Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization.
ECD
excitonic model
fragment diabatization
guanine quadruplexes
Journal
Chirality
ISSN: 1520-636X
Titre abrégé: Chirality
Pays: United States
ID NLM: 8914261
Informations de publication
Date de publication:
05 2023
05 2023
Historique:
revised:
24
01
2023
received:
09
12
2022
accepted:
24
01
2023
medline:
14
4
2023
pubmed:
13
2
2023
entrez:
12
2
2023
Statut:
ppublish
Résumé
In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K
Substances chimiques
DNA
9007-49-2
Guanine
5Z93L87A1R
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
298-310Subventions
Organisme : Consiglio Nazionale delle Ricerche
Organisme : ICSC - Centro Nazionale di Ricerca in High Performance Computing, Big Data and Quantum Computing
Organisme : CN3 - National Center for Gene Therapy and Drugs based on RNA technology
Organisme : NextGenerationEU
Informations de copyright
© 2023 The Authors. Chirality published by Wiley Periodicals LLC.
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