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首页> 外文期刊>Biophysical Chemistry: An International Journal Devoted to the Physical Chemistry of Biological Phenomena >Quantifying length-dependent DNA end-binding by nucleoproteins
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Quantifying length-dependent DNA end-binding by nucleoproteins

机译：量化核蛋白的长度依赖性DNA末端结合

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摘要

The ends of nucleic acids oligomers alter the statistics of interior nonspecific ligand binding and act as binding sites with altered properties. While the former aspect of "end effects" has received much theoretical attention in the literature, the physical nature of end-binding, and hence its potential impact on a wide range of studies with oligomers, remains poorly known. Here, we report for the first time end-binding to DNA using a model helix-turn-helix motif, the DNA-binding domain of ETV6, as a function of DNA sequence length. Spectral analysis of ETV6 intrinsic tryptophan fluorescence by singular value decomposition showed that end-binding to nonspecific fragments was negligible at > 0.2 kbp and accumulated to 8% of total binding to 23-bp oligomers. The affinity for end-binding was insensitive to salt but tracked the affinity of interior binding, suggesting translocation from interior sites rather than free solution as its mechanism. As the presence of a cognate site in the 23-bp oligomer suppressed end-binding, neglect of end-binding to the short cognate DNA does not introduce significant error. However, the same applies to nonspecific DNA only if longer fragments (> 0.2 kbp) are used.
机译：核酸寡聚体的末端改变内部非特异性配体结合的统计，并用作具有改变性质的结合位点。虽然“结束效应”的前面是在文献中获得了很大的理论关注，但最终结合的物理性质，因此对寡聚体的各种研究潜在影响仍然是众所周知的。在这里，我们使用型号螺旋转向螺旋基序，ETV6的DNA结合结构域作为DNA序列长度的函数报告对DNA的第一次结合到DNA的第一次结合。奇异值分解的ETV6内在色氨酸荧光的光谱分析显示，与非特异性片段的结束结合在> 0.2kbp上可忽略不计，并累积至总结合的8％至23bp寡聚体。对末端结合的亲和力对盐不敏感，但追踪内部结合的亲和力，表明来自内部部位的易位而不是自由溶液作为其机制。由于23-BP低聚物中的同源位点的存在抑制的终止结合，忽略与短同源DNA的终止结合不会引入显着的误差。然而，只有使用较长的碎片（> 0.2kbp），就相同的是非特异性DNA。

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