Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study,Journal of Computational Chemistry

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Photophysical properties of fluorescent imaging biological probes of nucleic acids: SAC-CI and TD-DFT Study
Journal of Computational Chemistry ( IF 3.4 ) Pub Date : 2018-08-24 , DOI: 10.1002/jcc.25553
Takafumi Shiraogawa ₁ , G Candel ₂ , Ryoichi Fukuda _{3,

4} , Ilaria Ciofini ₂ , Carlo Adamo _{2,

5} , Akimitsu Okamoto _{6,

7} , Masahiro Ehara _{1,

3,

8}

Affiliation

Recently, exciton‐controlled hybridization‐sensitive fluorescent oligonucleotide (ECHO) probe, which shows strong emission in the near‐infrared region via hybridization to the target DNA and/or RNA strand, has been developed. In this work, photophysical properties of the chromophores of these probes and the fluorescent mechanism have been investigated by the SAC‐CI and TD‐DFT calculations. Three fluorescent cyanine chromophores whose excitation is challenging for TD‐DFT methods, have been examined regarding the photo‐absorption and emission spectra. The SAC‐CI method well reproduces the experimental values with respect to transition energies, while the quantitative prediction by TD‐DFT calculations is difficult for these chromophores. Some stable structures of H‐aggregate system were computationally located and two of the configurations were examined for the photo‐absorption. The present results support for the assumption based on experimental measurement in which strong fluorescence is due to the monomer unit in nearly planar structure and its suppression of probes is to the H‐aggregates of two exciton units. Stokes shifts of these three chromophores were qualitatively reproduced by the theoretical calculations, while the energy splitting due to H‐aggregate in the hybridized probe was slightly overestimated. © 2018 Wiley Periodicals, Inc.

中文翻译：

核酸荧光成像生物探针的光物理特性：SAC-CI 和 TD-DFT 研究

最近，已经开发出激子控制的杂交敏感荧光寡核苷酸 (ECHO) 探针，该探针通过与目标 DNA 和/或 RNA 链的杂交在近红外区域显示出强发射。在这项工作中，通过 SAC-CI 和 TD-DFT 计算研究了这些探针发色团的光物理性质和荧光机制。三种荧光花青色团的激发对于 TD-DFT 方法具有挑战性，已经在光吸收和发射光谱方面进行了检查。SAC-CI 方法很好地再现了关于跃迁能的实验值，而通过 TD-DFT 计算对这些发色团进行定量预测是困难的。H-聚集体系统的一些稳定结构被计算定位，并检查了其中两个配置的光吸收。目前的结果支持基于实验测量的假设，其中强荧光是由于近平面结构中的单体单元造成的，它对探针的抑制是由于两个激子单元的 H 聚集体。这三个发色团的斯托克斯位移通过理论计算得到了定性再现，而杂交探针中 H 聚集体引起的能量分裂被稍微高估了。© 2018 Wiley Periodicals, Inc. 目前的结果支持基于实验测量的假设，其中强荧光是由于近平面结构中的单体单元造成的，它对探针的抑制是由于两个激子单元的 H 聚集体。这三个发色团的斯托克斯位移通过理论计算得到了定性再现，而杂交探针中 H 聚集体引起的能量分裂被稍微高估了。© 2018 Wiley Periodicals, Inc. 目前的结果支持基于实验测量的假设，其中强荧光是由于近平面结构中的单体单元造成的，它对探针的抑制是由于两个激子单元的 H 聚集体。这三个发色团的斯托克斯位移通过理论计算得到了定性再现，而杂交探针中 H 聚集体引起的能量分裂被稍微高估了。© 2018 Wiley Periodicals, Inc.

更新日期：2018-08-24

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