Backbone dynamics in the DNA HhaI protein binding site
The dynamics of the phosphodiester backbone in the [5′-GCGC-3′] 2 moiety of the DNA oligomer [d(G1A2T 3A4G5C6G7C 8T9A10T11C12)] 2 are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs nonstereospecifically deuterated on the 5′ methylene group of nucleotides within the [5′-GCGC-3′]2 moiety indicated that all of these positions are structurally flexible. Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone and furanose ring of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through not only a loss of mobility but also a change of direction of motion. These NMR data indicate that the [5′-GCGC-3′]2 moiety is dynamic, with the largest amplitude motions occurring nearest the methylation site. The change of orientation of this moiety in DNA upon methylation may make the molecule less amenable to binding to the HhaI endonuclease.
Pederson, Kari, Gary A. Meints, Zahra Shajani, Paul A. Miller, and Gary P. Drobny. "Backbone Dynamics in the DNA Hha I Protein Binding Site." Journal of the American Chemical Society 130, no. 28 (2008): 9072-9079.
Journal of the American Chemical Society