Manola Moretti

The structure of DNA by direct imaging.

The DNA helix and its internal structures were directly imaged; characteristic lengths and inner components were measured and reported. The structure of DNA was determined in 1953 by x-ray fiber diffraction. Several attempts have been made to obtain a direct image of DNA with alternative techniques. The direct image is intended to allow a quantitative evaluation of all relevant characteristic lengths present in a molecule. A direct image of DNA, which is different from diffraction in the reciprocal space, is difficult to obtain for two main reasons: the intrinsic very low contrast of the elements that form the molecule and the difficulty of preparing the sample while preserving its pristine shape and size. We show that through a preparation procedure compatible with the DNA physiological conditions, a direct image of a single suspended DNA molecule can be obtained. In the image, all relevant lengths of A-form DNA are measurable. A high-resolution transmission electron microscope that operates at 80 keV with an ultimate resolution of 1.5 Å was used for this experiment. Direct imaging of a single molecule can be used as a method to address biological problems that require knowledge at the single-molecule level, given that the average information obtained by x-ray diffraction of crystals or fibers is not sufficient for detailed structure determination, or when crystals cannot be obtained from biological molecules or are not sufficient in understanding multiple protein configurations.

Adiabatic nanofocusing: spectroscopy, transport and imaging investigation of the nano world

Adiabatic compression plays a fundamental role in the realization of localized enhanced electromagnetic field hot spots, it provides the possibility to focus at nanoscale optical excitation. It differs from the well-known lightning rod effect since it is based on the lossless propagation of surface plasmon polaritons (SPPs) up to a nano-sized metal tip where the energy density is largely enhanced. Here we discuss two important applications of adiabatic compression: Raman and hot electron spectroscopy at nanometric resolution. The underlying phenomena are the conversion of SPPs into photons or hot electrons. New scanning probe spectroscopy techniques along with experimental results are discussed. We foresee that these techniques will play a key role in relating the functional and structural properties of matter at the nanoscale.

Visualization of single proteins from stripped native cell membranes: A protocol for high-resolution atomic force microscopy

Atomic force microscopy (AFM) proved to be able to obtain high‐resolution three‐dimensional images of single‐membrane proteins, isolated, crystallized, or included in reconstructed model membranes. The extension of this technique to native systems, such as the protein immersed in a cell membrane, needs a careful manipulation of the biological sample to meet the experimental constraints for high‐resolution AFM imaging. In this article, a general protocol for sample preparation is presented, based on the mechanical stretch of the cell membrane. The effectiveness for AFM imaging has been tested on the basis of an integrated optical and AFM approach and the proposed method has been applied to cells expressing cystic fibrosis transmembrane conductance regulator, a channel involved in cystic fibrosis, showing the possibility to identify and analyze single proteins in the plasma membrane. Microsc. Res. Tech. 76:723–732, 2013.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Superhydrophobic Devices Molecular Detection

Recent advances in the single-molecule detection and manipulation provided unexpected solutions for the understanding of the physio-pathological behavior of individual biological macromolecules. Modern techniques of patterning at the micro- and nanometer scale combined with chemical treatments are being used to create surfaces that stretch the hydrophobic behavior to the limit. The ability to create surfaces with high static water contact angles (usually greater than 150°) is essential for a variety of applications, ranging from the development of biosensors to the implementation of sensitive and reliable single-molecule collection and sample preparation methods. Thus, superhydrophobic devices could be considered as nano-biotechnological single-molecule detection tools that can be applied to a wide range of high-resolution studies. To outline the paper, single-molecule detection topics and theoretical principles of superhydrophobicity are first introduced. A comprehensive overview is then given, describing how different types of devices with superhydrophobic surfaces are realized. Finally, the usefulness of the presented devices for a wide range of applications and the concluding comments are proposed.