Department of Chemistry and Biochemistry and the Biodesign Institute, Arizona State University , PO Box 875601, Tempe, Arizona 85287, United States.
J Phys Chem B. 2014 Jan 9;118(1):152-63. doi: 10.1021/jp410976p. Epub 2013 Dec 20.
Photophysical measurements are reported for Cy3-DNA constructs in which both Cy3 nitrogen atoms are attached to the DNA backbone by short linkers. While this linking was thought to rigidify the orientation of the dye and hinder cis-isomerization, the relatively low fluorescence quantum yield and the presence of a short component in the time-resolved fluorescence decay of the dye indicated that cis-isomerization remained possible. Fluorescence correlation spectroscopy and transient absorption experiments showed that photoisomerization occurred with high efficiency. Molecular dynamics simulations of the trans dye system indicated the presence of stacked and unstacked states, and free energy simulations showed that the barriers for stacking/unstacking were low. In addition, simulations showed that the ground cis state was feasible without DNA distortions. Based on these observations, a model is put forward in which the doubly linked dye can photoisomerize in the unstacked state.
报道了 Cy3-DNA 构建体的光物理测量结果，其中 Cy3 的两个氮原子都通过短链接连接到 DNA 骨架上。虽然这种连接被认为可以使染料的取向刚性化并阻碍顺式异构化，但染料的时间分辨荧光衰减中存在短成分和相对较低的荧光量子产率表明顺式异构化仍然是可能的。荧光相关光谱和瞬态吸收实验表明光异构化发生的效率很高。顺式染料体系的分子动力学模拟表明存在堆叠和未堆叠状态，自由能模拟表明堆叠/解堆叠的势垒较低。此外，模拟表明，在没有 DNA 扭曲的情况下，基态顺式是可行的。基于这些观察结果，提出了一种模型，其中双连接的染料可以在未堆叠状态下发生光异构化。
