Data from: Simulation assisted analysis of the intrinsic stiffness for short DNA molecules imaged with scanning atomic force microscopy

Studying the mechanical properties of short segments of dsDNA can provide insight into various biophysical phenomena, from DNA looping to the organization of nucleosomes. Scanning atomic force microscopy (AFM) is able to acquire images of single DNA molecules with near-basepair resolution. From many images, one may use equilibrium statistical mechanics to quantify the intrinsic stiffness (or persistence length) of the DNA. However, this approach is highly dependent upon both the correct microscopic polymer model and a correct image analysis of DNA contours. These complications have led to significant debate over the flexibility of dsDNA at short length scales. We first show how to extract accurate measures of DNA contour lengths by calibrating to DNA traces of simulated AFM data. After this calibration, we show that DNA adsorbed on an aminopropyl-mica surface behaves as a worm-like chain (WLC) for contour lengths as small as ~20 nm. We also show that a DNA binding protein can modify the mechanics of the DNA from that of a WLC.

研究双链DNA（dsDNA）短片段的力学特性，可为从DNA环化到核小体组装等多种生物物理现象提供重要洞察。扫描原子力显微镜（AFM）可获取单DNA分子的图像，其分辨率可达近碱基对级别。通过多张此类图像，可借助平衡统计力学量化DNA的本征刚度（或称持久长度）。然而，该方法高度依赖于准确的微观聚合物模型，以及对DNA轮廓的精确图像分析。上述难点引发了学界关于短尺度下双链DNA柔性的广泛争议。本研究首先通过对标模拟原子力显微镜数据得到的DNA轨迹，阐明了如何精准提取DNA轮廓长度的方法。完成该校准步骤后，本研究证明：当吸附于氨丙基云母表面时，即使轮廓长度低至约20纳米，DNA仍表现为蠕虫状链（WLC）。此外，本研究还证实，DNA结合蛋白可改变DNA的力学特性，使其偏离蠕虫状链的行为模式。