Solid-state nuclear magnetic resonance spectroscopy studies of furanose ring dynamics in the DNA HhaI binding site.
The dynamics of the furanose rings in the GCGC 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 by using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs selectively deuterated on the furanose rings of nucleotides within the 5'-GCGC-3' moiety indicated that all of these positions are structurally flexible. The furanose ring within the deoxycytidine that is the methylation target displays the largest-amplitude structural changes according to the observed deuterium NMR line shapes, whereas the furanose rings of nucleotides more remote from the methylation site have less-mobile furanose rings (i.e., with puckering amplitudes < 0.3 A). Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through the furanose ring. These NMR data indicate that the 5'-GCGC-3' is dynamic, with the largest-amplitude motions occurring nearest the methylation site. The inherent flexibility of this moiety in DNA makes the molecule more amenable to the large-amplitude structural rearrangements that must occur when the DNA binds to the HhaI methyltransferase.
Meints
Gary A
GA
Department of Chemistry, Missouri State University, Springfield, Missouri 65897, and Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Miller
Paul A
PA
Pederson
Kari
K
Shajani
Zahra
Z
Drobny
Gary
G
D001665:Binding Sites; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D019175:DNA Methylation; D003841:Deoxycytidine / Q000737:chemistry; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism; D003903:Deuterium / Q000737:chemistry; D005663:Furans / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D009705:Nucleosides / Q000737:chemistry
D005663:Furans; D009705:Nucleosides; D003841:Deoxycytidine; D004247:DNA; D003903:Deuterium; D015252:Deoxyribonucleases, Type II Site-Specific; C037130:GCGC-specific type II deoxyribonucleases