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

Author:

Asha Haritha1,Green James A.2ORCID,Esposito Luciana1,Santoro Fabrizio3ORCID,Improta Roberto1

Affiliation:

1. Istituto di Biostrutture e Bioimmagini CNR Napoli Italy

2. Institut für Physikalische Theoretische Chemie Goethe‐Universität Frankfurt am Main Frankfurt am Main Germany

3. Istituto di Chimica dei Composti Organometallici (ICCOM‐CNR), Area della Ricerca del CNR Pisa Italy

Abstract

AbstractIn 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 cation in the calculation.

Funder

Consiglio Nazionale delle Ricerche

Publisher

Wiley

Subject

Organic Chemistry,Spectroscopy,Drug Discovery,Pharmacology,Catalysis,Analytical Chemistry

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