Site-Search Process for Synaptic Protein-DNA Complexes

被引:6
|
作者
Vemulapalli, Sridhar [1 ]
Hashemi, Mohtadin [1 ]
Lyubchenko, Yuri L. [1 ]
机构
[1] Univ Nebraska Med Ctr, Coll Pharm, Dept Pharmaceut Sci, Omaha, NE 68198 USA
关键词
high-speed AFM; SFiI; site-search; threading; site-bound segment transfer; synaptic complexes; DIFFUSION-DRIVEN MECHANISMS; RESTRICTION-ENDONUCLEASE; ASSOCIATION KINETICS; COUPLED DIFFUSION; NUCLEIC-ACIDS; FORCE; DYNAMICS; SFIL; TRANSLOCATION; LOOP;
D O I
10.3390/ijms23010212
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The assembly of synaptic protein-DNA complexes by specialized proteins is critical for bringing together two distant sites within a DNA molecule or bridging two DNA molecules. The assembly of such synaptosomes is needed in numerous genetic processes requiring the interactions of two or more sites. The molecular mechanisms by which the protein brings the sites together, enabling the assembly of synaptosomes, remain unknown. Such proteins can utilize sliding, jumping, and segmental transfer pathways proposed for the single-site search process, but none of these pathways explains how the synaptosome assembles. Here we used restriction enzyme SfiI, that requires the assembly of synaptosome for DNA cleavage, as our experimental system and applied time-lapse, high-speed AFM to directly visualize the site search process accomplished by the SfiI enzyme. For the single-site SfiI-DNA complexes, we were able to directly visualize such pathways as sliding, jumping, and segmental site transfer. However, within the synaptic looped complexes, we visualized the threading and site-bound segment transfer as the synaptosome-specific search pathways for SfiI. In addition, we visualized sliding and jumping pathways for the loop dissociated complexes. Based on our data, we propose the site-search model for synaptic protein-DNA systems.
引用
收藏
页数:11
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