Observing Single‐Molecule Dynamics at Millimolar Concentrations

Single‐molecule fluorescence microscopy is a powerful tool for revealing chemical dynamics and molecular association mechanisms, but has been limited to low concentrations of fluorescent species and is only suitable for studying high affinity reactions. Here, we combine nanophotonic zero‐mode waveguides (ZMWs) with fluorescence resonance energy transfer (FRET) to resolve single‐molecule association dynamics at up to millimolar concentrations of fluorescent species. This approach extends the resolution of molecular dynamics to >100‐fold higher concentrations, enabling observations at concentrations relevant to biological and chemical processes, and thus making single‐molecule techniques applicable to a tremendous range of previously inaccessible molecular targets. We deploy this approach to show that the binding of cGMP to pacemaking ion channels is weakened by a slower internal conformational change.     

Anisotropic Conductivity at the Single‐Molecule Scale

In most junctions built by wiring a single molecule between two electrodes, the electrons flow along only one axis: between the two anchoring groups. However, molecules can be anisotropic, and an orientation‐dependent conductance is expected. Here, we fabricated single‐molecule junctions by using the electrode potential to control the molecular orientation and access individual elements of the conductivity tensor. We measured the conductance in two directions, along the molecular plane as the benzene ring bridges two electrodes using anchoring groups (upright) and orthogonal to the molecular plane with the molecule lying flat on the substrate (planar). The perpendicular (planar) conductance is about 400 times higher than that along the molecular plane (upright). This offers a new method for designing a reversible room‐temperature single‐molecule electromechanical switch that controllably employs the electrode potential to orient the molecule in the junction in either “ON” or “OFF” conductance states.     

Detecting Single‐Molecule Dynamics on Lipid Membranes with Quenchers‐in‐a‐Liposome FRET

Tracking membrane‐interacting molecules and visualizing their conformational dynamics are key to understanding their functions. It is, however, challenging to accurately probe the positions of a molecule relative to a membrane. Herein, a single‐molecule method, termed LipoFRET, is reported to assess interplay between molecules and liposomes. It takes advantage of FRET between a single fluorophore attached to a biomolecule and many quenchers in a liposome. This method was used to characterize interactions between α‐synuclein (α‐syn) and membranes. These results revealed that the N‐terminus of α‐syn inserts into the membrane and spontaneously transitions between different depths. In contrast, the C‐terminal tail of α‐syn is regulated by calcium ions and floats in solution in two conformations. LipoFRET is a powerful tool to investigate membrane‐interacting biomolecules with sub‐nanometer precision at the single‐molecule level.     

Revealing Conformational Variants of Solution‐Phase Intrinsically Disordered Tau Protein at the Single‐Molecule Level

Intrinsically disordered proteins, such as tau protein, adopt a variety of conformations in solution, complicating solution‐phase structural studies. We employed an anti‐Brownian electrokinetic (ABEL) trap to prolong measurements of single tau proteins in solution. Once trapped, we recorded the fluorescence anisotropy to investigate the diversity of conformations sampled by the single molecules. A distribution of anisotropy values obtained from trapped tau protein is conspicuously bimodal while those obtained by trapping a globular protein or individual fluorophores are not. Time‐resolved fluorescence anisotropy measurements were used to provide an explanation of the bimodal distribution as originating from a shift in the compaction of the two different families of conformations.     

Single‐Molecule Observation of the Photoregulated Conformational Dynamics of DNA Origami Nanoscissors

We demonstrate direct observation of the dynamic opening and closing behavior of photocontrollable DNA origami nanoscissors using high‐speed atomic force microscopy (HS‐AFM). First the conformational change between the open and closed state controlled by adjustment of surrounding salt concentration could be directly observed during AFM scanning. Then light‐responsive moieties were incorporated into the nanoscissors to control these structural changes by photoirradiation. Using photoswitchable DNA strands, we created a photoresponsive nanoscissors variant and were able to distinguish between the open and closed conformations after respective irradiation with ultraviolet (UV) and visible (Vis) light by gel electrophoresis and AFM imaging. Additionally, these reversible changes in shape during photoirradiation were directly visualized using HS‐AFM. Moreover, four photoswitchable nanoscissors were assembled into a scissor–actuator‐like higher‐order object, the configuration of which could be controlled by the open and closed switching induced by irradiation with UV and Vis light.     

Single‐Molecule Photoactivation FRET: A General and Easy‐To‐Implement Approach To Break the Concentration Barrier

Single‐molecule fluorescence resonance energy transfer (sm‐FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm‐FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single‐molecule photoactivation FRET (sm‐PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm‐PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm‐FRET measurements. sm‐PAFRET serves as an easy‐to‐implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.     

Three‐State Single‐Molecule Naphthalenediimide Switch: Integration of a Pendant Redox Unit for Conductance Tuning

We studied charge transport through core‐substituted naphthalenediimide (NDI) single‐molecule junctions using the electrochemical STM‐based break‐junction technique in combination with DFT calculations. Conductance switching among three well‐defined states was demonstrated by electrochemically controlling the redox state of the pendent diimide unit of the molecule in an ionic liquid. The electrical conductances of the dianion and neutral states differ by more than one order of magnitude. The potential‐dependence of the charge‐transport characteristics of the NDI molecules was confirmed by DFT calculations, which account for electrochemical double‐layer effects on the conductance of the NDI junctions. This study suggests that integration of a pendant redox unit with strong coupling to a molecular backbone enables the tuning of charge transport through single‐molecule devices by controlling their redox states.     

In Situ Coupling of Single Molecules Driven by Gold‐Catalyzed Electrooxidation

A single‐molecule method has been developed based on the scanning tunneling microscope (STM) to selectively couple a series of aniline derivatives and create azobenzenes. The Au‐catalyzed oxidative coupling is driven by the local electrochemical potential at the nanostructured Au STM tip. The products are detected in situ by measuring the conductance and molecular junction elongation and compared with analogous measurements of the expected azobenzene derivatives prepared ex situ. This single‐molecule approach is robust, and it can quickly and reproducibly create reactions for a variety of anilines. We further demonstrate the selective synthesis of geometric isomers and the assembly of complex molecular architectures by sequential coupling of complementary anilines, demonstrating unprecedented control over bond formation at the nanoscale.