Deposition of Supercoiled DNA on Mica for Scanning Force Microscopy Imaging

The deposition of DNA molecules on mica is driven and controlled by the ionic densities around DNA and close to the surface of the substrate. Dramatic improvements in the efficiency and reproducibility of DNA depositions were due to the introduction of divalent cations in the deposition solutions. The ionic distributions on DNA and on mica determine the mobility of adsorbed DNA molecules, thus letting them assume thermodynamically equilibrated conformations, or alternatively trapping them in non-equilibrated conformations upon adsorption. With these prerequisites, mica does not seem like an inert substrate for DNA deposition for microscopy, and its properties greatly affect the efficiency of DNA deposition and the appearance of the molecules on the substrate. In our laboratory, we have some preliminary evidence that mica could also participate in DNA damage, most likely through its heavy metal impurities

Automated DNA Fragments Recognition and Sizing through AFM Image Processing

This paper presents an automated algorithm to determine DNA fragment size from atomic force microscope images and to extract the molecular profiles. The sizing of DNA fragments is a widely used procedure for investigating the physical properties of individual or protein-bound DNA molecules. Several atomic force microscope (AFM) real and computer-generated images were tested for different pixel and fragment sizes and for different background noises. The automated approach minimizes processing time with respect to manual and semi-automated DNA sizing. Moreover, the DNA molecule profile recognition can be used to perform further structural analysis. For computer-generated images, the root mean square error incurred by the automated algorithm in the length estimation is 0.6% for a 7.8 nm image pixel size and 0.34% for a 3.9 nm image pixel size. For AFM real images we obtain a distribution of lengths with a standard deviation of 2.3% of mean and a measured average length very close to the real one, with an error around 0.33%

Evidence of Orientation-Dependent Early States of Prion Protein Misfolded Structures from Single Molecule Force Spectroscopy

Prion diseases are neurodegenerative disorders characterized by the presence of oligomers and amyloid fibrils. These are the result of protein aggregation processes of the cellular prion protein (PrPC) into amyloidal forms denoted as prions or PrPSc. We employed atomic force microscopy (AFM) for single molecule pulling (single molecule force spectroscopy, SMFS) experiments on the recombinant truncated murine prion protein (PrP) domain to characterize its conformations and potential initial oligomerization processes. Our AFM-SMFS results point to a complex scenario of structural heterogeneity of PrP at the monomeric and dimer level, like other amyloid proteins involved in similar pathologies. By applying this technique, we revealed that the PrP C-terminal domain unfolds in a two-state process. We used two dimeric constructs with different PrP reciprocal orientations: one construct with two sequential PrP in the N- to C-terminal orientation (N-C dimer) and a second one in the C- to C-terminal orientation (C-C dimer). The analysis revealed that the different behavior in terms of unfolding force, whereby the dimer placed C-C dimer unfolds at a higher force compared to the N-C orientation. We propose that the C-C dimer orientation may represent a building block of amyloid fibril formation

Preparation and Properties of PTFE-PMMA Core-Shell Nanoparticles and Nanocomposites

he preparation of polytetrafluoroethylene-poly(methyl methacrylate) (PTFE-PMMA) core-shell particles was described, featuring controlled size and narrow size distribution over a wide compositional range, through a seeded emulsion polymerization starting from a PTFE seed of 26 nanometers. Over the entire MMA/PTFE range, the particle size increases as the MMA/PTFE ratio increases. A very precise control over the particle size can be exerted by properly adjusting the ratio between the monomer and the PTFE seed. Particles in the 80240 nm range can be prepared with uniformity indexes suited to build 2D and 3D colloidal crystals. These core-shell particles were employed to prepare nanocomposites with different compositions, through an annealing procedure at a temperature higher than the glass transition temperature of the shell forming polymer. A perfect dispersion of the PTFE particles within the PMMA matrix was obtained and optically transparent nanocomposites were prepared containing a very high PTFE amount

Microstructured soft devices for the growth and analysis of populations of homogenous multicellular tumor spheroids

: Multicellular tumor spheroids are rapidly emerging as an improved in vitro model with respect to more traditional 2D culturing. Microwell culturing is a simple and accessible method for generating a large number of uniformly sized spheroids, but commercially available systems often do not enable researchers to perform complete culturing and analysis pipelines and the mechanical properties of their culture environment are not commonly matching those of the target tissue. We herein report a simple method to obtain custom-designed self-built microwell arrays made of polydimethylsiloxane or agarose for uniform 3D cell structure generation. Such materials can provide an environment of tunable mechanical flexibility. We developed protocols to culture a variety of cancer and non-cancer cell lines in such devices and to perform molecular and imaging characterizations of the spheroid growth, viability, and response to pharmacological treatments. Hundreds of tumor spheroids grow (in scaffolded or scaffold-free conditions) at homogeneous rates and can be harvested at will. Microscopy imaging can be performed in situ during or at the end of the culture. Fluorescence (confocal) microscopy can be performed after in situ staining while retaining the geographic arrangement of spheroids in the plate wells. This platform can enable statistically robust investigations on cancer biology and screening of drug treatments

Statistical Mechanics of Elastica on Plane as a Model of Supercoiled DNA-Origin of the MKdV hierarchy-

In this article, I have investigated statistical mechanics of a non-stretched elastica in two dimensional space using path integral method. In the calculation, the MKdV hierarchy naturally appeared as the equations including the temperature fluctuation.I have classified the moduli of the closed elastica in heat bath and summed the Boltzmann weight with the thermalfluctuation over the moduli. Due to the bilinearity of the energy functional,I have obtained its exact partition function.By investigation of the system,I conjectured that an expectation value at a critical point of this system obeys the Painlev\'e equation of the first kind and its related equations extended by the KdV hierarchy.Furthermore I also commented onthe relation between the MKdV hierarchy and BRS transformationin this system.Comment: AMS-Tex Us

Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static

Preface

Both in research labs and in the world outside them, we are currently experiencing the mainstreaming of nanotechnology. After a few decades of discoveries and technological development of the new world at the bottom, now nanotechnology is at work in the industry as well as in many types of labs. Through mating with other sciences and technologies, it is helping to solve societal problems and to enable discoveries, often staying hidden under the hood of products and services. The mainstreaming is evident at all levels, including the goals of governments and funding bodies. Nowadays funds are granted primarily for innovation in the industry and for the solution of grand societal challenges. Nanotech can contribute to both, but it must synergize and sometimes compete with other technologies in order to do so. Nanotechnology cannot work alone; rather it complements and enhances all other tools of science and technology. The growth of nanotechnology is continuing and it does so with the awareness that to spread and have an impact it must be shared. Methods developed in focused labs must be shared with others and with those that will put them to work in the field and make them part of complex procedures and collaborative efforts organized around the current and future needs of our society. A book of methods is one of the enabling tools of this process as it is an often-missing link between the technology developers and the users. A few years have passed since the first edition of this book of methods on DNA nanotechnology. We have witnessed the further development of DNA nanotechnology to make ever more brilliantly conceived and realized nanostructures and to make them useful. More applications have come in the biosensing field. New uses and applications have arisen for DNA origami and many more researchers use them nowadays. This new edition contains new methods that enrich the library of the first edition to make a richer arsenal of methods for researchers and technologists expanding to DNA nanotechnology. Several chapters of this new edition focus on these applicative uses of nanostructures, especially toward biosensing. A number of chapters focus on the use of DNA origami for arranging matter in the nanoscale or on their manipulation with the aid of other technologies, such as nanolithography. There are also chapters detailing the procedures for making nucleic acids nanostructures of different kinds, as these can implement the available set of building blocks for nanotechnology. A few chapters focus on methods to simulate complex nanostructures or on gathering insightful thermodynamic information from probing nanostructures. This book has also been gifted with an introductory chapter written by Ned Seeman. The recognized father of the field of structural DNA nanotechnology traces some of its historical origins and charms us with a reminder that science and technology are still made by humans. I trust this book will be able to give its little contribution to the uptake of DNA nanotechnology