BioNanotechnology and Structure Formation Group, Department of Chemistry and Food Chemistry, Biotechnology Center, Technische Universität Dresden, D-01062 Dresden, Germany.
Nucleic Acids Res. 2010 Oct;38(19):6526-32. doi: 10.1093/nar/gkq434. Epub 2010 May 28.
YOYO-1 is a fluorescent dye widely used for probing the statistical-mechanical properties of DNA. However, currently contradicting data exist how YOYO-1 binding alters the DNA structure and rigidity. Here, we systematically address this problem using magnetic tweezers. Remarkably, we find that the persistence length of DNA remains constant independent of the amount of bound YOYO-1, which contrasts previous assumptions. While the ionic conditions can considerably alter the stability of YOYO-1 binding, the DNA bending rigidity seems not to be affected. We furthermore determine important structural parameters such as the binding site size, the elongation, as well as the untwisting angle per bound YOYO-1 molecule. We expect that our assay, in which all the parameters are determined within a single experiment, will be beneficial for a large range of other DNA binding drugs.
YOYO-1 是一种广泛用于探测 DNA 统计力学性质的荧光染料。然而，目前关于 YOYO-1 结合如何改变 DNA 结构和刚性存在相互矛盾的数据。在这里，我们使用磁镊系统地解决了这个问题。值得注意的是，我们发现 DNA 的持久性长度在不依赖于结合的 YOYO-1 量的情况下保持不变，这与以前的假设相反。虽然离子条件可以极大地改变 YOYO-1 结合的稳定性，但 DNA 的弯曲刚性似乎不受影响。我们还确定了重要的结构参数，如结合位点大小、伸长率以及每个结合的 YOYO-1 分子的扭结角度。我们期望我们的测定方法，其中所有参数都在单个实验中确定，将对其他大量 DNA 结合药物有益。
