Biomedical subjects

Luca Bertini

Publications and source records attributed to Luca Bertini.

3 recordsLinked to original sources

PubMed2026

Unraveling G-Quadruplex and i-Motif Coexistence Within a Double-Stranded DNA.

DNA can transiently fold into variable arrangements, which are expected to exploit regulatory functions. Guanine-rich sequences can fold into G-quadruplexes (G4s), while the complementary strand adopts potentially i-Motif (iM) arrangements. Their concomitant formation at the same genomic site is still under debate. However, recently, single-molecule analyses have shown the simultaneous G4 and iM presence within a double-stranded (ds) DNA context, addressing them as synergic blockers of replication fork progression. While these findings point to a functional interplay between G4 and iM, a deeper understanding of the factors enabling their coexistence remains unclear. In this work, we unravel the equilibria governing G4- and iM-folding within dsDNA, adopting an extensive biophysical approach allowing analysis of an optimized modular system, scalable across constructs of increasing molecular complexity. Our findings corroborate the simultaneous formation model and further clarify the thermodynamic determinants driving duplex denaturation and the favorable folding of stable G4 and iM structures.

G-Quadruplexes↗

PubMed2003

Guest-framework interaction in type I inorganic clathrates with promising thermoelectric properties: on the ionic versus neutral nature of the alkaline-earth metal guest A in A8Ga16Ge30 (A=Sr, Ba).

Periodic density functional calculations using pseudopotentials and a local basis set were performed on the type I clathrates A(8)Ga(16)Ge(30) (A=Sr, Ba). Both are known to show promising thermoelectric properties. Ab initio wave functions were analyzed within the framework of the quantum theory of atoms in molecules. This enabled us to analyze both the charge transfer and bonding properties of the clathrate from a rigorous quantum mechanical viewpoint. The Ba and Sr centers were found to be largely ionic (charge: ca. +1.7 e) both in the smaller 20-atom and in the larger 24-atom cages, consistent with a Zintl-phase view of these type I clathrates. The assertion that the Sr atoms in the different cages have similar oxidation states is shown to be consistent with multiwavelength diffraction experiments on Sr(8)Ga(16)Ge(30); while the assertion of ionicity of the Sr center is supported by the observation that the adsorption edge lies close to that previously found in the Sr K-edge XANES spectra of Sr(OH)(2).8 H(2)O. As such, this work contradicts previous experimental and theoretical studies that claim that the guest atoms are neutral. We show that the discrepancy is related to the definitions used for electron transfer. Definitions based on electron displacement (rearrangement) in space, as in previous works, do not account for the variation in shape and volume of the atomic catchment regions upon change in the number and average locations of the particles in the system. Eventually, such definitions lead to underestimation of charge transfer. The large binding energy found in earlier work for Ba and Sr in these materials is found to be consistent with a simple picture of charge transfer from the guest to the frame. Preliminary investigations on a clathrate of perfect stoichiometry appear to rule out any important relationship between the observed increase in the thermoelectric figure of merit with increasing external pressure and host-guest charge transfer.

Barium↗

PubMed2003

Chemical information from the source function.

The source function, which enables one to equate the value of the electron density at any point within a molecule to a sum of atomic contributions, has been applied to a number of cases. The source function is a model-independent, quantitative measure of the relative importance of an atom's or group's contribution to the density at any point in a system, and it represents a potentially interesting tool to provide chemical information. It is shown that the source contribution from H to the electron density rho(b) at the bond critical point in HX diatomics decreases with increasing X's electronegativity, and that this decrease is a result of significant changes in the Laplacian distribution within the H-basin. It is also demonstrated that the source function from Li to rho(b) in LiX diatomics is a more sensitive index of atomic transferability than it is the lithium atomic energy or population. The observed changes are such as to ensure a constant percentage source contribution from Li to rho(b) throughout the LiX series, rather than a constant source as one would expect in the limit of perfect atomic transferability. Application of the source function to planar lithium clusters has revealed that the source function clearly discriminates between a nonnuclear electron density maximum and a maximum associated to a nucleus, on the basis of the relative weight of the source contributions from the basin associated to the maximum and from the remaining basins in the cluster. The source function has also allowed for a classification of hydrogen bonds in terms of characteristic source contributions to the density at the H-bond critical point from the H involved in the H-bond, the H-donor D, and the H-acceptor A. The source contribution from the H appears as the most distinctive marker of the H-bond strength, being highly negative for isolated H-bonds, slightly negative for polarized assisted H-bonds, close to zero for resonance-assisted H-bonds, and largely positive for charge-assisted H-bonds. The contributions from atoms other than H, D, and A strongly increase with decreasing H-bond strength, consistently with the parallel increased electrostatic character of the interaction. The correspondence between the classification provided by the Electron Localization Function topologic approach and by the source function has been highlighted. It is concluded that the source function represents a practical tool to disclose the local and nonlocal character of the electron density distributions and to quantify such a locality and nonlocality in terms of a physically sound and appealing chemical partitioning.

Journal Article↗