Effect of HU protein on the conformation and compaction of DNA in a nanochannel
Effect of HU protein on the conformation and compaction of DNA in a nanochannel
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DOI：
10.1039/c7sm02118f
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发表时间：
2018-03-28
期刊：
影响因子：
3.4
通讯作者：
van der Maarel, Johan R. C.
中科院分区：
文献类型：
--
作者：
Guttula, Durgarao;Liu, Fan;van der Maarel, Johan R. C.
用荧光显微镜研究了热不稳定核结构蛋白 HU 对限制在纳米通道中的单个 DNA 分子构象的影响。随着 HU 浓度的增加，预孵育的 DNA 分子在通道的纵向上收缩。这种收缩主要是由于 HU 介导的远端 DNA 片段的桥接，并受通道直径以及缓冲液的离子组成和强度控制。当 HU 浓度超过阈值时，DNA 分子会压缩成浓缩形式。二价镁离子有利于桥联或缩合，但不是桥联或缩合所必需的。使用允许原位改变环境溶液条件的纳米流体装置研究了暴露于 HU 后的构象响应。核蛋白复合物的拉伸首先增加，在大约 20 分钟内达到顶点，随后在大约 2 小时后降低至与预孵育 DNA 分子相关的平衡值。通过结合 HU 蛋白的结构重排，然后通过桥联相互作用进行压实，这一观察结果在时间依赖性弯曲刚度方面得到了合理化。讨论了之前获得的核相关蛋白 H-NS 和 Hfq 的结果，对蛋白结合相关基因调控具有重要意义。
The effect of the heat unstable nucleoid structuring protein HU on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. Pre-incubated DNA molecules contract in the longitudinal direction of the channel with increasing concentration of HU. This contraction is mainly due to HU-mediated bridging of distal DNA segments and is controlled by channel diameter as well as ionic composition and strength of the buffer. For over-threshold concentrations of HU, the DNA molecules compact into an condensed form. Divalent magnesium ions facilitate, but are not required for bridging nor condensation. The conformational response following exposure to HU was investigated with a nanofluidic device that allows an in situ change in environmental solution conditions. The stretch of the nucleoprotein complex first increases, reaches an apex in similar to 20 min, and subsequently decreases to an equilibrium value pertaining to pre-incubated DNA molecules after similar to 2 h. This observation is rationalised in terms of a time-dependent bending rigidity by structural rearrangement of bound HU protein followed by compaction through bridging interaction. Results are discussed in regard to previous results obtained for nucleoid associated proteins H-NS and Hfq, with important implications for protein binding related gene regulation.