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15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
Published on: April 19, 2021
Rotational diffusion tensor of nucleic acids from 13C NMR relaxation
Jerome Boisbouvier1, Zhengrong Wu, Arika Ono
1Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A.
Journal of Biomolecular NMR
|August 13, 2003
Summary
This study reveals DNA dodecamer rotational diffusion using carbon-13 measurements. Solution NMR structures accurately reflect DNA dynamics, unlike crystal structures, providing insights into molecular motion.
Area of Science:
- Biophysical Chemistry
- Structural Biology
- Nuclear Magnetic Resonance (NMR) Spectroscopy
Background:
- Understanding DNA dynamics is crucial for molecular biology.
- Rotational diffusion provides insights into DNA structural flexibility and interactions.
- Previous studies often relied on static structural models, potentially missing dynamic aspects.
Purpose of the Study:
- To determine the rotational diffusion properties of the DNA dodecamer d(CGCGAATTCGCG)(2).
- To compare the accuracy of crystal versus solution NMR structures in reflecting DNA dynamics.
- To establish a reliable model for DNA rotational dynamics.
Main Methods:
- Utilized carbon-13 (13C) R(1rho) and R(1) relaxation measurements on specific carbon atoms (C(1'), C(3'), C(4')).
- Analyzed data from uniformly 13C-enriched DNA samples.
- Applied an axially symmetric rotational diffusion model to interpret relaxation data.
Main Results:
- R(1rho)/R(1) ratios showed poor agreement with crystal structures but good agreement with a solution NMR structure.
- Determined a diffusion anisotropy (D(\|)/D(perpendicular)) of 2.1+/-0.4.
- Calculated an overall rotational correlation time of 3.35 ns at 35°C in D(2)O.
Conclusions:
- Solution NMR structures better represent DNA dodecamer dynamics than crystal structures.
- The derived rotational diffusion parameters align well with hydrodynamic modeling predictions.
- This work highlights the sensitivity of NMR relaxation measurements to subtle structural differences and DNA dynamics.
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