Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA.
Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA.
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DOI：
10.1016/j.bpj.2013.03.053
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发表时间：
2013-06
影响因子：
3.4
通讯作者：
T. Uzawa;T. Isoshima;Yoshihiro Ito;K. Ishimori;D. Makarov;K. Plaxco
中科院分区：
文献类型：
--
作者：
T. Uzawa;T. Isoshima;Yoshihiro Ito;K. Ishimori;D. Makarov;K. Plaxco
分子内碰撞动力学在生物分子折叠和功能中发挥着重要作用，并且越来越多地在仿生技术的性能中发挥着重要作用。然而迄今为止，单链核酸动力学的定量研究还很有限。因此，我们在这里研究了单链 DNA 端到端碰撞动力学的序列组成、链长、粘度和温度依赖性。我们发现这些动力学的绝对碰撞率和温度依赖性都依赖于碱基组成，这表明碱基堆积相互作用是一个重要的贡献者。例如，虽然聚胸腺嘧啶的端到端碰撞动力学表现出简单的线性阿累尼乌斯行为，但较长的聚腺嘌呤结构的行为更为复杂。具体而言，20-和25-腺嘌呤构建体表现出双相温度依赖性，在高于335 K（对于20-腺嘌呤）和328 K（对于25-腺嘌呤），它们的温度依赖性实际上与多胸腺嘧啶的温度依赖性难以区分。聚胸腺嘧啶和聚腺嘌呤的不同阿伦尼乌斯行为以及聚腺嘌呤跨过而表现得像聚胸腺嘧啶的温度的链长依赖性可以通过势垒摩擦机制来解释，其中在低温下，聚腺嘌呤局部重排的能垒成为其端到端碰撞动力学的主要贡献者。
Intramolecular collision dynamics play an essential role in biomolecular folding and function and, increasingly, in the performance of biomimetic technologies. To date, however, the quantitative studies of dynamics of single-stranded nucleic acids have been limited. Thus motivated, here we investigate the sequence composition, chain-length, viscosity, and temperature dependencies of the end-to-end collision dynamics of single-stranded DNAs. We find that both the absolute collision rate and the temperature dependencies of these dynamics are base-composition dependent, suggesting that base stacking interactions are a significant contributor. For example, whereas the end-to-end collision dynamics of poly-thymine exhibit simple, linear Arrhenius behavior, the behavior of longer poly-adenine constructs is more complicated. Specifically, 20- and 25-adenine constructs exhibit biphasic temperature dependencies, with their temperature dependences becoming effectively indistinguishable from that of poly-thymine above 335 K for 20-adenines and 328 K for 25-adenines. The differing Arrhenius behaviors of poly-thymine and poly-adenine and the chain-length dependence of the temperature at which poly-adenine crosses over to behave like poly-thymine can be explained by a barrier friction mechanism in which, at low temperatures, the energy barrier for the local rearrangement of poly-adenine becomes the dominant contributor to its end-to-end collision dynamics.