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The dynamics of the phosphodiester backbone in the [5'-GCGC-3'][sub2] moiety of the DNA oligomer [d(G[sub1]A[sub2]T[sub3]A[sub4]G̱[sub5]C̱[sub6]G̱[sub7]C̱[sub8]T[sub9]A[sub10]T[sub11]C[sub12])][sub2] are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs nonstereospecifically deuterated on the 5' methylene group of nudleotides within the [5'-GCGC-3'][sub2] 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'][sub2] 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 Hhal endonuclease. [ABSTRACT FROM AUTHOR]

The dynamics of the furanose rings in the GCGC moiety of the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]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 Å). 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 Hhal methyltransferase. [ABSTRACT FROM AUTHOR]