0000000000392649
AUTHOR
Hugo Gattuso
Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures
We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…
Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin
In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extra…
Targeting G-quadruplexes with Organic Dyes: Chelerythrine–DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy
The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences&mdash
Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization
International audience; We report a computational investigation of the hydrogen abstraction (H-abstraction) induced by triplet benzophenone (3BP) on thymine nucleobase and backbone sugar. The chemical process is studied using both high level multiconfigurational perturbation and density functional theory. Both methods show good agreement in predicting small kinetic barriers. Furthermore the behavior of benzophenone in DNA is simulated using molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. The accessibility of benzophenone to the labile hydrogens within B-DNA is demonstrated, as well as the driving force for this reaction. We evidence a strong dependence of the H-…
Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA
Multiscale molecular dynamics simulations reveal out-of-plane distortions that favour DNA photostability. A novel photostability mechanism involving four proton transfers and triggered by a nearby Na+ ion is also unveiled.