Studying the excited electronic states of guanine rich DNA quadruples by quantum mechanical methods: main achievements and perspectives

Abstract

Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

“…Solvent effects of waTer have been included by the Polarizable Continuum Model (PCM) [ 44 ]. This approach has been already profitably used to the study the photoactivated behavior of oligonucleotides [ 43 ], including GQ [ 13 , 45 , 46 , 47 , 48 ]. The electronic couplings for the FHC approach were calculated using the ‘EET’ option within Gaussian, which utilises a transition density based approach to calculate the Coulombic couplings between LEs [ 22 ].…”

“…In fact, crystallographic methods, besides selecting the conformation prone to crystallization, are not the best option to study flexible structures in solution. Optical spectroscopies, especially electronic circular dichroism (ECD) [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ], have been shown to be particularly useful for the structural characterization of GQs, but they have a more limited atomic resolution. Integration with suitable computational methods in order to provide a greater atomic resolution is therefore very fruitful [ 13 , 16 , 17 , 18 , 19 ].…”

“…Optical spectroscopies, especially electronic circular dichroism (ECD) [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ], have been shown to be particularly useful for the structural characterization of GQs, but they have a more limited atomic resolution. Integration with suitable computational methods in order to provide a greater atomic resolution is therefore very fruitful [ 13 , 16 , 17 , 18 , 19 ]. However, considering that a GQ contains, at least, a dozen closely stacked nucleobases, without considering the loops, a brute-force approach, exploiting full quantum mechanical (QM) calculations, is extremely computationally demanding.…”

Facile room-temperature self-assembly of extended cation-free guanine-quartet network on Mo-doped Au(111) surface

“…Self-assembly of organic molecules with sufficient stability is highly desirable to develop intriguingly organized materials or molecular architectures for diverse applications from nanoelectronic circuits to drug design. [1][2][3][4] The emergence of various RNA/DNA quadruplex structures is a vital discovery in biomolecular science because of their antiproliferative behavior and the gene-regulating features of non-canonical RNA/DNA secondary structures. [5][6][7] Among various RNA/DNA quadruplexes, guanine is the only purine generated in human cells to date, 8,9 where stabilizing the G-quadruplex has become a practical rationale for therapeutic approaches to treat cancer with crucial selectivity that is required for clinical development.…”

Enhanced Rigidity Changes Ultraviolet Absorption: Effect of a Merocyanine Binder on G-Quadruplex Photophysics

“… 16 , 20 Most theoretical studies on the absorption of G4 have focused on unprobed G4s so far. 21 − 24 There exist calculations of UV/vis spectra of telomeric G4 structures, 23 , 24 but the spectroscopic properties of G4–probe complexes are only used as a G4 diagnostic tool to assess whether the probe binds. 25 Molecular dynamics studies have been carried out with G4 binders 26 − 28 with the aim to monitor the spatiotemporal status of G4s by means of fluorescent probes and shed light into the biological role of these DNA structures.…”