Feeling Inter‐ or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions

Single‐molecule force spectroscopy (SMFS) opens new avenues for elucidating the structures and functions of large coiled molecules such as synthetic and biopolymers at the single‐molecule level. In addition, some of the features in the force–extension curves (i.e. force spectra) are closely related to primary/secondary structures of the molecules being stretched. For example, the long force plateau in the DNA stretching curve is related to the double‐helix structure. These features can be regarded as the force fingerprints of individual macromolecules. These force fingerprints can therefore be used as indicators/criteria of single‐molecule manipulation during the measurement of some unknown intra‐ or intermolecular interactions. By comparing the force spectra of a single polymer chain before and after interaction with other molecules, the mode/strength of such molecular interactions can be derived. This Review focuses on recent advances in AFM‐based SMFS studies on molecular interactions in both synthetic and biopolymer systems using a single macromolecular chain as probe, including interactions between nucleic acids and proteins, mechanochemistry of covalent bonds, conformation‐regulated enzymatic reactions, adsorption and desorption of biopolymers on a flat surface or from the nanopore of a carbon nanotube, and polymer interactions in the condensed state.     

Internal Architecture and Adsorption Sites of Violet Lander Molecules Assembled on Native and KBr‐Passivated InSb(001) Surfaces

The adsorption of individual Violet Lander molecules self‐assembled on the c(8×2) reconstructed InSb(001) surface in its native form and on the surface passivated with one to three monolayers of KBr is investigated by means of low‐temperature scanning tunneling microscopy (STM). Preferred adsorption sites of the molecules are found on flat terraces as well as at atomic step edges. For molecules immobilized on flat terraces, several different conformations are identified from STM images acquired with submolecular resolution and are explained by the rotation of the 3,5‐di‐tert‐butylphenyl groups around σ bonds, which allows adjustment of the molecular geometry to the anisotropic substrate structure. Formation of ordered molecular chains is found at steps running along substrate reconstruction rows, whereas at the steps oriented perpendicularly no intermolecular ordering is recorded. It is also shown that the molecules deposited at two or more monolayers of the epitaxial KBr spacer do not have any stable adsorption sites recorded with STM. Prospects for the manipulation of single molecules by using the STM tip on highly anisotropic substrates are also explored, and demonstrate the feasibility of controlled lateral displacement in all directions.     

Label‐Free Biosensing over a Wide Concentration Range with Photonic Force Microscopy

We present a label‐free biosensor that measures molecular interactions between biomolecules on the surface of a probe bead and substrate over a wide concentration range. This system is capable of detecting target biomolecules with concentrations varying from 10 nM to 0.1 pM , with high selectivity and sensitivity.     

Direct Observation of the Reversible Two‐State Unfolding and Refolding of an α/β Protein by Single‐Molecule Atomic Force Microscopy

Directly observing protein folding in real time using atomic force microscopy (AFM) is challenging. Here the use of AFM to directly monitor the folding of an α/β protein, NuG2, by using low‐drift AFM cantilevers is demonstrated. At slow pulling speeds (<50 nm s^?1), the refolding of NuG2 can be clearly observed. Lowering the pulling speed reduces the difference between the unfolding and refolding forces, bringing the non‐equilibrium unfolding–refolding reactions towards equilibrium. At very low pulling speeds (ca. 2 nm s^?1), unfolding and refolding were observed to occur in near equilibrium. Based on the Crooks fluctuation theorem, we then measured the equilibrium free energy change between folded and unfolded states of NuG2. The improved long‐term stability of AFM achieved using gold‐free cantilevers allows folding–unfolding reactions of α/β proteins to be directly monitored near equilibrium, opening the avenue towards probing the folding reactions of other mechanically important α/β and all‐β elastomeric proteins.     

Adsorption of Large Organic Molecules on Clean and Hydroxylated Rutile TiO2(110) Surfaces

Behavior of large organic molecules equipped with spacer groups (Violet Landers, VL) on the TiO₂(110)‐(1×1) surfaces is investigated by means of high‐resolution scanning tunneling microscopy (STM). Two distinct adsorption geometries are observed. We demonstrate that the molecule adsorption morphology can be alternated by well‐controlled STM tip‐induced manipulation. It is used to probe the mobility of molecules and reveals locking in one of the analyzed adsorption sites, thus allow to enhance or reduce the mobility along the [001] direction. Field induced hydrogen desorption is used to perform lateral STM manipulation on a hydroxyl‐free surface, which provides insight into the influence of surface hydroxyl groups on the molecule behavior. The ability to image with submolecular resolution both the central board and the spacer groups of the VL molecule is demonstrated.     

Topological and Electron‐Transfer Properties of Yeast Cytochrome c Adsorbed on Bare Gold Electrodes

The redox metalloprotein yeast cytochrome c was directly self‐chemisorbed on “bare” gold electrodes through the free sulfur‐containing group Cys102. Topological, spectroscopic, and electron transfer properties of the immobilised molecules were investigated by in situ scanning probe microscopy and cyclic voltammetry. Atomic force and scanning tunnelling microscopy revealed individual protein molecules adsorbed on the gold substrate, with no evidence of aggregates. The adsorbed proteins appear to be firmly bound to gold and display dimensions in good agreement with crystallographic data. Cyclic voltammetric analysis showed that up to 84 % of the electrode surface is functionalised with electroactive proteins whose measured redox midpoint potential is in good agreement with the formal potential. Our results clearly indicate that this variant of cytochrome c is adsorbed on bare gold electrodes with preservation of morphological properties and redox functionality.     

Nano-Optical Tweezers: Methods and Applications for Trapping Single Molecules and Nanoparticles

Optical tweezers were developed in 1970 by Arthur Ashkin as a tool for the manipulation of micron-sized particles. Ashkin's original design was then adapted for a variety of purposes, such as trapping and manipulation of biological materials^[1] and the laser cooling of atoms.^[2,3] More recent development has led to nano-optical tweezers, for trapping particles on the scale of only a few nanometers, and holographic tweezers, which allow for dynamic control of multiple traps in real-time. These alternatives to conventional optical tweezers have made it possible to trap single molecules and to perform a variety of studies on them. Presented here is a review of recent developments in nano-optical tweezers and their current and future applications.