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(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 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.
Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Kari
K
Pederson
Gary A
GA
Meints
Zahra
Z
Shajani
Paul A
PA
Miller
Gary P
GP
Drobny
D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D019175:DNA Methylation; D015257:DNA-Cytosine Methylases / Q000737:chemistry* / Q000378:metabolism*; D003903:Deuterium; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D013816:Thermodynamics
D009841:Oligonucleotides; D004247:DNA; D003903:Deuterium; C037664:DNA modification methylase HhaI; D015257:DNA-Cytosine Methylases