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Reconfiguring primase DNA-recognition sequences by using a data-driven approach

Adam Soffer, Morya Ifrach, Stefan Ilic, Ariel Afek, Dan Vilenchik, View ORCID ProfileBarak Akabayov
doi: https://doi.org/10.1101/2020.09.29.317842
Adam Soffer
aDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
bData Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
cSchool of Computer and Electrical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Morya Ifrach
aDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Stefan Ilic
aDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Ariel Afek
aDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Dan Vilenchik
bData Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
cSchool of Computer and Electrical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Barak Akabayov
aDepartment of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
bData Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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  • ORCID record for Barak Akabayov
  • For correspondence: akabayov@bgu.ac.il
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Abstract

DNA–protein interactions are essential in all aspects of every living cell. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is challenging but important, since it may contribute to finding the means to regulate metabolic pathways involving DNA–protein interactions. Using a massive experimental benchmark dataset of binding scores for DNA sequences and a machine learning workflow, we describe the binding to DNA of T7 primase, as a model system for specific DNA–protein interactions. Effective binding of T7 primase to its specific DNA recognition se-quences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • The title abstract and the first paragraph of the introduction have been slightly modified. Non of the results/discussion/conclusions were modified.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 14, 2020.
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Reconfiguring primase DNA-recognition sequences by using a data-driven approach
Adam Soffer, Morya Ifrach, Stefan Ilic, Ariel Afek, Dan Vilenchik, Barak Akabayov
bioRxiv 2020.09.29.317842; doi: https://doi.org/10.1101/2020.09.29.317842
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Reconfiguring primase DNA-recognition sequences by using a data-driven approach
Adam Soffer, Morya Ifrach, Stefan Ilic, Ariel Afek, Dan Vilenchik, Barak Akabayov
bioRxiv 2020.09.29.317842; doi: https://doi.org/10.1101/2020.09.29.317842

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