in live cells. It is now conceptually possible to relate the dynamic organization of molecular machinery to cellular function. However, inherent heterogeneities, as well as disparities between spatial and temporal scales, pose substantial challenges in deriving such a relationship. New approaches are required to link discrete single-molecule behavior with continuous cellular-level processes. Here we combined intercalated molecular and cellular imaging with a computational framework to detect reproducible transient changes in the behavior of individual molecules that are linked to cellular behaviors. Applying our approach to integrin transmembrane receptors revealed a spatial density gradient underlying characteristic molecular density increases and mobility decreases, indicating the subsequent onset of local protrusive activity. Integrin mutants further revealed that these density and mobility transients are separable and depend on different binding domains within the integrin cytoplasmic tail. Our approach provides a generalizable paradigm for dissecting dynamic spatiotemporal molecular behaviors linked to local cellular events.

Photon-induced generation and spatial control of extreme pressure at the nanoscale with a gold bowtie nano-antenna platform.

Precise spatial and temporal control of pressure stimulation at the nanometer scale is essential for the fabrication and manipulation of nano-objects, and for exploring single-molecule behaviour of matter under extreme conditions. However, state-of-the-art nano-mechanical transducers require sophisticated driving hardware and are currently limited to moderate pressure regimes. Here we report a gold plasmonic bowtie (AuBT) nano-antennas array that can generate extreme pressure stimulus of ∼100 GPa in the ps (10-12 s) time scale with sub-wavelength resolution upon irradiation with ultra-short laser pulses. Our method leverages the non-linear interaction of photons with water molecules to excite a nano-plasma in the plasmon-enhanced near-field and induce extreme thermodynamic states. The proposed method utilizes laser pulses, which in contrast to micro- and nano-mechanical actuators offers simplicity and versatility. We present time-resolved shadowgraphic imaging, electron microscopy and simulation data that suggest that our platform can efficiently create cavitation nano-bubbles and generate intense pressure in specific patterns, which can be controlled by the selective excitation of plasmon modes of distinct polarizations. This novel platform should enable probing non-invasively the mechanical response of cells and single-molecules at time and pressure regimes that are currently difficult to reach with other methods.

Observing Single, Heterogeneous, One-Electron Transfer Reactions

Understanding electrochemical events on the single-molecule level is crucial for fields such as catalysis and biological systems. A variety of techniques exist to study the electrochemistry of single molecules, but few provide correlated chemical information. Herein, we study the electrochemistry of rhodamine 6G in nonaqueous conditions and demonstrate the first statistic electrochemical single-molecule SERS (EC-SMSERS) proof of single-electron transfer events. We find that the distribution of reduction events is broader than that in a bulk electrochemical experiment. The distribution of the reduction potentials can be explained by molecular reorientation and variations of the local surface site or chemical potential of the Ag nanoparticle. Our results contribute toward understanding electrochemical behavior of single molecules on the nanoscale monitored by SERS and the ultimate goal of controlling single-electron transfer processes.

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics

Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics

Kinesin-2 KIF3AC and KIF3AB Can Drive Long-Range Transport along Microtubules

Mammalian KIF3AC is classified as a heterotrimeric kinesin-2 that is best known for organelle transport in neurons, yet in vitro studies to characterize its single molecule behavior are lacking. The results presented show that a KIF3AC motor that includes the native helix α7 sequence for coiled-coil formation is highly processive with run lengths of ∼1.23 μm and matching those exhibited by conventional kinesin-1. This result was unexpected because KIF3AC exhibits the canonical kinesin-2 neck-linker sequence that has been reported to be responsible for shorter run lengths observed for another heterotrimeric kinesin-2, KIF3AB. However, KIF3AB with its native neck linker and helix α7 is also highly processive with run lengths of ∼1.62 μm and exceeding those of KIF3AC and kinesin-1. Loop L11, a component of the microtubule-motor interface and implicated in activating ADP release upon microtubule collision, is significantly extended in KIF3C as compared with other kinesins. A KIF3AC encoding a truncation in KIF3C loop L11 (KIF3ACΔL11) exhibited longer run lengths at ∼1.55 μm than wild-type KIF3AC and were more similar to KIF3AB run lengths, suggesting that L11 also contributes to tuning motor processivity. The steady-state ATPase results show that shortening L11 does not alter kcat, consistent with the observation that single molecule velocities are not affected by this truncation. However, shortening loop L11 of KIF3C significantly increases the microtubule affinity of KIF3ACΔL11, revealing another structural and mechanistic property that can modulate processivity. The results presented provide new, to our knowledge, insights to understand structure-function relationships governing processivity and a better understanding of the potential of KIF3AC for long-distance transport in neurons.

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics.

We report Single Molecule Cluster Analysis (SiMCAn), which utilizes hierarchical clustering of hidden Markov modeling-fitted single-molecule fluorescence resonance energy transfer (smFRET) trajectories to dissect the complex conformational dynamics of biomolecular machines. We used this method to study the conformational dynamics of a precursor mRNA during the splicing cycle as carried out by the spliceosome. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify the signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified an open conformation adopted late in splicing by a 3' splice-site mutant, invoking a mechanism for substrate proofreading. SiMCAn enables rapid interpretation of complex single-molecule behaviors and should prove useful for the comprehensive analysis of a plethora of dynamic cellular machines.

Slow Magnetic Relaxation Observed in Dysprosium Compounds Containing Unsupported Near-Linear Hydroxo- and Fluoro-Bridges.

The encapsulating N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) ligand was employed to isolate two novel Dy(III) compounds which contain rare bridging pathways for lanthanide systems. Compound 1, [Na2Dy(III)2(valdien)2(μ-OH)(dbm)2(H2O)2][Na2Dy(III)2(valdien)2(μ-OH)(NO3)2(dbm)2], where dbm(-) is dibenzoylmethanido, and compound 2, [Na3Dy(III)2(valdien)2(μ-F)(μ3-F)2(Cl)2(MeOH)2]n·0.5(MeOH)·(H2O), both exhibit linear lone hydroxo- and fluoro-bridges, respectively, between the metal centers. The unit cell of 1 comprises two discrete dinuclear molecules, which differ slightly, forming a cation-anion pair, while 2 forms a coordination polymer. The magnetic investigations indicate that both compounds display ferromagnetic coupling between the Dy(III) ions. Magnetic susceptibility measurements in the temperature range 1.8-300 K reveal that the Dy(III) ions in 1 are weakly coupled, resulting in a mononuclear single-molecule magnet-like behavior under an applied field. In the case of 2, the stronger coupling arising from the fluoride-bridge, leads to zero-field single-molecule magnet (SMM) behavior with a non-negligible anisotropy barrier (Ueff) of 42 K.

Synthesis, Electrochemistry, and Single-Molecule Conductance of Bimetallic 2,3,5,6-Tetra(pyridine-2-yl)pyrazine-Based Complexes.

The ligands 4'-(4-(methylthio)phenyl)-2,2':6',2″-terpyridine (L(1)), 4'-((4-(methylthio)phenyl)ethynyl)- 2,2':6',2″-terpyridine (L(2)), and bis(tridentate) bridging ligand 2,3,5,6-tetra(pyridine-2-yl)pyrazine (tpp) were used to prepare the complexes [Ru(L(1))2][PF6]2 ([1][PF6]2, [Ru(L(2))2][PF6]2 ([2][PF6]2), [{(L(1))Ru}(μ-tpp){Ru(L(1))}][PF6]4 ([3][PF6]4), and [{(L(2))Ru}(μ-tpp){Ru(L(2))}][PF6]4 ([4][PF6]4). Crystallographically determined structures give S···S distances of up to 32.0 Å in [4](4+). On the basis of electrochemical estimates, the highest occupied molecular orbitals of these complexes fall between -5.55 and -5.85 eV, close to the work function of clean gold (5.1-5.3 eV). The decay of conductance with molecular length across this series of molecules is approximately exponential, giving rise to a decay constant (pseudo β-value) of 1.5 nm(-1), falling between decay factors for oligoynes and oligophenylenes. The results are consistent with a tunnelling mechanism for the single-molecule conductance behavior.

Fluorescence Recovery after Photobleaching and Single-Molecule Tracking Measurements of Anisotropic Diffusion within Identical Regions of a Cylinder-Forming Diblock Copolymer Film.

This work demonstrates ensemble and single-molecule diffusion measurements within identical regions of a cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer (PS-b-PEO) film using fluorescence recovery after photobleaching (FRAP) and single-molecule tracking (SMT). A PS-b-PEO film (∼4 μm thick) with aligned cylindrical PEO microdomains containing 10 μM sulforhodamine B (SRB) was prepared by directional solvent-vapor penetration (SVP) of 1,4-dioxane. The ensemble diffusion behavior of SRB in the microdomains was assessed in FRAP studies of circular photobleached regions (∼7 μm in diameter). The SRB concentration was subsequently reduced by additional photobleaching, and the diffusion of individual SRB molecules was explored using SMT in the identical area (∼16 × 16 μm(2)). The FRAP data showed anisotropic fluorescence recovery, yielding the average microdomain orientation. The extent of fluorescence recovery observed (∼90%) demonstrated long-range microdomain connectivity, while the recovery time dependence provided an ensemble measurement of the SRB diffusion coefficient within the cylindrical microdomains. The SMT data exhibited one-dimensional diffusion of individual SRB molecules along the SVP direction across the entire film thickness, as consistent with the FRAP results. Importantly, the average of the single-molecule diffusion coefficients was close to the value obtained from FRAP in the identical area. In some cases, SMT offered smaller diffusion coefficients than FRAP, possibly due to contributions from SRB molecules confined within short PEO microdomains. The implementation of FRAP and SMT measurements in identical areas provides complementary information on molecular diffusion with minimal influence of sample heterogeneity, permitting direct comparison of ensemble and single-molecule diffusion behavior.