NanoInnovationLAB Highlights

We demonstrate that, contrary to current understanding, the density of probe molecules is not responsible for the lack of hybridization in high density single-stranded DNA (ss-DNA) self-assembled monolayers (SAMs). To this end, we use nanografting to fabricate well packed ss-DNA nanopatches within a “carpet matrix” SAM of inert thiols on gold surfaces. The DNA surface density is varied by changing the “writing” parameters, for example, tip speed, and number of scan lines. Since ss-DNA is 50 times more flexible than ds-DNA, hybridization leads to a transition to a “standing up” phase. Therefore, accurate height and compressibility measurements of the nanopatches before and after hybridization allow reliable, sensitive, and label-free detection of hybridization. Side-by-side comparison of self-assembled and nanografted DNA-monolayers shows that the latter, while denser than the former, display higher hybridization efficiencies.

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Quantitative study of the effect of coverage on the hybridization efficiency of surface-bound DNA nanostructures, Mirmontaz E., Castronovo, M., Grunwald, C., Bano, F., Scaini, D., Ensafi, A.A., Scoles, G., Casalis, L., Nanoletters 8, 4134 (2008)

The immobilization of bio-molecules (e.g. DNA, proteins, enzymes) on surfaces with controlled orientations is important in the development of most powerful and sensitive sensors. To this end, we make the use of an emerging Atomic force microscopy (AFM) based nanofabrication tool known as nanografting, that allows for the fabrication of ordered and packed patches of biomolecular monolayer of variable density on ultra-flat gold surfaces. These surface-bound nanostructures appear to be a good candidate for advancing our understanding of protein-protein and protein-nucleic acids interactions. The effect of the reaction (for instance the reaction of DNA with a complementary strand) will persuade changes in the length of the DNA molecules involved that can be accurately measured by AFM height and/or friction measurements.

In particular the lab has developed the expertise in AFM-based protein immobilization at the nanoscale through bioaffinity immobilization (e.g. NTA - His-tag system), Dna Directed Immobilization, covalent immobilization of protein. The nanofabricated intarfaces are then exploited for the investigation of  biochemical activity of proteins, to evidence bio-recognition phenomena in a broad dynamical range, and the study of protein protein and protein ligand interaction expecially in the field of neurodegenerative diseases

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Toward multiprotein nanoarrays using nanografting and DNA directed immobilization of proteins, Bano, F., Fruk, L., Sanavio, B., Glettenberg, M., Casalis, L., Niemeyer, C.M., Scoles, G. , Nanoletters 9, 2614 (2009)

Oriented Immobilization of Prion Protein Demonstrated via Precise Interfacial Nanostructure Measurements, Barbara Sanavio, Denis Scaini, Christian Grunwald, Giuseppe Legname, Giacinto Scoles, and Loredana Casalis, ACS Nano 4, 6607 (2010)

Self-Assembled Monolayers (SAMs) of thiols on metal surfaces are ubiquitous in the field of nanoscience with potential applications ranging from molecular electronics to biomembranes and nanopatterning. Yet, despite significant efforts, the structure of these systems is still debated.

Contraddictory results are obtained even for the prototypical case of methylthiolate (MT), CH₃S, adsorbed on the Au(111) crystal surface. While theoretical simulations have proposed a bridge onding site for the S atom of MT adsorbed on a flat Au(111) terrace, the most recent experimental investigations by Photoelectron Diffraction (PED) and Normal Incidence X-ray Standing Waves (NIXSW)suggest a preference for the ontop site.

Given the hypothesis of a restructuring of the Au- thiolate interface, we decided to employ Density Functional Theory (DFT)-based molecular dynamics (MD) calculations to determine a realistic structural model, from which to fit our experimental data obtained using PED and Grazing Incidence X-Ray Diffraction (GXRD).

The model we arrive at in this way contains a certain amount of disorder but resolves the theory-experiment discrepancy that has been prominent in the literature and suggests that the well known formation of superlattices may be a result of an ordering among binding sites and vacancies.

In general, our results underscore the importance of disorder at molecule/metal interfaces. At present we are examining the case of chais with 6 and 10 carbon atoms to conferm of contraddict the hypohtesis discussed above.

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Structure of a CH3S monolayer on Au(111) solved by the interplay between molecular dynamics calculations and diffraction measurements, Mazzarello, R., Cossaro, A., Verdini, A., Rousseau, R., Casalis, L., Danisman, M.F., Floreano, L., Scandolo, S., Morgante, A., Scoles, G., Physical Review Letters 98, 016102 (2007)

X-ray diffraction and computation yield the structure of alkanethiols on gold(111), Cossaro, A., Mazzarello, R., Rousseau, R., Casalis, L.,Verdini, A., Kohlmeyer, A., Floreano, L. , Scandolo, S., Morgante, A., Klein, M.L., Scoles, G., Science 321, 943 (2008)

Mechanical stabilization effect of water on a membrane-like system Castronovo, M., Bano, F., Raugei, S., Scaini, D., Dell'Angela, M., Hudej, R., Casalis, L., Scoles, G., JACS 129, 2636 (2007)

We developed a new generation of Carbon Endowed Electrodes (CEEs) for neuronal applications characterized by the presence of carbon in the form of conductive and biocompatible material. Nanoelectrodes that closely mimic the natural tissue microenvironment with its complex chemical and physical cues are essential for improving the quality and reliability of measurements, especially those performed on biological samples, as electroactive cells like neurons and cardiocytes.

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Carbon nanotubes might improve neuronal performance by favouring electrical shortcuts, Cellot, G., Cilia, E., Cipollone, S., Rancic, V., Sucapane, A., Giordani, S. , Gambazzi, L., Markram, H., Grandolfo, M., Scaini, D., Gelain, F., Casalis, L. , Prato, M., Giugliano, M., Ballerini, L., Nature Nanotechnology 4, 126 (2009)

CT-AFM is commonly used for electrical characterization of organic and inorganic surface systems. Understanding electron transfer at the molecular level may lead to the development of molecular assemblies with unique properties and is of great importance for the advancement of both organic, molecular and bio-electronics. In our lab we follow an approach to the study of Metal-Molecule-Metal surface junctions that uses a combination of different AFM-based techniques. We first use Nanografting to build nanopatches of the molecules of interest into a hosting reference self assembled monolayer (SAM) typically made of alkanethiols. After the tip is changed to a conductive one, CT-AFM is used to characterize electrically the whole system recording, at the same time, the system topography. Some of the advantages of this approach are the possibility to build and study a wide range of different monolayers side-by-side on the same sample and the in-situ control of the quality both of the hosting monolayer and that of the grafted patches.  This peculiarity allows us to directly compare the current values of the alkanethiol chains.

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Electron transfer mediating properties of hydrocarbons as a function of chain length: A differential scanning conductive tip atomic force microscopy investigation, Scaini, D., Castronovo, M., Casalis, L., Scoles, G. , ACS Nano 2, 507 (2008)