DNA complexes with human apurinic/apyrimidinic endonuclease 1: structural insights revealed by pulsed dipolar EPR with orthogonal spin labeling.
Base Sequence
Binding Sites
Cloning, Molecular
DNA
/ chemistry
DNA Damage
DNA-(Apurinic or Apyrimidinic Site) Lyase
/ chemistry
Electron Spin Resonance Spectroscopy
Escherichia coli
/ genetics
Gene Expression
Genetic Vectors
/ chemistry
Humans
Molecular Dynamics Simulation
Nucleic Acid Conformation
Oligonucleotides
/ chemistry
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Recombinant Proteins
/ chemistry
Spin Labels
/ chemical synthesis
Substrate Specificity
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
05 09 2019
05 09 2019
Historique:
accepted:
11
07
2019
revised:
04
07
2019
received:
24
04
2019
pubmed:
23
7
2019
medline:
4
12
2019
entrez:
23
7
2019
Statut:
ppublish
Résumé
A DNA molecule is under continuous influence of endogenous and exogenous damaging factors, which produce a variety of DNA lesions. Apurinic/apyrimidinic sites (abasic or AP sites) are among the most common DNA lesions. In this work, we applied pulse dipolar electron paramagnetic resonance (EPR) spectroscopy in combination with molecular dynamics (MD) simulations to investigate in-depth conformational changes in DNA containing an AP site and in a complex of this DNA with AP endonuclease 1 (APE1). For this purpose, triarylmethyl (TAM)-based spin labels were attached to the 5' ends of an oligonucleotide duplex, and nitroxide spin labels were introduced into APE1. In this way, we created a system that enabled monitoring the conformational changes of the main APE1 substrate by EPR. In addition, we were able to trace substrate-to-product transformation in this system. The use of different (orthogonal) spin labels in the enzyme and in the DNA substrate has a crucial advantage allowing for detailed investigation of local damage and conformational changes in AP-DNA alone and in its complex with APE1.
Identifiants
pubmed: 31329919
pii: 5536976
doi: 10.1093/nar/gkz620
pmc: PMC6735896
doi:
Substances chimiques
Oligonucleotides
0
Recombinant Proteins
0
Spin Labels
0
DNA
9007-49-2
APEX1 protein, human
EC 4.2.99.18
DNA-(Apurinic or Apyrimidinic Site) Lyase
EC 4.2.99.18
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7767-7780Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
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