Luca Bertini | Search PubMed

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

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↗