Force-fluorescence setup for observing protein-DNA interactions under load

This chapter explores advanced single-molecule techniques for studying protein-DNA interactions, particularly focusing on Replication Protein A (RPA) using a force-fluorescence setup. It combines magnetic tweezers (MT) with total internal reflection fluorescence (TIRF) microscopy, enabling detailed observation of DNA behavior under mechanical stress. The chapter details the use of DNA hairpins and bare DNA to examine RPA's binding dynamics and its influence on DNA's mechanical properties. This approach provides deeper insights into RPA's role in DNA replication, repair, and recombination, highlighting its significance in maintaining genomic stability.

Nanoengineering Triplet-Triplet Annihilation Upconversion: From Materials to Real-World Applications

Using light to control matter has captured the imagination of scientists for generations, as there is an abundance of photons at our disposal. Yet delivering photons beyond the surface to many photoresponsive systems has proven challenging, particularly at scale, due to light attenuation via absorption and scattering losses. Triplet-triplet annihilation upconversion (TTA-UC), a process which allows for low energy photons to be converted to high energy photons, is poised to overcome these challenges by allowing for precise spatial generation of high energy photons due to its nonlinear nature. With a wide range of sensitizer and annihilator motifs available for TTA-UC, many researchers seek to integrate these materials in solution or solid-state applications. In this Review, we discuss nanoengineering deployment strategies and highlight their uses in recent state-of-the-art examples of TTA-UC integrated in both solution and solid-state applications. Considering both implementation tactics and application-specific requirements, we identify critical needs to push TTA-UC-based applications from an academic curiosity to a scalable technology.

Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers

Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.

Angle-dependent strength of a single chemical bond by stereographic force spectroscopy

A wealth of chemical bonds and polymers have been studied with single-molecule force spectroscopy, usually by applying a force perpendicular to the anchoring surface. However, the direction-dependence of the bond strength lacks fundamental understanding. Here we establish stereographic force spectroscopy to study the single-bond strength for various pulling angles. Surprisingly, we find that the apparent bond strength increases with increasing pulling angle relative to the anchoring surface normal, indicating a sturdy mechanical anisotropy of a chemical bond. This finding can be rationalized by a fixed pathway for the rupture of the bond, resulting in an effective projection of the applied pulling force onto a nearly fixed rupture direction. Our study is fundamental for the molecular understanding of the role of the direction of force application in molecular adhesion and friction. It is also a prerequisite for the nanoscale tailoring of the anisotropic strength of bottom-up designed materials.

Stereographic force spectroscopy reveals that a chemical bond ruptures along a fixed pathway such that the apparent bond strength strongly depends on the angle of force application.

Multicolor Mechanofluorophores for the Quantitative Detection of Covalent Bond Scission in Polymers

The fracture of polymer materials is a multiscale process starting with the scission of a single molecular bond advancing to a site of failure within the bulk. Quantifying the bonds broken during this process remains a big challenge yet would help to understand the distribution and dissipation of macroscopic mechanical energy. We here show the design and synthesis of fluorogenic molecular optical force probes (mechanofluorophores) covering the entire visible spectrum in both absorption and emission. Their dual fluorescent character allows to track non-broken and broken bonds in dissolved and bulk polymers by fluorescence spectroscopy and microscopy. Importantly, we develop an approach to determine the absolute number and relative fraction of intact and cleaved bonds with high local resolution. We anticipate that our mechanofluorophores in combination with our quantification methodology will allow to quantitatively describe fracture processes in materials ranging from soft hydrogels to high-performance polymers.

Precise sequencing of single protected-DNA fragment molecules for profiling of protein distribution and assembly on DNA

Multiple DNA-interacting protein molecules are often dynamically distributed and/or assembled along a DNA molecule to adapt to their intricate functions temporally. However, analytical technology for measuring such binding behaviours is still missing. Here, we demonstrate the unique capacity of a supernuclease for a highly efficient cutting of the unprotected-DNA segments and with complete preservation of the protein-occluded DNA segments at near single-nucleotide resolution. By exploring this high-resolution cutting, an unprecedented assay that allows a precise sequencing of single protected-DNA fragment molecules (SPDFMS) was developed. As relevant applications, relevant information was gained on the respective distribution/assembly patterns and coordinated displacement of single-stranded DNA-binding protein and recombinase RecA, two model proteins, on DNA. Benefiting from this assay, we also for the first time provide direct measurement of the length of single RecA nucleofilaments, showing the predominant stoichiometry of 5-7 RecA monomers per RecA nucleofilament under physiologically relevant conditions. This innovative assay appears as a promising analytical tool for studying diverse protein-DNA interactions implicated in DNA replication, transcription, recombination, repair, and gene editing.

Anti-Stokes Stress Sensing: Mechanochemical Activation of Triplet-Triplet Annihilation Photon Upconversion

The development of methods to detect damage in macromolecular materials is of paramount importance to understand their mechanical failure and the structure-property relationships of polymers. Mechanofluorophores are useful and sensitive molecular motifs for this purpose. However, to date, tailoring of their optical properties remains challenging and correlating emission intensity to force induced material damage and the respective events on the molecular level is complicated by intrinsic limitations of fluorescence and its detection techniques. Now, this is tackled by developing the first stress-sensing motif that relies on photon upconversion. By combining the Diels-Alder adduct of a π-extended anthracene with the porphyrin-based triplet sensitizer PtOEP in polymers, triplet-triplet annihilation photon upconversion of green to blue light is mechanochemically activated in solution as well as in the solid state.

High-intensity focused ultrasound-induced mechanochemical transduction in synthetic elastomers

While study in the field of polymer mechanochemistry has yielded mechanophores that perform various chemical reactions in response to mechanical stimuli, there is not yet a triggering method compatible with biological systems. Applications such as using mechanoluminescence to generate localized photon flux in vivo for optogenetics would greatly benefit from such an approach. Here we introduce a method of triggering mechanophores by using high-intensity focused ultrasound (HIFU) as a remote energy source to drive the spatially and temporally resolved mechanical-to-chemical transduction of mechanoresponsive polymers. A HIFU setup capable of controlling the excitation pressure, spatial location, and duration of exposure is employed to activate mechanochemical reactions in a cross-linked elastomeric polymer in a noninvasive fashion. One reaction is the chromogenic isomerization of a naphthopyran mechanophore embedded in a polydimethylsiloxane (PDMS) network. Under HIFU irradiation evidence of the mechanochemical transduction is the observation of a reversible color change as expected for the isomerization. The elastomer exhibits this distinguishable color change at the focal spot, depending on ultrasonic exposure conditions. A second reaction is the demonstration that HIFU irradiation successfully triggers a luminescent dioxetane, resulting in localized generation of visible blue light at the focal spot. In contrast to conventional stimuli such as UV light, heat, and uniaxial compression/tension testing, HIFU irradiation provides spatiotemporal control of the mechanochemical activation through targeted but noninvasive ultrasonic energy deposition. Targeted, remote light generation is potentially useful in biomedical applications such as optogenetics where a light source is used to trigger a cellular response.

High-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and an Atomic Force Microscopy-Based Toolbox

To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins. As a well-studied model system, we use native purple membrane from Halobacterium salinarum, whose membrane protein bacteriorhodopsin was His-tagged to bind nitrilotriacetate (NTA) ligands. First, by confocal microscopy we localize the extracellular and cytoplasmic surfaces of purple membrane. Then, we apply AFM to image single bacteriorhodopsins approaching sub-nanometer resolution. Afterwards, the binding of NTA ligands to bacteriorhodopsins is localized and quantified by FD-based AFM. Finally, we apply AFM-based SMFS to characterize the (un)folding of the membrane protein and to structurally map inter- and intramolecular interactions. The multimethodological approach is generally applicable to characterize biological membranes and membrane proteins at physiologically relevant conditions.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.