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Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Backbone dynamics in the DNA HhaI protein binding site
Kari Pederson1, Gary A Meints, Zahra Shajani
1Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Journal of the American Chemical Society
|June 24, 2008
Summary
Deuterium solid-state NMR reveals DNA backbone flexibility. Methylation alters DNA dynamics, reducing mobility and changing motion direction, potentially affecting enzyme binding.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- The DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 contains a [5'-GCGC-3']2 moiety.
- Previous studies indicated that methylation impacts DNA backbone and furanose ring dynamics.
Purpose of the Study:
- To investigate the dynamics of the phosphodiester backbone in the [5'-GCGC-3']2 moiety of a specific DNA oligomer.
- To understand how methylation affects DNA backbone dynamics and its implications for enzyme interactions.
Main Methods:
- Deuterium solid-state Nuclear Magnetic Resonance (SSNMR) spectroscopy was employed.
- DNA was nonstereospecifically deuterated at the 5' methylene group of nucleotides within the [5'-GCGC-3']2 moiety.
Main Results:
- SSNMR spectra demonstrated significant structural flexibility at all studied positions of the [5'-GCGC-3']2 moiety.
- Methylation was observed to reduce backbone mobility and alter the direction of motion.
- The largest amplitude motions were localized nearest to the methylation site.
Conclusions:
- The [5'-GCGC-3']2 moiety in the DNA oligomer exhibits dynamic behavior.
- Methylation perturbs DNA backbone dynamics by decreasing mobility and changing motion orientation.
- Altered DNA dynamics due to methylation may reduce the affinity for HhaI endonuclease binding.
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