Rosa Di Felice

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The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not(More)
Attempts to resolve the energy-level structure of single DNA molecules by scanning tunnelling spectroscopy span over the past two decades, owing to the unique ability of this technique to probe the local density of states of objects deposited on a surface. Nevertheless, success was hindered by extreme technical difficulties in stable deposition and(More)
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our(More)
EF-hand calcium sensors respond structurally to changes in intracellular Ca(2+) concentration, triggering diverse cellular responses and resulting in broad interactomes. Despite impressive advances in decoding their structure-function relationships, the folding mechanism of neuronal calcium sensors is still elusive. We used single-molecule optical tweezers(More)
We use a stepwise pulling protocol in molecular dynamics simulations to identify how a G-quadruplex selects and conducts Na(+), K(+), and NH4(+) ions. By estimating the minimum free-energy changes of the ions along the central channel via Jarzynski's equality, we find that the G-quadruplex selectively binds the ionic species in the following order: K(+) >(More)
Neuronal calcium sensor-1 (NCS-1) is a protein able to trigger signal transduction processes by binding a large number of substrates and re-shaping its structure depending on the environmental conditions. The X-ray crystal structure of the unmyristoilated NCS-1 shows a large solvent-exposed hydrophobic crevice (HC); this HC is partially occupied by the(More)
We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic structure calculations to formulate a coarse-grained charge(More)
We briefly present the results of recent experiments of transverse scanning tunneling spectroscopy of homogeneous poly(dG)-poly(dC) DNA molecules and discuss them in the light of theoretical investigation. A semiempirical theoretical model is adopted to describe the transverse tunneling current across a DNA molecule placed between a metallic gold substrate(More)
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