Department of Chemistry , New York University , New York , New York 10003 , United States.
Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States.
Biochemistry. 2019 Feb 12;58(6):575-581. doi: 10.1021/acs.biochem.8b01148. Epub 2018 Dec 28.
The PX motif of DNA is a four-stranded structure in which two parallel juxtaposed double-helical domains are fused by crossovers at every point where the strands approach each other. Consequently, its twist and writhe are approximately half of those of conventional DNA. This property has been shown to relax supercoiled plasmid DNA under circumstances in which head-to-head homology exists within the plasmid; the homology can be either complete homology or every-other-half-turn homology, known as PX homology. It is clearly of interest to establish whether the cell contains proteins that interact with this unusual and possibly functional motif. We have examined Escherichia coli extracts to seek such a protein. We find by gel mobility studies that the PX motif is apparently bound by a cellular component. Fractionation of this binding activity reveals that the component is DNA polymerase I (Pol I). Although the PX motif binds to Pol I, we find that PX-DNA is not able to serve as a substrate for the extension of a shortened strand. We cannot say at this time whether the binding is a coincidence or whether it represents an activity of Pol I that is currently unknown. We have modeled the interaction of Pol I and PX-DNA using symmetry considerations and molecular dynamics.
PX 基序是 DNA 的一种四链结构，其中两个平行并列的双螺旋结构域通过在每条链相互接近的每一点上的交叉连接融合在一起。因此，它的扭转和缠绕大约是常规 DNA 的一半。已经证明，在质粒中存在同源性的情况下，这种特性可以使超螺旋质粒 DNA 松弛；这种同源性可以是完全同源性，也可以是每半圈同源性，称为 PX 同源性。显然，人们有兴趣确定细胞中是否含有与这种不寻常且可能具有功能的基序相互作用的蛋白质。我们已经检查了大肠杆菌提取物以寻找这样的蛋白质。通过凝胶迁移研究，我们发现 PX 基序显然被细胞成分所结合。这种结合活性的分级分离表明，该成分是 DNA 聚合酶 I（Pol I）。尽管 PX 基序与 Pol I 结合，但我们发现 PX-DNA 不能作为缩短链延伸的底物。目前，我们无法确定这种结合是巧合还是代表 Pol I 的一种未知活性。我们已经使用对称性考虑和分子动力学对 Pol I 和 PX-DNA 的相互作用进行了建模。
