Physics Depsartment & Institute for Nanotechnology, Bar Ilan University, Ramat Gan, Israel.
Physics Depsartment & Institute for Nanotechnology, Bar Ilan University, Ramat Gan, Israel.
Biophys J. 2022 Jun 7;121(11):2127-2134. doi: 10.1016/j.bpj.2022.04.033. Epub 2022 Apr 30.
Measuring the mechanical properties of single-stranded DNA (ssDNA) is a complex challenge that has been addressed lately by different methods. We measured the persistence length of ring ssDNA using a combination of a special DNA origami structure, a self-avoiding ring polymer simulation model, and nonparametric estimation statistics. The method overcomes the complexities set forth by previously used methods. We designed the DNA origami nano structures and measured the ring ssDNA polymer conformations using atomic force microscopy. We then calculated their radius of gyration, which was used as a fitting parameter for finding the persistence length. As there is no simple formulation for the radius of gyration distribution, we developed a simulation program consisting of a self-avoiding ring polymer to fit the persistence length to the experimental data. ssDNA naturally forms stem-loops, which should be taken into account in fitting a model to the experimental measurement. To overcome that hurdle, we found the possible loops using minimal energy considerations and used them in our fitting procedure of the persistence length. Due to the statistical nature of the loops formation, we calculated the persistence length for different percentages of loops that are formed. In the range of 25-75% loop formation, we found the persistence length to be 1.9-4.4 nm, and for 50% loop formation we get a persistence length of 2.83 ± 0.63 nm. This estimation narrows the previously known persistence length and provides tools for finding the conformations of ssDNA.
测量单链 DNA（ssDNA）的机械性能是一个复杂的挑战，最近已经有不同的方法来解决这个问题。我们使用特殊的 DNA 折纸结构、自回避环聚合物模拟模型和非参数估计统计数据的组合来测量环 ssDNA 的持久长度。该方法克服了以前使用的方法所带来的复杂性。我们设计了 DNA 折纸纳米结构，并使用原子力显微镜测量了环 ssDNA 聚合物构象。然后，我们计算了它们的旋转半径，这是用于找到持久长度的拟合参数。由于旋转半径分布没有简单的公式，我们开发了一个包含自回避环聚合物的模拟程序，将持久长度拟合到实验数据中。ssDNA 自然形成茎环，在拟合模型到实验测量时应考虑到这一点。为了克服这个障碍，我们使用最小能量考虑找到可能的环，并在我们的持久长度拟合过程中使用它们。由于环形成的统计性质，我们计算了不同百分比形成的环的持久长度。在 25-75%的环形成范围内，我们发现持久长度为 1.9-4.4nm，而在 50%的环形成时，我们得到的持久长度为 2.83 ± 0.63nm。这种估计缩小了以前已知的持久长度，并为寻找 ssDNA 的构象提供了工具。
