A Solid-State Deuterium NMR Study of the Localized Dynamics at the C9pG10 Step in the DNA Dodecamer [d(CGCGAATTCGCG)]₂

Abstract

A solid-state deuterium NMR study of localized mobility at the C9pG10 step in the DNA dodecamer [d(CGCGAATTCGCG)]2 is described. In contrast to the results of earlier deuterium NMR studies of furanose ring and backbone dynamics within the d(AATT) moiety, the furanose ring and helix backbone of dC9 display large amplitudes of motion on the 0.1 ms time scale at hydration levels characteristic of the B form structure. Solid-state deuterium NMR line shape data obtained from labeled dC9 DNA are interpreted using a composite motion model, in which the DNA oligomer is treated as rotating as a whole about the helix axis, while the base, furanose ring, and phosphodiester backbone execute localized motions. Consistent with past solid-state NMR studies, the amplitude and rate of the uniform rotation of the dC9-labeled oligomer are found to be sensitive to hydration level. Amplitudes of localized reorientational motions of C−D bonds in the furanose ring and backbone of dC9 are found to be larger than the librational amplitudes for the C−D bonds in the base of dC9, indicating that the pyrimidine base sugar does not move as a rigid entity and intersects a locally flexible region of the phosphodiester backbone. At hydration levels corresponding to 10−12 waters per nucleotide, Zeeman relaxation times for the furanose ring and backbone deuterons of dC9 in B form DNA equal 0.025 and 0.03 ms, respectively, and are the shortest relaxation times observed thus far for any deuteron in the DNA dodecamer at comparable hydration levels. The results of this solid-state NMR study suggest the existence of a significant dynamic component of sequence-specific recognition in this system.

Conformational dynamics of an intact virus: Order parameters for the coat protein of Pf1 bacteriophage

“…We presume that the observed large-amplitude submicrosecond dynamics occur within a highly hydrated interior of the virus (39). To estimate the hydration of a cavity around the viral DNA, we used the coordinates of 1PFI, the only available Pf1 model with DNA coordinates, to calculate the possible number of explicit water molecules within the volume defined by the unison of all spheres with radius of 8 Å from each atom of the DNA by using GROMACS (40).…”

“…For instance, solid-state studies of a hydrated, Watson-Crick basepaired DNA molecule show considerable submicrosecond dynamics in the backbone and the deoxyribose ring (39,42). By comparison, an extended DNA in Pf1 with bases directed outward toward the capsid (11,15) may have additional dynamic modes or different amplitudes in the normal modes, such as greater torsional motion about the N-glycosidic bonds (43).…”

Simulations of molecular dynamics in solid-state NMR spectra of spin-1 nuclei including effects of CSA- and EFG-terms up to second order

“…In this context methods for determination of 2 H dynamics have been of particular significance with a broad range of applications ranging from studies of glass formers [1], small molecules in larger host matrices [2][3][4], ionic rotors [5], selectively deuterated sites [6,7] or functional groups in macromolecules [8,9].…”

Preparation of Base-Deuterated 2?-Deoxyadenosine Nucleosides and Their Site-Specific Incorporation Into Dna

“…Therefore, structural information about ground states needs to be augmented with knowledge about the movements of functionally important residues. Solid state deuterium NMR is a valuable tool to study motions of specific sites in nucleic acids [1][2][3] . *Corresponding author.…”

“…For example, solid state deuterium NMR was used to detect large amplitude motions in the sugar-phosphate backbone at the GC-AT duplex junction of the EcoR1 restriction site 5 0 -d(CGAATTCG) 2 , precisely where this enzyme cuts 3 . This cleavage reaction can be suppressed by base-methylation at position 5 of 2 0 -deoxycytidine (dC) and interestingly, the methylation reduces the amplitudes of motion of the sugar-phosphate backbone 3 .…”