Effect of HU protein on the conformation and compaction of DNA in a nanochannel,Soft Matter

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Effect of HU protein on the conformation and compaction of DNA in a nanochannel
Soft Matter ( IF 2.9 ) Pub Date : 2018-02-12 00:00:00 , DOI: 10.1039/c7sm02118f
Durgarao Guttula _{1,

2,

3,

4} , Fan Liu _{1,

2,

3,

4} , Jeroen A. van Kan _{1,

2,

3,

4} , Véronique Arluison _{5,

6,

7,

8,

9} , Johan R. C. van der Maarel _{1,

2,

3,

4}

Affiliation

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 ∼20 min, and subsequently decreases to an equilibrium value pertaining to pre-incubated DNA molecules after ∼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.

中文翻译：

HU蛋白对纳米通道中DNA构象和紧实的影响

用荧光显微镜研究了热不稳定的类核苷酸结构蛋白HU对限制在纳米通道中的单个DNA分子构象的影响。预培养的DNA分子在通道的纵向上随着HU浓度的增加而收缩。该收缩主要是由于HU介导的远端DNA片段的桥接，并且受通道直径以及缓冲液的离子组成和强度控制。对于HU的阈值以上浓度，DNA分子会压缩成浓缩形式。二价镁离子促进但不要求桥接或缩合。暴露于HU后的构象反应已通过允许原位使用的纳米流体装置进行了研究环境解决方案条件的变化。核蛋白复合物的延伸首先增加，在约20分钟内达到顶点，然后在约2小时后下降至与预孵育的DNA分子有关的平衡值。通过结合HU蛋白的结构重排，然后通过桥连相互作用进行压实，可以在时间相关的弯曲刚度方面合理化该观察结果。讨论了有关与核苷相关的蛋白质H-NS和Hfq获得的先前结果的结果，对蛋白质结合相关基因的调控具有重要意义。

更新日期：2018-02-12

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