title: Exploration of the biological micro-surrounding effect on the excited states of the size-expanded fluorescent base x-cytosine in DNA.
abstract: We present the results of a detailed and systematic computational investigation into the excited-state properties of the fluorescent cytosine analogue x-cytosine (xC). Also examined were the influences of hydration, linking to deoxyribose, base pairing with guanine (G), and base stacking on its absorption and emission processes. The calculated excitation and emission energies agree well with the experimentally measured data. It was found that hydration, linking to deoxyribose, and base pairing with G have a hyperchromic effect on the excitation maximum of xC. The linking sugar will red-shift the fluorescence emission of xC by 7 nm, while hydration and base pairing with G, on the contrary, results in a blue-shift of the fluorescence emission by 8 and 9 nm, respectively. In addition, hydration of xCG will further blue-shift the fluorescence emission of xC by about 17 nm. Furthermore, the fluorescence quantum yield of xC would be increased after hydration, linking to deoxyribose, and base pairing with G. When sandwiched by two identical natural bases, a significant decrease of the oscillator strength as well as a red-shift of the dipole-allowed transition with respect to free xC is observed in all cases. The fluorescence quantum yield of xC was expected to be lowered in the stacked complexes due to a static quenching mechanism.
authors.affiliation: The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, PR China.
authors.forename: Laibin
authors.initials: L
authors.lastname: Zhang
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Chen
authors.forename: Haiying
authors.initials: H
authors.lastname: Liu
authors.forename: Li
authors.initials: L
authors.lastname: Han
authors.forename: Robert I
authors.initials: RI
authors.lastname: Cukier
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Bu
mesh_terms: D020029:Base Pairing; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D011789:Quantum Theory; D013050:Spectrometry, Fluorescence
chemical_list: D003596:Cytosine; D004247:DNA