Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.
J Phys Chem Lett. 2021 May 20;12(19):4576-4584. doi: 10.1021/acs.jpclett.1c00962. Epub 2021 May 10.
The conformational dynamics of single-stranded DNA (ss-DNA) are implicated in the mechanisms of several key biological processes such as DNA replication and damage repair and have been modeled with those of semiflexible or flexible polymer. The high flexibility and customizability of ss-DNA also make it an excellent polymeric material for materials engineering. Polythymidine (poly(T)) is an excellent model ss-DNA as a flexible polymer since it does not form any secondary structure. However, only limited experimental results have been reported of poly(T) conformational dynamics with a very short length that is not relevant to the aforementioned processes and applications. Here, we provide the first experimental results of the conformational dynamics of poly(T) with lengths in the range of 130-170 nucleotides at the single-molecule level. Our experiments are based on single-molecule FRET and a DNA hairpin structure of which the folding kinetics are governed by the conformational dynamics of poly(T). We found that the folding kinetics deviate far from those of a flexible polymer model with a harmonic bending potential. To this end, we derived a simple model for the kinetics of DNA hairpin folding from the self-avoiding-walk (SAW). Our model describes the conformational dynamics of poly(T) very well and enables estimation of the conformational dimensionality. The estimated dimensionalities suggest that ss-DNA is completely flexible at 100 mM or a higher NaCl concentration, but not at 50 mM. These results will help understand the conformational dynamics of ss-DNA implicated in several key biological processes and maximize the utility of ss-DNA for materials engineering. Also, our system and model provide an excellent platform to investigate the conformational dynamics of ss-DNA.
单链 DNA（ss-DNA）的构象动力学与多种关键生物过程的机制有关，例如 DNA 复制和损伤修复，并已通过半刚性或柔性聚合物对其进行建模。ss-DNA 的高灵活性和可定制性使其成为材料工程中极好的聚合物材料。聚胸腺嘧啶核苷酸（poly(T)) 作为一种柔性聚合物是极好的 ss-DNA 模型，因为它不会形成任何二级结构。然而，仅报道了非常短长度的 poly(T)构象动力学的有限实验结果，这些结果与上述过程和应用无关。在这里，我们在单分子水平上提供了长度在 130-170 个核苷酸范围内的 poly(T)构象动力学的第一个实验结果。我们的实验基于单分子 FRET 和 DNA 发夹结构，其折叠动力学受 poly(T)构象动力学的控制。我们发现折叠动力学与具有谐弯曲势的柔性聚合物模型大相径庭。为此，我们从无规行走（SAW）出发，为 DNA 发夹折叠动力学推导了一个简单的模型。我们的模型很好地描述了 poly(T)的构象动力学，并能够估计构象的维度。估计的维度表明，ss-DNA 在 100mM 或更高的 NaCl 浓度下是完全灵活的，但在 50mM 下则不是。这些结果将有助于理解与多种关键生物过程相关的 ss-DNA 的构象动力学，并最大限度地提高 ss-DNA 在材料工程中的应用。此外，我们的系统和模型为研究 ss-DNA 的构象动力学提供了一个极好的平台。
