Electronic transitions and ESIPT kinetics of the thienyl-3-hydroxychromone nucleobase surrogate in DNA duplexes: a DFT/MD-TDDFT study.
Alain SougnabéDaniel LissouckFabien Fontaine-ViveMama NsangouYves MelyAlain BurgerCyril Assongo KenfackPublished in: RSC advances (2020)
The fluorescent nucleobase surrogate M (2-thienyl-3-hydroxychromone fluorophore) when imbedded in DNA opposite an abasic site exhibits a two colour response highly sensitive to environment changes and base composition. Its two colour emission originates from an excited state intramolecular proton transfer (ESIPT), which converts the excited normal N* form into its T* tautomer. To get deeper insight on the spectroscopic properties of M in DNA duplexes, quantum chemical calculations were performed on M stacked with different base pairs in model trimers extracted from MD simulations. The photophysics of M in duplexes appeared to be governed by stacking interactions as well as charge and hole transfer. Indeed, stacking of M in DNA screens M from H-bonding with water molecules, which favours ESIPT and thus, the emission of the T* form. With A and T flanking bases, the electronic densities in the frontier MOs were localized on M, in line with its effective absorption and emission. In addition, reduction of the free rotation between the thienyl and chromone groups together with the shielding of the dye from water molecules largely explain its enhanced quantum yield in comparison to the free M in solution. By contrast, the localisation of the electron density on the flanking G residues in the ground state and the energetically favorable hole transfer from M to G in the excited state explains the reduced quantum yield of M sandwiched between CG pairs. Finally, the much higher brightness of M as compared to 2-aminopurine when flanked by A and T residues could be related to the much stronger oscillator strength of its S 0 → S 1 transition and the ineffective charge transfer from M to A or T residues.
Keyphrases
- molecular dynamics
- fluorescent probe
- circulating tumor
- cell free
- living cells
- density functional theory
- single molecule
- energy transfer
- monte carlo
- electron transfer
- solar cells
- quantum dots
- molecular docking
- magnetic resonance
- nucleic acid
- circulating tumor cells
- solid state
- highly efficient
- computed tomography
- molecular dynamics simulations
- genome wide
- gold nanoparticles
- reduced graphene oxide
- gene expression
- ionic liquid