Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level.
Conformational Dynamics of Poly(T) Single-Stranded DNA at the Single-Molecule Level.
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DOI：
10.1021/acs.jpclett.1c00962
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发表时间：
2021-05-20
影响因子：
5.7
通讯作者：
Lee, Tae-Hee
中科院分区：
文献类型：
--
作者：
Kim, Shi Ho;Lee, Tae-Hee
单链DNA（ss-DNA）的构象动力学与DNA复制和损伤修复等重要生物学过程的机制密切相关，并已被半柔性或柔性聚合物所模拟。ss-DNA的高度灵活性和可定制性也使其成为材料工程的优秀聚合物材料。聚胸苷（poly（T））是一种优良的柔性聚合物模型ss-DNA，因为它不形成任何二级结构。然而，只有有限的实验结果已经报道的聚（T）构象动力学与非常短的长度，是不相关的上述过程和应用。在这里，我们提供了第一个实验结果的构象动力学的聚（T）的长度在130 - 170个核苷酸的范围内，在单分子水平。我们的实验是基于单分子FRET和DNA发夹结构的折叠动力学是由聚（T）的构象动力学。我们发现，折叠动力学偏离远从一个灵活的聚合物模型与谐波弯曲势。为此，我们推导出一个简单的模型的动力学的DNA发夹折叠的自回避行走（SAW）。我们的模型很好地描述了poly（T）的构象动力学，并且能够估计构象维度。估计的维数表明，ss-DNA是完全灵活的，在100 mM或更高的NaCl浓度，但不是在50 mM。这些结果将有助于了解的构象动力学的ss-DNA牵连在几个关键的生物过程，并最大限度地利用ss-DNA的材料工程。此外，我们的系统和模型提供了一个很好的平台，研究ss-DNA的构象动力学。
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 semi-flexible or flexible polymer. The high flexibility and customizability of ss-DNA also make it an excellent polymeric material for materials engineering. Poly-thymidine (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.
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DOI：
10.1073/pnas.1119057109
发表时间：
2012-01-17
影响因子：
11.1
作者：
Chen, Huimin;Meisburger, Steve P.;Pollack, Lois
通讯作者：
Pollack, Lois
DOI：
10.1073/pnas.151242898
发表时间：
2001-07-31
影响因子：
11.1
作者：
Bar-Ziv, R;Libchaber, A
通讯作者：
Libchaber, A
影响因子：
4.8
作者：
Lee, Jaehyoun;Crickard, J. Brooks;Lee, Tae-Hee
通讯作者：
Lee, Tae-Hee
影响因子：
3.4
作者：
Murphy, MC;Rasnik, I;Ha, TJ
通讯作者：
Ha, TJ
影响因子：
10.8
作者：
Kim, Shi Ho;Liu, Yu;Lee, Tae-Hee
通讯作者：
Lee, Tae-Hee