The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded–double-stranded DNA (ssDNA–dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA–dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2dimer probes. With the application of these methods, the (iCy3)2dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein–DNA complex assembly and function.

中文翻译：

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使用位点特异性激子耦合二聚体探针光谱研究局部 DNA 主链构象和构象紊乱

基因组表达、调节和修复过程需要蛋白质和 DNA 在位于单链-双链 DNA (ssDNA-dsDNA) 连接处及其附近的特定位点处直接相互作用。在这里，我们回顾了最近开发的光谱方法和分析的应用，将线性吸光度和圆二色性光谱与非线性二维荧光光谱相结合，以研究内部已内部修饰的 ssDNA-dsDNA 叉结构的糖磷酸骨架的局部构象和构象紊乱。用激子耦合花青 (iCy3) 标记2二聚体探针。通过应用这些方法，(iCy3)2二聚体可以作为 dsDNA 糖磷酸主链在各个关键位置的平均局部构象和构象分布的可靠探针。我们的研究结果提出了一个可能的结构框架，用于理解 DNA 呼吸在驱动蛋白质-DNA 复合物组装和功能过程中的作用。