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Distinguishing binding modes of a new phosphonium dye with DNA by surface-enhanced Raman spectroscopy

机译：用表面增强拉曼光谱分析DNA的新鏻染料的结合模式

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To understand the disruption of the cell processes induced by small molecule binding to DNA, numerous structural studies of DNA complexes have been done, whereby a variety of methods has been applied. The use of various techniques is required, not only for the unique information on the structure provided by each of the methods, but also for limitations that arise during the sample preparation or measurement procedures. Here, surface-enhanced Raman scattering (SERS) spectroscopy has been employed to study binding of a new mitochondria-specific dye with ds-DNA polynucleotides. Concentration dependent differences in the SERS spectra of the dye were attributed to concentration induced changes in position of the dye molecules on the enhancing metal surface and assigned to aggregated molecules formed due to π-stacking interactions at higher dye concentration (5.0 × 10 ~(?5) mol L ~(?1) ) and to single molecules at lower dye concentration (5.0 × 10 ~(?6) mol L ~(?1) ). The characteristic SERS spectra were further on correlated with the spectra of the dye/DNA complexes, implying binding of the monomeric dye molecules at the excess of the adenine–thymine polynucleotide, [dye]/[AT] = 1/10, and in form of the stacked dye molecules at the higher [dye]/[AT] ratio of 1/2. In addition, the distinctive SERS spectra of the complexes with the AT alternating and homo-polymer indicated different placement of the dye molecules within the minor groove, affected by the polynucleotide groove width. Beside well-known quantitative, this study emphasized structural sensitivity of SERS, able to distinguish various molecular forms of the small molecules in the complex structures such as those formed with biomacromolecules.
机译：为了理解由小分子结合到DNA的小分子诱导的细胞过程的破坏，已经完成了DNA复合物的许多结构研究，从而应用了各种方法。需要使用各种技术，而不仅仅是关于每个方法提供的结构的独特信息，而且还需要用于样品制备或测量程序期间出现的限制。这里，已经采用表面增强的拉曼散射（SERS）光谱学研究了与DS-DNA多核苷酸的新型线粒体特异性染料的结合。染料的SERS光谱的浓度依赖性差异归因于浓度诱导的染料分子在增强金属表面上的位置变化，并且在较高染料浓度（5.0×10〜（？ 5）Mol L〜（α1））和以较低染料浓度的单分子（5.0×10〜（α6）mol l〜（α1））。特征阶SERS光谱进一步与染料/ DNA复合物的光谱相关，暗示单体染料分子在过量的腺嘌呤 - 胸腺嘧啶多核苷酸，液[染料] / [AT] = 1/10中的结合，以及形式堆叠的染料分子在较高的[染料] / [AT]的比例为1/2。另外，具有交替和均聚合物的复合物的独特SERS光谱表明染料分子在受核苷酸槽宽度影响的染色分子的不同放置。除了众所周知的定量之外，该研究强调了SERS的结构敏感性，能够将各种分子形式的小分子在复杂结构中区分开，例如由生物致摩洛族形成的诸如那些。

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