Human topoisomerase II-DNA interaction study by using atomic force microscopy

Structural insights into the DNA topoisomerase II of the African swine fever virus

Type II topoisomerases are ubiquitous enzymes that play a pivotal role in modulating the topological configuration of double-stranded DNA. These topoisomerases are required for DNA metabolism and have been extensively studied in both prokaryotic and eukaryotic organisms. However, our understanding of virus-encoded type II topoisomerases remains limited. One intriguing example is the African swine fever virus, which stands as the sole mammalian-infecting virus encoding a type II topoisomerase. In this work, we use several approaches including cryo-EM, X-ray crystallography, and biochemical assays to investigate the structure and function of the African swine fever virus type II topoisomerase, pP1192R. We determine the structures of pP1192R in different conformational states and confirm its enzymatic activity in vitro. Collectively, our results illustrate the basic mechanisms of viral type II topoisomerases, increasing our understanding of these enzymes and presenting a potential avenue for intervention strategies to mitigate the impact of the African swine fever virus.

Atomic force microscopy-A tool for structural and translational DNA research

Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.

Nano-Motion Analysis for Rapid and Label Free Assessing of Cancer Cell Sensitivity to Chemotherapeutics

Background and Objectives: Optimization of chemotherapy is crucial for cancer patients. Timely and costly efficient treatments are emerging due to the increasing incidence of cancer worldwide. Here, we present a methodology of nano-motion analysis that could be developed to serve as a screening tool able to determine the best chemotherapy option for a particular patient within hours. Materials and Methods: Three different human cancer cell lines and their multidrug resistant (MDR) counterparts were analyzed with an atomic force microscope (AFM) using tipless cantilevers to adhere the cells and monitor their nano-motions. Results: The cells exposed to doxorubicin (DOX) differentially responded due to their sensitivity to this chemotherapeutic. The death of sensitive cells corresponding to the drop in signal variance occurred in less than 2 h after DOX application, while MDR cells continued to move, even showing an increase in signal variance. Conclusions: Nano-motion sensing can be developed as a screening tool that will allow simple, inexpensive and quick testing of different chemotherapeutics for each cancer patient. Further investigations on patient-derived tumor cells should confirm the method’s applicability.

Mechanism and Control of Meiotic DNA Double-Strand Break Formation in S. cerevisiae

Developmentally programmed formation of DNA double-strand breaks (DSBs) by Spo11 initiates a recombination mechanism that promotes synapsis and the subsequent segregation of homologous chromosomes during meiosis. Although DSBs are induced to high levels in meiosis, their formation and repair are tightly regulated to minimize potentially dangerous consequences for genomic integrity. In S. cerevisiae, nine proteins participate with Spo11 in DSB formation, but their molecular functions have been challenging to define. Here, we describe our current view of the mechanism of meiotic DSB formation based on recent advances in the characterization of the structure and function of DSB proteins and discuss regulatory pathways in the light of recent models.

Structural and functional characterization of the Spo11 core complex

Spo11, which makes DNA double-strand breaks (DSBs) essential for meiotic recombination, has long been recalcitrant to biochemical study. We provide molecular analysis of S. cerevisiae Spo11 purified with partners Rec102, Rec104 and Ski8. Rec102 and Rec104 jointly resemble the B subunit of archaeal Topoisomerase VI, with Rec104 occupying a position similar to the Top6B GHKL-type ATPase domain. Unexpectedly, the Spo11 complex is monomeric (1:1:1:1 stoichiometry), consistent with dimerization controlling DSB formation. Reconstitution of DNA binding reveals topoisomerase-like preferences for duplex-duplex junctions and bent DNA. Spo11 also binds noncovalently but with high affinity to DNA ends mimicking cleavage products, suggesting a mechanism to cap DSB ends. Mutations that reduce DNA binding in vitro attenuate DSB formation, alter DSB processing, and reshape the DSB landscape in vivo. Our data reveal structural and functional similarities between the Spo11 core complex and Topo VI, but also highlight differences reflecting their distinct biological roles.

Atomic Force Microscopy: The Characterisation of Amyloid Protein Structure in Pathology

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Proteins are versatile macromolecules that perform a variety of functions and participate in virtually all cellular processes. The functionality of a protein greatly depends on its structure and alterations may result in the development of diseases. Most well-known of these are protein misfolding disorders, which include Alzheimer’s and Parkinson’s diseases as well as type 2 diabetes mellitus, where soluble proteins transition into insoluble amyloid fibrils. Atomic Force Microscopy (AFM) is capable of providing a topographical map of the protein and/or its aggregates, as well as probing the nanomechanical properties of a sample. Moreover, AFM requires relatively simple sample preparation, which presents the possibility of combining this technique with other research modalities, such as confocal laser scanning microscopy, Raman spectroscopy and stimulated emission depletion microscopy. In this review, the basic principles of AFM are discussed, followed by a brief overview of how it has been applied in biological research. Finally, we focus specifically on its use as a characterisation method to study protein structure at the nanoscale in pathophysiological conditions, considering both molecules implicated in disease pathogenesis and the plasma protein fibrinogen. In conclusion, AFM is a userfriendly tool that supplies multi-parametric data, rendering it a most valuable technique.

PEGylated surfaces for the study of DNA-protein interactions by atomic force microscopy

DNA-protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA-protein interactions at nanometre resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working in biologically relevant protein concentrations, where proteins may be present in large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGy block copolymers to achieve selective adsorption of DNA on a mica surface for AFM studies. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, we show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113/PLL1000-2000 mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. We show - through the use of biotinylated DNA and streptavidin - that this selective adsorption extends to DNA-protein complexes and that DNA-bound streptavidin can be unambiguously distinguished in spite of an excess of unbound streptavidin in solution. Finally, we apply this to the nuclear enzyme PARP1, resolving the binding of individual PARP1 molecules to DNA by in-liquid AFM.

Stokesian dynamics of sedimenting elastic rings

We consider elastic microfilaments which form closed loops. We investigate how the loops change shape and orientation while settling under gravity in a viscous fluid. Loops are circular at the equilibrium. Their dynamics are investigated numerically based on the Stokes equations for the fluid motion and the bead-spring model of the microfilament. The Rotne-Prager approximation for the bead mobility is used. We demonstrate that the relevant dimensionless parameter is the ratio of the bending resistance of the filament to the gravitation force corrected for buoyancy. The inverse of this ratio, called the elasto-gravitation number B, is widely used in the literature for sedimenting elastic linear filaments. We assume that B is of the order of 104-106, which corresponds to easily deformable loops. We find out that initially tilted circles evolve towards different sedimentation modes, depending on B. Very stiff or stiff rings attain almost planar, oval shapes, which are vertical or tilted, respectively. More flexible loops deform significantly and converge towards one of several characteristic periodic motions. These sedimentation modes are also detected when starting from various shapes, and for different loop lengths. In general, multi-stability is observed: an elastic ring converges to one of several sedimentation modes, depending on the initial conditions. This effect is pronounced for very elastic loops. The surprising diversity of long-lasting periodic motions and shapes of elastic rings found in this work gives a new perspective for the dynamics of more complex deformable objects at micrometer and nanometer scales, sedimenting under gravity or rotating in a centrifuge, such as red blood cells, ring polymers or circular DNA.

Atomic force microscopy study of EDTA induced desorption of metal ions immobilized DNA from mica surface

Adsorption of DNA molecules onto substrate, such as mica, is well documented. However, desorption of the immobilized DNA molecules from substrate, which is also an important aspect of DNA behavior on substrate, has not been paid much attention. Here, DNA molecules were first immobilized on mica surface by using divalent metal ions as the bridge agents. Desorption of the immobilized DNA from mica surface was realized via ethylenediamine tetraacetic acid disodium salt (EDTA) treatment. EDTA is a chelating agent; it can remove the bridging metal ions between DNA and mica, which leads to the release of DNA molecules from mica substrate. The divalent metal ions assisted DNA adsorption onto mica surface and the EDTA induced DNA desorption from mica surface were followed by atomic force microscopy (AFM). Randomly dispersed DNA strands and DNA networks are two distinct adsorption morphologies of DNA on mica surface and their desorption processes from mica surface induced by EDTA are also different. Other factors that influence the EDTA-induced DNA desorption, such as type of bridging metal ion and DNA molecule length, have also been systematically studied. Moreover, EDTA treatment has no effect on the integrity of DNA molecule. The EDTA induced desorption of metal ions immobilized DNA from mica surface is simple and effective, which has potential applications in DNA separation and purification, DNA biophysics, and DNA-based nanotechnology.

Analysis of single, cisplatin-induced DNA bends by atomic force microscopy and simulations

Bent DNA, or DNA that is locally more flexible, is a recognition motif for many DNA binding proteins. These DNA conformational properties can thus influence many cellular processes, such as replication, transcription, and DNA repair. The importance of these DNA conformational properties is juxtaposed to the experimental difficulty to accurately determine small bends, locally more flexible DNA, or a combination of both (bends with increased flexibility). In essence, many current bulk methods use average quantities, such as the average end-to-end distance, to extract DNA conformational properties; they cannot access the additional information that is contained in the end-to-end distance distributions. We developed a method that exploits this additional information to determine DNA conformational parameters. The method is based on matching end-to-end distance distributions obtained experimentally by atomic force microscopy imaging to distributions obtained from simulations. We applied this method to investigate cisplatin GG biadducts. We found that cisplatin induces a bend angle of 36° and softens the DNA locally around the bend.

The antibacterial activity and modes of LI-F type antimicrobial peptides against Bacillus cereus in vitro

AIMS

LI-Fs are a family of highly potent cyclic lipodepsipeptide antibiotics with a broad antimicrobial spectrum (Gram-positive bacteria and fungi). In this study, LI-F-type antimicrobial peptides (AMP-jsa9) composing of LI-F03a, LI-F03b, LI-F04a, LI-F04b and LI-F05b were isolated from Paenibacillus polymyxa JSA-9. To better understand the antimicrobial mechanism of AMP-jsa9, the potency and action(s) of AMP-jsa9 against Bacillus cereus were examined.

METHODS AND RESULTS

Flow cytometry, confocal laser microscopy, scanning electron microscopy, transmission electron microscopy (TEM) and atomic force microscopy observation, as well as determination of peptidoglycan and cell wall-associated protein and other methods were used. The results indicate that AMP-jsa9 exhibits strong, broad-spectrum antimicrobial activity. Moreover, AMP-jsa9 targets the cell wall and membrane of B. cereus to impair membrane integrity, increase membrane permeability and enhance cytoplasm leakage (e.g. K⁺ , protein, nucleic acid). This leads to bacterial cells with irregular, withered and coarse surfaces. In addition, AMP-jsa9 is also able to bind to DNA and break down B. cereus biofilms.

CONCLUSIONS

In this study, the action mechanism of LI-Fs against B. cereus was clarified in details.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study provide a theoretical basis for utilizing AMP-jsa9 or similar analogues as natural and effective preservatives in the food and feed industries. These efforts could also stimulate research activities interested in understanding the specific effects of other antimicrobial agents.

DNA-protein interactions explored by atomic force microscopy

DNA-protein interactions play an important role in all living organisms on Earth. The advent of atomic force microscopy permitted for the first time to follow and to characterize interaction forces between these two molecular species. After a short description of the AFM and its imaging modes we review, in a chronological order some of the studies that we think importantly contributed to the field.

The dynamic interplay between DNA topoisomerases and DNA topology

Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

The Dynamic Interplay Between DNA Topoisomerases and DNA Topology

Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

Real-time monitoring of protein conformational changes using a nano-mechanical sensor

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice.

Time-lapse AFM imaging of DNA conformational changes induced by daunorubicin

Cancer is a major health issue that absorbs the attention of a large part of the biomedical research. Intercalating agents bind to DNA molecules and can inhibit their synthesis and transcription; thus, they are increasingly used as drugs to fight cancer. In this work, we show how atomic force microscopy in liquid can characterize, through time-lapse imaging, the dynamical influence of intercalating agents on the supercoiling of DNA, improving our understanding of the drug's effect.