Title :

The ‘hidden side’ of spin labelled oligonucleotides: Molecular dynamics study focusing on the EPR-silent components of base pairing

Author(s) :

Dantu, Sarath Chandra [Auteur]
Max-Planck-Institut für Biophysikalische Chemie - Max Planck Institute for Biophysical Chemistry [Göttingen]
Sicoli, Giuseppe [Auteur]
Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516

Journal title :

Journal of Magnetic Resonance

Volume number :

324

Publication date :

2021

English keyword(s) :

Nitroxide labels
EPR
MD
base pair geometry
RNA

HAL domain(s) :

Chimie

English abstract : [en]

Nitroxide labels are combined with nucleic acid structures and are studied using electron paramagnetic resonance experiments (EPR). As X-ray/NMR structures are unavailable with the nitroxide labels, detailed residue level ...
Show more >Nitroxide labels are combined with nucleic acid structures and are studied using electron paramagnetic resonance experiments (EPR). As X-ray/NMR structures are unavailable with the nitroxide labels, detailed residue level information, down to atomic resolution, about the effect of these nitroxide labels on local RNA structures is currently lacking. This information is critical to evaluate the choice of spin label. In this study, we compare and contrast the effect of TEMPO-based (NT) and rigid spin (Ç) labels (in both 2′-O methylated and not-methylated forms) on RNA duplexes. We also investigate sequence- dependent effects of NT label on RNA duplex along with the more complex G-quadruplex RNA. Distances measured from molecular dynamics simulations between the two spin labels are in agreement with the EPR experimental data. To understand the effect of labelled oligonucleotides on the structure, we studied the local base pair geometries and global structure in comparison with the unlabelled structures. Based on the structural analysis, we can conclude that TEMPO-based and Ç labels do not significantly perturb the base pair arrangements of the native oligonucleotide. When experimental structures for the spin labelled DNA/RNA molecules are not available, general framework offered by the current study can be used to provide information critical to the choice of spin labels to facilitate future EPR studies.Show less >

Language :

Anglais

Audience :

Non spécifiée

Popular science :

Non

Administrative institution(s) :

ENSCL
Université de Lille
CNRS

Collections :

• Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516

Research team(s) :

Propriétés magnéto structurales des matériaux (PMSM)

Submission date :

2024-02-21T17:11:56Z
2024-02-27T10:24:50Z