Dynamics and ordering in a spin-labeled oligonucleotide observed by 220 GHz electron paramagnetic resonance

Area of Science:

• Biophysics
• Chemical Physics
• Molecular Biology

Background:

• Electron paramagnetic resonance (EPR) is a spectroscopic technique used to study materials with unpaired electrons.
• Spin-labeling involves attaching a paramagnetic molecule to a target molecule to study its structure and dynamics.
• Understanding local motions in DNA is crucial for various biological processes.

Purpose of the Study:

• To investigate the dynamics of a newly synthesized cytosine spin-label and a spin-labeled DNA pentamer using high-frequency EPR.
• To differentiate between local and global motions in spin-labeled macromolecules.
• To explore the utility of high-field EPR in studying DNA dynamics.

Main Methods:

• High-frequency (220 GHz) electron paramagnetic resonance (EPR) spectroscopy.
• Spin-labeling of a cytosine monomer and a TTC*TT pentamer.
• Temperature-dependent studies in aqueous buffer with glycerol.
• Analysis using models of fully anisotropic rotation (FAR) and microscopic ordering with macroscopic disorder (MOMD).

Main Results:

• The dynamics of the spin-labeled monomer were well-described by the fully anisotropic rotation (FAR) model.
• High-field EPR spectra of the pentamer were best interpreted using the microscopic ordering with macroscopic disorder (MOMD) model.
• Local order parameters (0.60-0.70) suggest a micelle-like structure for the label within the pentamer.
• High-field EPR demonstrated excellent orientation selectivity, providing insights into local base motions.

Conclusions:

• High-frequency EPR of spin-labels provides new dynamic information about local base motions in DNA.
• This technique allows accurate discrimination between local and global motions in spin-labeled macromolecules.
• The findings suggest potential micelle-like structures formed by hydrophobic bases interacting with the spin-label.