Kari Pederson - Backbone Dynamics in the DNA HhaI Protein Binding Site

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      Publication Details (including relevant citation   information):

      Pederson, K.; Meints, G. A.; Shajani, Z.; Miller, P.; Drobny, G.   P. J. Am. Chem. Soc. 2008, 130, 9072-9079.

      Abstract:

      The dynamics of the phosphodiester backbone in the   [5′-GCGC-3′]2 moiety of the DNA oligomer   [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2  are studied using deuterium solid-state NMR (SSNMR).  SSNMR   spectra obtained from DNAs selectively 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   makes the molecule less amenable to binding to the HhaI   endonuclease.

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