Study of biomacromolecule conformational changes by Scanning Force Microscopy

L?objectif de ce travail de thèse est l?étude des changements conformationels des biomacromolecules à l?échelle d?une molécule unique. Pour cela on a utilisé la Microscopie à Force Atomique (AFM) appliqué à l?étude des protéines et des acides nucléiques déposés sur une surface. Dans ce type de microscopie, une pointe très fine attachée à l?extrémité d?un levier est balayée au dessus d?une surface. L?interaction de la pointe avec la surface de l?échantillon induit la déflection du levier et ce phénomène permet de reconstruire la topographie de l?échantillon. Très importante dans cette technique est la possibilité de travailler en liquide. Cela permet de étudier les biomolécules en conditions quasi-physiologiques sans qu?elles perdent leur activité. On a étudié GroEL, la chaperonin de E.coli, qui est un homo oligomère avec une structure à double anneau qui joue un rôle très important dans le repliement des protéines dénaturées et celles qui viennent d?être synthétisées. En particulier on a focalisé notre attention sur la stabilité mécanique et sur les changements conformationels qui ont lieu pendant l?activité de GroEL. Une analyse détaillée des changements dans la stabilité mécanique et des effets produits par la liaison et l?hydrolyse de l?ATP est présentée dans ce travail. On a montré que le point le plus faible dans la structure de GroEL est l?interface entre les deux anneaux et que l?étape critique dans l?affaiblissement de la structure est l?hydrolyse de l?ATP. En ce qui concerne le changement conformationel, le passage d?une surface hydrophobe à hydrophile, induit par l?hydrolyse de l?ATP, a été montré. Ensuite on a étudié le changement dans la conformation et dans la topologie de l?ADN résultant de l?interaction avec des molécules spécifiques et en réponse à l?exposition des cellules de E.coli à des conditions de stress. Le niveau de surenroulement est un paramètre très sensible, de façon variée, à tous ces facteurs. Les cellules qui ont crus à de températures plus élevées que leur température optimale ont la tendance à diminuer le nombre de surenroulements négatif pour augmenter la stabilité thermique de leur plasmides. L?interaction avec des agents intercalant induit une transition d?un surenroulement négatif à un surenroulement positif d?une façon dépendante de la température. Finalement, l?effet de l?interaction de l?ADN avec des surfaces différentes a été étudié et une application pratique sur les noeuds d?ADN est présentée.<br/><br/>The aim of the present thesis work is to study the conformational changes of biomacromolecules at the single molecule level. To that end, Atomic Force Microcopy (AFM) imaging was performed on proteins and nucleic acids adsorbed onto a surface. In this microcopy technique a very sharp tip attached at the end of a soft cantilever is scanned over a surface, the interaction of the tip with the sample?s surface will induce the deflection of the cantilever and thus it will make possible to reconstruct the topography. A very important feature of AFM is the possibility to operate in liquid, it means with the sample immersed in a buffer solution. This allows one to study biomolecules in quasi-physiological conditions without loosing their activity. We have studied GroEL, the chaperonin of E.coli, which is a double-ring homooligomer which pays a very important role in the refolding of unfolded and newly synthetized polypeptides. In particular we focus our attention on its mechanical stability and on the conformational change that it undergoes during its activity cycle. A detailed analysis of the change in mechanical stability and how it is affected by the binding and hydrolysis of nucleotides is presented. It has been shown that the weak point of the chaperonin complex is the interface between the two rings and that the critical step to weaken the structure is the hydrolysis of ATP. Concerning the conformational change we have directly measured, with a nanometer scale resolution, the switching from a hydrophobic surface to a hydrophilic one taking place inside its cavity induced by the ATP hydrolysis. We have further studied the change in the DNA conformation and topology as a consequence of the interaction with specific DNA-binding molecules and the exposition of the E.coli cells to stress conditions. The level of supercoiling has been shown to be a very sensitive parameter, even if at different extents, to all these factors. Cells grown at temperatures higher than their optimum one tend to decrease the number of the negative superhelical turns in their plasmids in order to increase their thermal stability. The interaction with intercalating molecules induced a transition from positive to negative supercoiling in a temperature dependent way. The effect of the interaction of the DNA with different surfaces has been investigated and a practical application to DNA complex knots is reported.<br/><br/>Observer les objets biologiques en le touchant Schématiquement le Microscope a Force Atomique (AFM) consiste en une pointe très fine fixée a l?extrémité d?un levier Lors de l?imagerie, la pointe de l?AFM gratte la surface de l?échantillon, la topographie de celui-ci induit des déflections du levier qui sont enregistrées au moyen d?un rayon laser réfléchi par le levier. Ces donnés sont ensuit utilisés par un ordinateur pour reconstituer en 3D la surface de l?échantillon. La résolution de l?instrument est fonction entre autre de la dureté, de la rugosité de l?échantillon et de la forme de la pointe. Selon l?échantillon et la pointe utilisée la résolution de l?AFM peut aller de 0.1 A (sur des cristaux) a quelque dizaine de nanomètres (sur des cellules). Cet instrument est particulierment intéressant en biologie en raison de sa capacité à imager des échantillons immergés dans un liquide, c?est à dire dans des conditions quasiphysiologiques. Dans le cadre de ce travail nous avons étudié les changements conformationels de molécules biologiques soumises à des stimulations externes. Nous avons essentielment concentré notre attention sur des complexes protéiques nommé Chaperons Moléculaires et sur des molécules d?ADN circulaire (plasmides). Les Chaperons sont impliqués entre autre dans la résistance des organismes vivants aux stress thermiques et osmotiques. Leur activité consiste essentielment à aider les autres protéines à être bien pliés dans leur conformation finale et, en conséquence, à eviter que ils soient dénaturées et que ils puissent s?agréger. L?ADN, quant à lui est la molécule qui conserve, dans sa séquence, l?information génétique de tous les organismes vivants. Ce travail a spécifiquement concerné l?étude des changements conformationels des chaperonins suit a leur activation par l?ATP. Ces travaux ont montrés a l?échelle de molécule unique la capacité de ces protéines de changer leur surface de hydrophobique a hydrophilique. Nous avons également utilisé l?AFM pour étudier le changement du nombre des surenroulements des molécules d?ADN circulaire lors d?une exposition à un changement de température et de force ionique. Ces travaux ont permis de montrer comment la cellule regle le nombre de surenroulements dans ces molécules pour répondre et contrôler l?expression génétique même dans de conditions extrêmes. Pour les deux molécules en général, c?était très important d?avoir la possibilité de observer leur transitions d?une conformation a l?autre directement a l?échelle d?une seul molécule et, surtout, avec une résolution largement au dessous des la longueur d?onde de la lumière visible que représente le limite pour l?imagerie optique.

Influence of the buffer environment on the Relative Biological Effectiveness of carbon ion radiation, investigated by Scanning Force Microscopy and gel electrophoresis

This work focuses on the analysis of the influence of environment on the relative biological effectiveness (RBE) of carbon ions on molecular level. Due to the high relevance of RBE for medical applications, such as tumor therapy, and radiation protection in space, DNA damages have been investigated in order to understand the biological efficiency of heavy ion radiation. The contribution of this study to the radiobiology research consists in the analysis of plasmid DNA damages induced by carbon ion radiation in biochemical buffer environments, as well as in the calculation of the RBE of carbon ions on DNA level by mean of scanning force microscopy (SFM). In order to study the DNA damages, besides the common electrophoresis method, a new approach has been developed by using SFM. The latter method allows direct visualisation and measurement of individual DNA fragments with an accuracy of several nanometres. In addition, comparison of the results obtained by SFM and agarose gel electrophoresis methods has been performed in the present study. Sparsely ionising radiation, such as X-rays, and densely ionising radiation, such as carbon ions, have been used to irradiate plasmid DNA in trishydroxymethylaminomethane (Tris buffer) and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES buffer) environments. These buffer environments exhibit different scavenging capacities for hydroxyl radical (HO0), which is produced by ionisation of water and plays the major role in the indirect DNA damage processes. Fragment distributions have been measured by SFM over a large length range, and as expected, a significantly higher degree of DNA damages was observed for increasing dose. Also a higher amount of double-strand breaks (DSBs) was observed after irradiation with carbon ions compared to X-ray irradiation. The results obtained from SFM measurements show that both types of radiation induce multiple fragmentation of the plasmid DNA in the dose range from D = 250 Gy to D = 1500 Gy. Using Tris environments at two different concentrations, a decrease of the relative biological effectiveness with the rise of Tris concentration was observed. This demonstrates the radioprotective behavior of the Tris buffer solution. In contrast, a lower scavenging capacity for all other free radicals and ions, produced by the ionisation of water, was registered in the case of HEPES buffer compared to Tris solution. This is reflected in the higher RBE values deduced from SFM and gel electrophoresis measurements after irradiation of the plasmid DNA in 20 mM HEPES environment compared to 92 mM Tris solution. These results show that HEPES and Tris environments play a major role on preventing the indirect DNA damages induced by ionising radiation and on the relative biological effectiveness of heavy ion radiation. In general, the RBE calculated from the SFM measurements presents higher values compared to gel electrophoresis data, for plasmids irradiated in all environments. Using a large set of data, obtained from the SFM measurements, it was possible to calculate the survive rate over a larger range, from 88% to 98%, while for gel electrophoresis measurements the survive rates have been calculated only for values between 96% and 99%. While the gel electrophoresis measurements provide information only about the percentage of plasmids DNA that suffered a single DSB, SFM can count the small plasmid fragments produced by multiple DSBs induced in a single plasmid. Consequently, SFM generates more detailed information regarding the amount of the induced DSBs compared to gel electrophoresis, and therefore, RBE can be calculated with more accuracy. Thus, SFM has been proven to be a more precise method to characterize on molecular level the DNA damage induced by ionizing radiations.

A novel assay for drug-DNA binding mode, affinity, and exclusion number: scanning force microscopy.

Determining the mode-of-binding of a DNA ligand is not always straightforward. Here, we establish a scanning force microscopic assay for mode-of-binding that is (i) direct: lengths of individual DNA-ligand complexes are directly measured; (ii) rapid: there are no requirements for staining or elaborate sample preparation; and (iii) unambiguous: an observed increase in DNA length upon addition of a ligand is definitive evidence for an intercalative mode-of-binding. Mode-of-binding, binding affinity, and site-exclusion number are readily determined from scanning force microscopy measurements of the changes in length of individual drug-DNA complexes as a function of drug concentration. With this assay, we resolve the ambiguity surrounding the mode of binding of 2,5-bis(4-amidinophenyl) furan (APF) to DNA and show that it binds to DNA by nonintercalative modes. APF is a member of an important class of aromatic dicationic drugs that show significant activity in the treatment of Pneumocystis carinii pneumonia, an opportunistic infection that is the leading cause of death in AIDS patients.

Large secretory structures at the cell surface imaged with scanning force microscopy.

Scanning force microscopy was used to image rat basophilic leukemia (RBL-2H3) cell surfaces under different stimulation conditions that either permit or inhibit secretion. Cross-linking the surface IgE receptors with dinitrophenol-conjugated bovine serum albumin initiates secretion in RBL cells with concomitant spreading of the cell body. Structures at the cell surface approximately 1.5 microns in diameter relate to secretion both spatially and temporally. The position of these surface pits and their sizes suggest that they may be related to the dense-core granules positioned along the cytoskeletal filaments in detergent-extracted, unactivated RBL cell processes. Topographic scanning force microscopy images of RBL cell surfaces at 2, 5, and 35 min after activation show that these structures persist and change in cross-sectional profile with time after activation. These structures may be related to the membrane retrieval mechanism of cells after intense stimulation.

Electrical scanning probe microscopy on organic optoelectronic structures

In the field of organic optoelectronics, the nanoscale structure of the materials has huge im-pact on the device performance. Here, scanning force microscopy (SFM) techniques become increasingly important. In addition to topographic information, various surface properties can be recorded on a nanometer length scale, such as electrical conductivity (conductive scanning force microscopy, C-SFM) and surface potential (Kelvin probe force microscopy, KPFM).rnrnIn the context of this work, the electrical SFM modes were applied to study the interplay be-tween morphology and electrical properties in hybrid optoelectronic structures, developed in the group of Prof. J. Gutmann (MPI-P Mainz). In particular, I investigated the working prin-ciple of a novel integrated electron blocking layer system. A structure of electrically conduct-ing pathways along crystalline TiO2 particles in an insulating matrix of a polymer derived ceramic was found and insulating defect structures could be identified. In order to get insights into the internal structure of a device I investigated a working hybrid solar cell by preparing a cross cut with focused ion beam polishing. With C-SFM, the functional layers could be identified and the charge transport properties of the novel active layer composite material could be studied. rnrnIn C-SFM, soft surfaces can be permanently damaged by (i) tip induced forces, (ii) high elec-tric fields and (iii) high current densities close to the SFM-tip. Thus, an alternative operation based on torsion mode topography imaging in combination with current mapping was intro-duced. In torsion mode, the SFM-tip vibrates laterally and in close proximity to the sample surface. Thus, an electrical contact between tip and sample can be established. In a series of reference experiments on standard surfaces, the working mechanism of scanning conductive torsion mode microscopy (SCTMM) was investigated. Moreover, I studied samples covered with free standing semiconducting polymer nano-pillars that were developed in the group of Dr. P. Theato (University Mainz). The application of SCTMM allowed non-destructive imag-ing of the flexible surface at high resolution while measuring the conductance on individual pillarsrnrnIn order to study light induced electrical effects on the level of single nanostructures, a new SFM setup was built. It is equipped with a laser sample illumination and placed in inert at-mosphere. With this photoelectric SFM, I investigated the light induced response in function-alized nanorods that were developed in the group of Prof. R. Zentel (University Mainz). A block-copolymer containing an anchor block and dye moiety and a semiconducting conju-gated polymer moiety was synthesized and covalently bound to ZnO nanorods. This system forms an electron donor/acceptor interface and can thus be seen as a model system of a solar cell on the nanoscale. With a KPFM study on the illuminated samples, the light induced charge separation between the nanorod and the polymeric corona could not only be visualized, but also quantified.rnrnThe results demonstrate that electrical scanning force microscopy can study fundamental processes in nanostructures and give invaluable feedback to the synthetic chemists for the optimization of functional nanomaterials.rn

Atomic force microscopy assisted with electron and ion beam microscopy for the direct measurement of biostructures and DNA samples

Dissertation to obtain a Master degree in Biotechnology

Atomic force microscopy of nucleoprotein complexes.

Recent data on the AFM studies of nucleoprotein complexes of different types are reviewed in this paper. The first section describes the progress in the sample preparation methods for AFM studies of nucleic acids and nucleoprotein complexes. The second part of this paper reviews AFM data on studies of complexes of DNA with regulatory proteins. These studies include two different types of DNA distortion induced by proteins binding: local bending of DNA at sites of protein binding and formation of large loops due to protein-protein interactions between molecules bound to distant sites along the DNA molecules (DNA looping). The prospects for use of AFM for physical mapping of genomes are discussed in this section as well. The third part of the paper reviews data on studies of complexes of DNA with non-sequence specific binding proteins. Special emphasis is given to studies of chromatin which have resulted in progress in the understanding of structure of native chromatin fiber. In this section, novel data on AFM studies of RecA-DNA filaments and complexes of dsRNA with the dsRNA-specific protein p25 are also presented. Discussion of the substrate preparation procedures in relation to the AFM studies of nucleoprotein complexes is given in the final section.

Kelvin Probe Force Microscopy (KPFM) characterization of lanthanum lutetium oxide high-k dielectric thin films

Lanthanum lutetium oxide (LaLuO3) thin films were investigated considering their perspective application for industrial microelectronics. Scanning probe microscopy (SPM) techniques permitted to visualize the surface topography and study the electric properties. This work compared both the material properties (charge behavior for samples of 6 nm and 25 nm width) and the applied SPM modes. Particularly, Kelvin probe force microscopy (KPFM) was applied to characterize local potential difference with high lateral resolution. Measurements showed the difference in morphology, chargeability and charge dissipation time for both samples. The polarity effect was detected for this material for the first time. Lateral spreading of the charged spots indicate the diffusive mechanism to be predominant in charge dissipation. This allowed to estimate the diffusion coefficient and mobility. Using simple electrostatic model it was found that charge is partly leaking into the interface oxide layer.

Peak Force Kelvin Probe Force Microscopy Investigation of ZrO2 Nanocomposites for Hygroelectricity Power Element

ZrO2 nanocomposites were investigated considering their perspective application in hygroelectric power elements. Scanning probe microscopy (SPM) techniques allowed to visualize the surface topography and electrical properties. In this work was compared spacial charge behaviour of sample in humid and dry air conditions. Also different SPM modes were compared. Kelvin probe force microscopy (KPFM) was applied to characterize the spacial charge distribution on surface of the sample. Measurements showed, that trapped charge is not dissipated and can be manipulated with low voltages. Humidity influence on the electric potential of the sample was shown.

Low voltage and variable-pressure scanning electron microscopy of fractured composites

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Label-free DNA detection of hepatitis C virus based on modified conducting polypyrrole films at microelectrodes and atomic force microscopy tip-integrated electrodes

We present a new strategy for the label-free electrochemical detection of DNA hybridization for detecting hepatitis C virus based on electrostatic modulation of the ion-exchange kinetics of a polypyrrole film deposited at microelectrodes. Synthetic single-stranded 18-mer HCV genotype-1-specific probe DNA has been immobilized at a 2,5-bis(2-thienyl)-N-(3-phosphoryl-n-alkyl)pyrrole film established by electropolymerization at the previously formed polypyrrole layer. HCV DNA sequences (244-mer) resulting from the reverse transcriptase-linked polymerase chain reaction amplification of the original viral RNA were monitored by affecting the ion-exchange properties of the polypyrrole film. The performance of this miniaturized DNA sensor system was studied in respect to selectivity, sensitivity, and reproducibility. The limit of detection was determined at 1.82 x 10(-21) mol L-1. Control experiments were performed with cDNA from HCV genotypes 2a/c, 2b, and 3 and did not show any unspecific binding. Additionally, the influence of the spacer length of 2,5-bis(2-thienyl)-N-(3-phosphoryl-n-alkyl)pyrrole on the behavior of the DNA sensor was investigated. This biosensing scheme was finally extended to the electrochemical detection of DNA at submicrometer-sized DNA biosensors integrated into bifunctional atomic force scanning electrochemical microscopy probes. The 18-mer DNA target was again monitored by following the ion-exchange properties of the polypyrrole film. Control experiments were performed with 12-base pair mismatched sequences.

Piezoresponse force microscopy behaviour of Bi4Ti3O12 ceramics with various excess bismuth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Nanoscopic studies of conjugated polymer blends by (electric) scanning probe microscopy

Conjugated polymers and conjugated polymer blends have attracted great interest due to their potential applications in biosensors and organic electronics. The sub-100 nm morphology of these materials is known to heavily influence their electromechanical properties and the performance of devices they are part of. Electromechanical properties include charge injection, transport, recombination, and trapping, the phase behavior and the mechanical robustness of polymers and blends. Electrical scanning probe microscopy techniques are ideal tools to measure simultaneously electric (conductivity and surface potential) and dielectric (dielectric constant) properties, surface morphology, and mechanical properties of thin films of conjugated polymers and their blends.rnIn this thesis, I first present a combined topography, Kelvin probe force microscopy (KPFM), and scanning conductive torsion mode microscopy (SCTMM) study on a gold/polystyrene model system. This system is a mimic for conjugated polymer blends where conductive domains (gold nanoparticles) are embedded in a non-conductive matrix (polystyrene film), like for polypyrrole:polystyrene sulfonate (PPy:PSS), and poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). I controlled the nanoscale morphology of the model by varying the distribution of gold nanoparticles in the polystyrene films. I studied the influence of different morphologies on the surface potential measured by KPFM and on the conductivity measured by SCTMM. By the knowledge I gained from analyzing the data of the model system I was able to predict the nanostructure of a homemade PPy:PSS blend.rnThe morphologic, electric, and dielectric properties of water based conjugated polymer blends, e.g. PPy:PSS or PEDOT:PSS, are known to be influenced by their water content. These properties also influence the macroscopic performance when the polymer blends are employed in a device. In the second part I therefore present an in situ humidity-dependence study on PPy:PSS films spin-coated and drop-coated on hydrophobic highly ordered pyrolytic graphite substrates by KPFM. I additionally used a particular KPFM mode that detects the second harmonic electrostatic force. With this, I obtained images of dielectric constants of samples. Upon increasing relative humidity, the surface morphology and composition of the films changed. I also observed that relative humidity affected thermally unannealed and annealed PPy:PSS films differently. rnThe conductivity of a conjugated polymer may change once it is embedded in a non-conductive matrix, like for PPy embedded in PSS. To measure the conductivity of single conjugated polymer particles, in the third part, I present a direct method based on microscopic four-point probes. I started with metal core-shell and metal bulk particles as models, and measured their conductivities. The study could be extended to measure conductivity of single PPy particles (core-shell and bulk) with a diameter of a few micrometers.