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PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I

Gao, Xiang and Gethers, Matthew and Han, Si-ping and Goddard, William A., III and Sha, Ruojie and Cunningham, Richard P. and Seeman, Nadrian C. (2019) PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I. Biochemistry, 58 (6). pp. 575-581. ISSN 0006-2960. http://resolver.caltech.edu/CaltechAUTHORS:20190219-082108610

[img] PDF (PX binding of protein fractions collected from Q-sepharose columns (Figure S1), PX binding of protein fractions in the presence of duplex competitors (Figure S2), PX binding of protein fractions collected from DNA cellulose columns (Figure S3), ...) - Supplemental Material
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Abstract

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1021/acs.biochem.8b01148DOIArticle
https://pubs.acs.org/doi/suppl/10.1021/acs.biochem.8b01148PublisherSupporting Information
ORCID:
AuthorORCID
Goddard, William A., III0000-0003-0097-5716
Seeman, Nadrian C.0000-0002-9680-4649
Additional Information:© 2018 American Chemical Society. Received: October 30, 2018; Revised: December 10, 2018; Published: December 17, 2018. This work was supported by the following grants to N.C.S.: GM-29554 from the National Institute of General Medical Sciences, CMMI-1120890, EFRI-1332411 (also to W.A.G.), and CCF-1526650 from the National Science Foundation, MURI W911NF-11-1-0024 from the Army Research Office, N000141110729 and N000140911118 from the Office of Naval Research, DE-SC0007991 from the Department of Energy for DNA synthesis and partial salary support, GBMF3849 from the Gordon and Betty Moore Foundation, and RGP0010/2017 from the Human Frontiers Science Program. This work was also supported by National Institutes of Health Grant CO6RR0154464 to R.P.C. The authors declare no competing financial interest. The authors thank Prof. Kenneth J. Marians for his generous gift of ParC and Prof. Paramjit Arora for valuable discussions.
Funders:
Funding AgencyGrant Number
NIHGM-29554
NSFCMMI-1120890
NSFEFMA-1332411
NSFCCF-1526650
Army Research Office (ARO)W911NF-11-1-0024
Office of Naval Research (ONR)N000141110729
Office of Naval Research (ONR)N000140911118
Department of Energy (DOE)DE-SC0007991
Gordon and Betty Moore FoundationGBMF3849
Human Frontier Science ProgramRGP0010/2017
NIHCO6RR0154464
Other Numbering System:
Other Numbering System NameOther Numbering System ID
WAG1318
Record Number:CaltechAUTHORS:20190219-082108610
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20190219-082108610
Official Citation:The PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I. Xiang Gao, Matthew Gethers, Si-ping Han, William A. Goddard, III, Ruojie Sha, Richard P. Cunningham, and Nadrian C. Seeman. Biochemistry 2019 58 (6), 575-581. DOI: 10.1021/acs.biochem.8b01148
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:92966
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Feb 2019 18:31
Last Modified:23 Feb 2019 02:08

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