Rosa Di Felice

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides the framework for the integration of DNA sequence and shape analyses in genome-wide studies. The HT methodology uses a sliding-window approach to mine DNA structural information obtained from Monte Carlo simulations. It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist). The results of rigorous validations of the HT predictions based on DNA structures solved by X-ray crystallography and NMR spectroscopy, hydroxyl radical cleavage data, statistical analysis and cross-validation, and molecular dynamics simulations provide strong confidence in this approach. The DNAshape web server is freely available at http://rohslab.cmb.usc.edu/DNAshape/.

Adsorption modes of cysteine on Au(111): thiolate, amino-thiolate, disulfide.

The adsorption of cysteine on the (111) surface of gold has been studied by means of periodic supercell density-functional theory calculations. A number of different adsorption modes are examined, including adsorption through the thiol group in either thiolate or disulfide form, and adsorption through both the thiol and amino functional groups. We find that at intermediate coverage densities the latter mode of adsorption is favored, followed by thiolate adsorption at the bridge (slightly displace toward fcc) site. The N-Au and S-Au bond strengths in the amino-thiolate adsorption are estimated to be of the order of 6 and 47 kcal/mol, respectively. The electronic structure of the different systems is analyzed, with focus on the total and projected density of states, as well as on the detailed character of the electronic states at the interface. States near the Fermi energy are found to have a metal-molecule antibonding character, whereas metal-molecule bonding states mostly occur near the lower edge of the Au-d band.

Long-range charge transport in single G-quadruplex DNA molecules

DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to differences in the measured molecules and experimental set-ups, and transporting significant current through individual DNA-based molecules remains a considerable challenge. Here, we report reproducible charge transport in guanine-quadruplex (G4) DNA molecules adsorbed on a mica substrate. Currents ranging from tens of picoamperes to more than 100 pA were measured in the G4-DNA over distances ranging from tens of nanometres to more than 100 nm. Our experimental results, combined with theoretical modelling, suggest that transport occurs via a thermally activated long-range hopping between multi-tetrad segments of DNA. These results could re-ignite interest in DNA-based wires and devices, and in the use of such systems in the development of programmable circuits.

Highly conductive self-assembled nanoribbons of coordination polymers.

Organic molecules can self-assemble into well-ordered structures, but the conductance of these structures is limited, which is a disadvantage for applications in molecular electronics. Conductivity can be improved by using coordination polymers-in which metal centres are incorporated into a molecular backbone-and such structures have been used as molecular wires by self-assembling them into ordered films on metal surfaces. Here, we report electrically conductive nanoribbons of the coordination polymer [Pt(2)I(S(2)CCH(3))(4)](n) self-assembled on an insulating substrate by direct sublimation of polymer crystals. Conductance atomic force microscopy is used to probe the electrical characteristics of a few polymer chains ( approximately 10) within the nanoribbons. The observed currents exceed those previously sustained in organic and metal-organic molecules assembled on surfaces by several orders of magnitude and over much longer distances. These results, and the results of theoretical calculations based on density functional theory, confirm coordination polymers as candidate materials for applications in molecular electronics.

Protein–surface interactions: challenging experiments and computations

Protein–surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnology to medicine. A recent workshop highlighted the current achievements and the main challenges in the field. Copyright

Ab initio study of model guanine assemblies: The role of π-π coupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principles calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the

Hydroxyl-Rich β-Sheet Adhesion to the Gold Surface in Water by First-Principle Simulations

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Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

orbitals in adjacent guanine molecules.

First Principles Effective Electronic Couplings for Hole Transfer in Natural and Size-Expanded DNA

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Electrical conductivity in platinum-dimer columns.

coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The band structure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.