Inferring primase-DNA specific recognition using a data driven approach.

Binding Sites DNA / chemistry DNA Primase / chemistry Machine Learning Nucleotide Motifs Protein Binding

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
18 11 2021
Historique:
accepted: 04 10 2021
revised: 01 10 2021
received: 23 08 2021
pubmed: 1 11 2021
medline: 24 12 2021
entrez: 31 10 2021
Statut: ppublish

Résumé

DNA-protein interactions play essential roles in all living cells. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is both challenging and 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 sequences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.

Identifiants

DOI: 10.1093/nar/gkab956 PMID: 34718733 PMC: PMC8599759
pubmed: 34718733
pii: 6414050
doi: 10.1093/nar/gkab956
pmc: PMC8599759
doi:

Substances chimiques

DNA 9007-49-2
DNA Primase EC 2.7.7.-

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

11447-11458

Informations de copyright

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Adam Soffer (A)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
Data Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
School of Computer and Electrical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Sarah A Eisdorfer (SA)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Morya Ifrach (M)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Stefan Ilic (S)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Ariel Afek (A)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Hallel Schussheim (H)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Dan Vilenchik (D)

Data Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
School of Computer and Electrical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Barak Akabayov (B)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
Data Science Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
ORCID: 0000-0002-3882-2742

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Classifications MeSH

Recherchemedicale.com › Phénomènes chimiques › Phénomènes biochimiques › Sites de fixation › Inferring primase-DNA specific recognition...
Recherchemedicale.com › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Inferring primase-DNA specific recognition...
Recherchemedicale.com › Enzymes et coenzymes › Enzymes › Transferases › Phosphotransferases › Nucleotidyltransferases › RNA nucleotidyltransferases › DNA-directed RNA polymerases › DNA primase › Inferring primase-DNA specific recognition...
Recherchemedicale.com › Sciences de l'information › Méthodologies informatiques › Algorithmes › Intelligence artificielle › Apprentissage machine › Inferring primase-DNA specific recognition...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Motifs nucléotidiques › Inferring primase-DNA specific recognition...
Recherchemedicale.com › Métabolisme › Liaison aux protéines › Inferring primase-DNA specific recognition...