Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein-DNA Complexes That Carry Out DNA Repair

The roles of non-productive complexes of DNA repair proteins with DNA lesions

A multitude of different types of lesions is continuously introduced into the DNA inside our cells, and their rapid and efficient repair is fundamentally important for the maintenance of genomic stability and cellular viability. This is achieved by a number of DNA repair systems that each involve different protein factors and employ versatile strategies to target different types of DNA lesions. Intriguingly, specialized DNA repair proteins have also evolved to form non-functional complexes with their target lesions. These proteins allow the marking of innocuous lesions to render them visible for DNA repair systems and can serve to directly recruit DNA repair cascades. Moreover, they also provide links between different DNA repair mechanisms or even between DNA lesions and transcription regulation. I will focus here in particular on recent findings from single molecule analyses on the alkyltransferase-like protein ATL, which is believed to initiate nucleotide excision repair (NER) of non-native NER target lesions, and the base excision repair (BER) enzyme hOGG1, which recruits the oncogene transcription factor Myc to gene promoters under oxidative stress.

Single-molecule imaging of genome maintenance proteins encountering specific DNA sequences and structures

DNA repair pathways are tightly regulated processes that recognize specific hallmarks of DNA damage and coordinate lesion repair through discrete mechanisms, all within the context of a three-dimensional chromatin landscape. Dysregulation or malfunction of any one of the protein constituents in these pathways can contribute to aging and a variety of diseases. While the collective action of these many proteins is what drives DNA repair on the organismal scale, it is the interactions between individual proteins and DNA that facilitate each step of these pathways. In much the same way that ensemble biochemical techniques have characterized the various steps of DNA repair pathways, single-molecule imaging (SMI) approaches zoom in further, characterizing the individual protein-DNA interactions that compose each pathway step. SMI techniques offer the high resolving power needed to characterize the molecular structure and functional dynamics of individual biological interactions on the nanoscale. In this review, we highlight how our lab has used SMI techniques - traditional atomic force microscopy (AFM) imaging in air, high-speed AFM (HS-AFM) in liquids, and the DNA tightrope assay - over the past decade to study protein-nucleic acid interactions involved in DNA repair, mitochondrial DNA replication, and telomere maintenance. We discuss how DNA substrates containing specific DNA sequences or structures that emulate DNA repair intermediates or telomeres were generated and validated. For each highlighted project, we discuss novel findings made possible by the spatial and temporal resolution offered by these SMI techniques and unique DNA substrates.

Using Different Surface Energy Models to Assess the Interactions between Antiviral Coating Films and phi6 Model Virus

High molecular weight chitosan (HMWCh), quaternised cellulose nanofibrils (qCNF), and their mixture showed antiviral potential in liquid phase, while this effect decreased when applied to facial masks, as studied in our recent work. To gain more insight into material antiviral activity, spin-coated thin films were prepared from each suspension (HMWCh, qCNF) and their mixture with a 1:1 ratio. To understand their mechanism of action, the interactions between these model films with various polar and nonpolar liquids and bacteriophage phi6 (in liquid phase) as a viral surrogate were studied. Surface free energy (SFE) estimates were used as a tool to evaluate the potential adhesion of different polar liquid phases to these films by contact angle measurements (CA) using the sessile drop method. The Fowkes, Owens-Wendt-Rabel-Kealble (OWRK), Wu, and van Oss-Chaudhury-Good (vOGC) mathematical models were used to estimate surface free energy and its polar and dispersive contributions, as well as the Lewis acid and Lewis base contributions. In addition, the surface tension SFT of liquids was also determined. The adhesion and cohesion forces in wetting processes were also observed. The estimated SFE of spin-coated films varied between mathematical models (26-31 mJ/m²) depending on the polarity of the solvents tested, but the correlation between models clearly indicated a significant dominance of the dispersion components that hinder wettability. The poor wettability was also supported by the fact that the cohesive forces in the liquid phase were stronger than the adhesion to the contact surface. In addition, the dispersive (hydrophobic) component dominated in the phi6 dispersion, and since this was also the case in the spin-coated films, it can be assumed that weak physical van der Waals forces (dispersion forces) and hydrophobic interactions occurred between phi6 and the polysaccharide films, resulting in the virus not being in sufficient contact with the tested material during antiviral testing of the material to be inactivated by the active coatings of the polysaccharides used. Regarding the contact killing mechanism, this is a disadvantage that can be overcome by changing the previous material surface (activation). In this way, HMWCh, qCNF, and their mixture can attach to the material surface with better adhesion, thickness, and different shape and orientation, resulting in a more dominant polar fraction of SFE and thus enabling the interactions within the polar part of phi6 dispersion.

Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization

Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions.

Dynamic human MutSα-MutLα complexes compact mismatched DNA

DNA mismatch repair (MMR) corrects errors that occur during DNA replication. In humans, mutations in the proteins MutSα and MutLα that initiate MMR cause Lynch syndrome, the most common hereditary cancer. MutSα surveilles the DNA, and upon recognition of a replication error it undergoes adenosine triphosphate-dependent conformational changes and recruits MutLα. Subsequently, proliferating cell nuclear antigen (PCNA) activates MutLα to nick the error-containing strand to allow excision and resynthesis. The structure-function properties of these obligate MutSα-MutLα complexes remain mostly unexplored in higher eukaryotes, and models are predominately based on studies of prokaryotic proteins. Here, we utilize atomic force microscopy (AFM) coupled with other methods to reveal time- and concentration-dependent stoichiometries and conformations of assembling human MutSα-MutLα-DNA complexes. We find that they assemble into multimeric complexes comprising three to eight proteins around a mismatch on DNA. On the timescale of a few minutes, these complexes rearrange, folding and compacting the DNA. These observations contrast with dominant models of MMR initiation that envision diffusive MutS-MutL complexes that move away from the mismatch. Our results suggest MutSα localizes MutLα near the mismatch and promotes DNA configurations that could enhance MMR efficiency by facilitating MutLα nicking the DNA at multiple sites around the mismatch. In addition, such complexes may also protect the mismatch region from nucleosome reassembly until repair occurs, and they could potentially remodel adjacent nucleosomes.

Single gold-bridged nanoprobes for identification of single point DNA mutations

Consensus ranking of protein affinity to identify point mutations has not been established. Therefore, analytical techniques that can detect subtle variations without interfering with native biomolecular interactions are required. Here we report a rapid method to identify point mutations by a single nanoparticle sensing system. DNA-directed gold crystallization forms rod-like nanoparticles with bridges based on structural design. The nanoparticles enhance Rayleigh light scattering, achieving high refractive-index sensitivity, and enable the system to monitor even a small number of protein-DNA binding events without interference. Analysis of the binding affinity can compile an atlas to distinguish the potential of various point mutations recognized by MutS protein. We use the atlas to analyze the presence and type of single point mutations in BRCA1 from samples of human breast and ovarian cancer cell lines. The strategy of synthesis-by-design of plasmonic nanoparticles for sensors enables direct identification of subtle biomolecular binding distortions and genetic alterations.