High-Resolution Field-Cycling NMR Studies of A DNA Octamer As A Probe of Phosphodiester Dynamics and Comparison with Computer Simulation

Mary F. Roberts, Qizhi Cui, Christopher J. Turner, David A. Case, Alfred G. Redfield

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40 Scopus citations

Abstract

Phosphorus-spin longitudinal relaxation rates of the DNA duplex octamer [d(GGAATTCC)]2 have been measured from 0.1 to 17.6 T by means of conventional and new field-cycling NMR methods. The high-resolution field-cycling method is identical to a conventional relaxation experiment, except that after preparation the sample is moved pneumatically from its usual position at the center of the high-resolution magnet upward to a lower field above its normal position and then returned to the center for readout after it has relaxed for the programmed relaxation delay at the low field. This is the first measurement of all longitudinal relaxation rates R1 of a nuclear species in a macromolecule over virtually the entire accessible magnetic field range. For detailed analysis, three magnetic field regions can be delineated: (i) dipolar relaxation dominates at fields below 2 T, (ii) chemical shift anisotropy (CSA) relaxation is roughly constant from 2 to 6 T, and (iii) a square-law increasing dependence is seen at fields higher than ∼6 T due to internal motion CSA relaxation. The analysis provides a rotational correlation time (τr = 4.1 ± 0.3 ns) for the duplex at both 1.5 and 0.25 mM concentrations (of duplex) at 22 °C. For comparison, extraction of τr in the conventional way from the ratio of T1/T2 at 14 T yields 3.2 ns. The τ r discrepancy disappears when we exclude the contribution of internal motion from the R1 in the ratio. The low-field dipolar relaxation provides a weighted inverse sixth power sum of the distances from the phosphorus to the protons responsible for relaxation. This average is similar for all phosphates in the octamer and similar to that in previous B-DNA structures (its inverse sixth root is about 2.40 Å for two different concentrations of octamer). The CSA relaxation at intermediate field provides an estimate of the order parameter squared, Sc2, for each phosphorus. Sc2 is about 0.7-1, clearly different for different phosphate linkages in the octamer duplex. The increasing R 1 at high fields reflects CSA relaxation due to internal motions, for which a correlation time, τhf, can be approximately extracted with the aid of additional measurements at 14.0 and 17.6 T. We conclude that τhf values are relatively large, in the range of about 150 ps. Insight into the motions leading to this correlation time was gained by a 28 ns molecular dynamics simulation of the molecule. S2 and τs (corresponding to τhf) predicted by this simulation were in good agreement with the experimental values from the field-cycling data. Both the effect of Mg2+ on the dynamic parameters extracted from 31P relaxation rates and the field dependence of relaxation rates for several protons of the octamer were measured. High-resolution field cycling opens up the possibility of monitoring residue-specific dipolar interactions and dynamics for the phosphorus nuclei of diverse oligonucleotides.

Original languageEnglish (US)
Pages (from-to)3637-3650
Number of pages14
JournalBiochemistry
Volume43
Issue number12
DOIs
StatePublished - Mar 30 2004
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry

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