Solid-State Nuclear Magnetic Resonance Spectroscopy Studies of Furanose Ring Dynamics in the DNA HhaI Binding Site

Abstract

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.

Static solid-state 2H NMR methods in studies of protein side-chain dynamics

“…In this example and its extension for the protein system,(29) the square potential form was used and was clearly a better fit compared with the Gaussian potential. An interesting example of the sensitivity of biomolecular systems to the form of the potential function is presented in Meints et al(72). …”

Effects of jump dynamics on solid state nuclear magnetic resonance line shapes and spin relaxation times

“…However, the number of adjustable parameters is still uncomfortably large, especially for models of small angle motion along a multi-dimensional angular trajectory. An excellent example of one way to proceed in this commonly occurring situation has recently been described by Meints et al [61], who used the procedure of Nadler and Shulten [62] to make a discrete, tri-diagonal approximation to the Smoluchkowski operator for rotational diffusion subject to a multi-dimensional potential energy function. A different option, perhaps more appropriate for disordered systems, is described in Section 4.…”

Solid State 2H NMR Analysis of Furanose Ring Dynamics in DNA Containing Uracil

“…The fundamental theoretical relationships used to interpret the spectroscopic data describing the internal motions of DNA subunits — in particular the furanose ring — have been described 23,34. A dynamically modulated deuterium NMR line shape is obtained via a quadrupolar echo experiment [( π /2) x – τ – ( π /2) y – τ – acq)].…”

“…The model can be generalized to include the reorientation of the C– 2 H bond 23,24,34. For each value of pseudorotation phase angle ϕ , there corresponds a set of angles ( Θ PC , ϕ PC ) specifying the orientation of a C2′– 2 H2″ bond relative to a coordinate system fixed to the framework of the planar furanose ring.…”