A Molecular Tuning Fork in Single‐Molecule Mechanochemical Sensing

The separate arrangement of target recognition and signal transduction in conventional biosensors often compromises the real‐time response and can introduce additional noise. To address these issues, we combined analyte recognition and signal reporting by mechanochemical coupling in a single‐molecule DNA template. We incorporated a DNA hairpin as a mechanophore in the template, which, under a specific force, undergoes stochastic transitions between folded and unfolded hairpin structures (mechanoescence). Reminiscent of a tuning fork that vibrates at a fixed frequency, the device was classified as a molecular tuning fork (MTF). By monitoring the lifetime of the folded and unfolded hairpins with equal populations, we were able to differentiate between the mono‐ and bivalent binding modes during individual antibody‐antigen binding events. We anticipate these mechanospectroscopic concepts and methods will be instrumental for the development of novel bioanalyses.     

Single‐Molecule Mechanochemical Sensing Using DNA Origami Nanostructures

While single‐molecule sensing offers the ultimate detection limit, its throughput is often restricted as sensing events are carried out one at a time in most cases. 2D and 3D DNA origami nanostructures are used as expanded single‐molecule platforms in a new mechanochemical sensing strategy. As a proof of concept, six sensing probes are incorporated in a 7‐tile DNA origami nanoassembly, wherein binding of a target molecule to any of these probes leads to mechanochemical rearrangement of the origami nanostructure, which is monitored in real time by optical tweezers. Using these platforms, 10 pM platelet‐derived growth factor (PDGF) are detected within 10 minutes, while demonstrating multiplex sensing of the PDGF and a target DNA in the same solution. By tapping into the rapid development of versatile DNA origami nanostructures, this mechanochemical platform is anticipated to offer a long sought solution for single‐molecule sensing with improved throughput.     

DCDHF Fluorophores for Single‐Molecule Imaging in Cells

There is a persistent need for small‐molecule fluorescent labels optimized for single‐molecule imaging in the cellular environment. Application of these labels comes with a set of strict requirements: strong absorption, efficient and stable emission, water solubility and membrane permeability, low background emission, and red‐shifted absorption to avoid cell autofluorescence. We have designed and characterized several fluorophores, termed “DCDHF” fluorophores, for use in live‐cell imaging based on the push–pull design: an amine donor group and a 2‐dicyanomethylene‐3‐cyano‐2,5‐dihydrofuran (DCDHF) acceptor group, separated by a π‐rich conjugated network. In general, the DCDHF fluorophores are comparatively photostable, sensitive to local environment, and their chemistries and photophysics are tunable to optimize absorption wavelength, membrane affinity, and solubility. Especially valuable are fluorophores with sophisticated photophysics for applications requiring additional facets of control, such as photoactivation. For example, we have reengineered a red‐emitting DCDHF fluorophore so that it is dark until photoactivated with a short burst of low‐intensity violet light. This molecule and its relatives provide a new class of bright photoactivatable small‐molecule fluorophores, which are needed for super‐resolution imaging schemes that require active control (here turning‐on) of single‐molecule emission.     

Analysis of Single‐Molecule Fluorescence Spectroscopic Data with a Markov‐Modulated Poisson Process

We present a photon‐by‐photon analysis framework for the evaluation of data from single‐molecule fluorescence spectroscopy (SMFS) experiments using a Markov‐modulated Poisson process (MMPP). A MMPP combines a discrete (and hidden) Markov process with an additional Poisson process reflecting the observation of individual photons. The algorithmic framework is used to automatically analyze the dynamics of the complex formation and dissociation of Cu²⁺ ions with the bidentate ligand 2,2′‐bipyridine‐4,4′dicarboxylic acid in aqueous media. The process of association and dissociation of Cu²⁺ ions is monitored with SMFS. The dcbpy‐DNA conjugate can exist in two or more distinct states which influence the photon emission rates. The advantage of a photon‐by‐photon analysis is that no information is lost in preprocessing steps. Different model complexities are investigated in order to best describe the recorded data and to determine transition rates on a photon‐by‐photon basis. The main strength of the method is that it allows to detect intermittent phenomena which are masked by binning and that are difficult to find using correlation techniques when they are short‐lived.     

Fast Biosynthesis of GFP Molecules: A Single‐Molecule Fluorescence Study

It's not easy being green : Real‐time visualization of labeled ribosomes and de novo synthesized green fluorescent protein molecules using single‐molecule‐sensitive fluorescence microscopy demonstrates that the mutant GFPem is produced with a characteristic time of five minutes. Fluorescence of the fastest GFP molecules appears within one minute (see picture).

     

Butterfly‐Shaped Pentanuclear Dysprosium Single‐Molecule Magnets

Two new “butterfly‐shaped” pentanuclear dysprosium(III) clusters, [Dy₅(μ₃‐OH)₃(opch)₆(H₂O)₃] ? 3 MeOH ? 9 H₂O ( 1 ) and [Dy₅(μ₃‐OH)₃(Hopch)₂(opch)₄(MeOH)(H₂O)₂] ? (ClO₄)₂ ? 6 MeOH ? 4 H₂O ( 2 ), which were based on the heterodonor‐chelating ligand o‐vanillin pyrazine acylhydrazone (H₂opch), have been successfully synthesized by applying different reaction conditions. Single‐crystal X‐ray diffraction analysis revealed that the butterfly‐shaped cores in both compounds were comparable. However, their magnetic properties were drastically different. Indeed, compound 1 showed dual slow‐relaxation processes with a transition between them that corresponded to energy gaps (Δ) of 8.1 and 37.9 K and pre‐exponential factors (τ₀) of 1.7×10^?5 and 9.7×10^?8 s for the low‐ and high‐temperature domains, respectively, whilst only a single relaxation process was noted for compound 2 (Δ=197 K, τ₀=3.2×10^?9 s). These significant disparities are most likely due to the versatile coordination of the H₂opch ligands with particular keto–enol tautomerism, which alters the strength of the local crystal field and, hence, the nature or direction of the easy axes of anisotropic dysprosium ions.     

Single‐Molecule Electroluminescence of a Phosphorescent Organometallic Complex

Lighting one by one: The electroluminescence (EL) from single molecules of a red phosphorescent iridium complex dispersed in a hole‐transporting polymer matrix is studied. The single‐molecule EL dynamics is determined by local structural inhomogeneities in the matrix polymer (see picture).

     

Identifying Multiple Populations from Single‐Molecule Lifetime Distributions

A major advantage of single‐molecule methods over ensemble‐averaging techniques involves the ability to characterize heterogeneity through the identification of multiple molecular populations. It can be challenging, however, to determine absolute values of dynamic parameters (and to relate these values to those determined from a conventional method) because characteristic timescales of various populations may vary over many orders of magnitude, and under a given set of experimental conditions instrumental sensitivity to various populations may be unequal. Using data obtained from the single‐molecule tracking microscopy of fibrinogen protein adsorption and desorption, it is shown that by performing a combined analysis of molecular trajectories obtained using a range of acquisition times, it is possible to extract quantitative absolute values of multiple population fractions and residence times (with well‐defined uncertainties), even when these values span many orders of magnitude. In particular, as many as six distinct populations are rigorously identified, exhibiting characteristic timescales that vary over nearly three orders of magnitude with population fractions as small as one part in a thousand. This approach will lead to better comparability between single‐molecule experiments and may be useful in connecting single‐molecule to ensemble‐averaged observations.     

Reversible Unfolding–Refolding of Rubredoxin: A Single‐Molecule Force Spectroscopy Study

In metalloproteins, metal centers serve as active sites for a range of functional purposes and as important structural elements to facilitate protein folding and assembly. It is challenging to observe the reversible unfolding and refolding of metalloproteins because of a loss or decomposition of the metal center. Here, the reversible unfolding–refolding of the iron–sulfur protein rubredoxin was observed directly using single‐molecule force spectroscopy. The results demonstrate that the iron can remain attached to the CXXC motif when rubredoxin is unfolded. Upon relaxation, the unfolded rubredoxin can refold into its native holo state with the reconstituted FeS₄ center. The possible loss of iron from the unfolded protein prevents rubredoxin from refolding into its native holo state. These results demonstrated that unfolding of rubredoxin is reversible, as long as the iron remains attached, and provide experimental evidence for the iron‐priming mechanism for the folding of rubredoxin.     

Cell‐Derived Vesicles for Single‐Molecule Imaging of Membrane Proteins

A new approach is presented for the application of single‐molecule imaging to membrane receptors through the use of vesicles derived from cells expressing fluorescently labeled receptors. During the isolation of vesicles, receptors remain embedded in the membrane of the resultant vesicles, thus allowing these vesicles to serve as nanocontainers for single‐molecule measurements. Cell‐derived vesicles maintain the structural integrity of transmembrane receptors by keeping them in their physiological membrane. It was demonstrated that receptors isolated in these vesicles can be studied with solution‐based fluorescence correlation spectroscopy (FCS) and can be isolated on a solid substrate for single‐molecule studies. This technique was applied to determine the stoichiometry of α3β4 nicotinic receptors. The method provides the capability to extend single‐molecule studies to previously inaccessible classes of receptors.     

Magnetic Bistability of Individual Single‐Molecule Magnets Grafted on Single‐Wall Carbon Nanotubes

A POM to remember : Hexanuclear Fe^III polyoxometalate (POM) single‐molecule magnets (see structure) can be noncovalently assembled on the surface of single‐wall carbon nanotubes. Complementary characterization techniques (see TEM image and magnetic hysteresis loops) demonstrate the integrity and bistability of the individual molecules, which could be used to construct single‐molecule memory devices.