College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China.
Phys Chem Chem Phys. 2018 Jun 20;20(24):16641-16649. doi: 10.1039/c8cp02295j.
Fluorescent base analogues are of great importance as sensitive probes to detect the dynamic structures of DNA. In this research, the structural and photophysical properties of 13-mer oligonucleotides containing 4-aminophthalimide:2,4-diaminopyrimidine (4AP:DAP) (4AP0, 4AP') were characterized using both molecular dynamics simulations and quantum mechanics methods. The results indicate that the 4AP:DAP pair is well adapted to the overall B-DNA structure with higher stability and π-stacking abilities. The structural overlap of 4AP' and 4AP0 with the neighboring adenines only lies in the 5'-direction which results in the structure distortion from native B-DNA. Furthermore, the photophysical properties of the fluorescent base monomers and the B-DNA duplex were explored in detail. A very important result is that the hydrogen bond interaction does not have more effect on the fluorescence band apart from the slight red-shifts. In particular, the identity of the neighboring bases stacked with 4AP has an important effect on the fluorescence band. How the local environment can alter the photophysical features of the nucleobases when they are incorporated into the DNA duplex is elucidated.
荧光碱基类似物是探测 DNA 动态结构的灵敏探针，具有重要意义。本研究采用分子动力学模拟和量子力学方法，对含有 4-氨基邻苯二甲酰亚胺：2,4-二氨基嘧啶（4AP：DAP）（4AP0、4AP'）的 13 -mer 寡核苷酸的结构和光物理性质进行了表征。结果表明，4AP：DAP 对与整体 B-DNA 结构具有更高的稳定性和π-堆积能力。4AP'和 4AP0 与相邻腺嘌呤的结构重叠仅位于 5'-方向，导致结构从天然 B-DNA 扭曲。此外，详细研究了荧光碱基单体和 B-DNA 双链的光物理性质。一个非常重要的结果是，氢键相互作用除了略微红移外，对荧光带没有更多影响。特别是，与 4AP 堆积的相邻碱基的身份对荧光带有重要影响。阐明了当碱基整合到 DNA 双链中时，局部环境如何改变碱基的光物理特征。
