Structure determination of a DNA octamer in solution by NMR spectroscopy. Effect of fast local motions
- Univ. of Utrecht (Netherlands)
- State Univ. of Leiden (Netherlands)
NMR structures of biomolecules are primarily based on nuclear Overhauser effects (NOEs) between protons. For the interpretation of NOEs in terms of distances, usually the assumption of a single rotational correlation time corresponding to a rigid molecule approximation is made. Here the authors investigate the effect of fast internal motions of the interproton vectors in the context of the relaxation matrix approach for structure determination of biomolecules. From molecular dynamics simulations generalized order parameters were calculated for the DNA octamer d(GCGTTCGC){center dot}d(CGCAACGC), and these were used in the calculation of NOE intensities. The magnitudes of the order parameters showed some variation for the different types of interproton vectors. The interproton distances changed only slightly, with a maximum of 10%; nevertheless, the changes were significant and resulted in constraints that were better satisfied. The structure of the DNA octamer was determined by using restrained molecular dynamics simulations with H{sub 2}O as a solvent, with and without the inclusion of local internal motions. Starting from A- or B-DNA, the structures showed a high local convergence, while the global convergence for the octamer was ca. 2.6 {angstrom}.
- OSTI ID:
- 5595043
- Journal Information:
- Biochemistry; (United States), Vol. 30:15; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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OLIGONUCLEOTIDES
NUCLEAR MAGNETIC RESONANCE
DNA
MOLECULAR STRUCTURE
NMR SPECTRA
OVERHAUSER EFFECT
PROTONS
BARYONS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
ORGANIC COMPOUNDS
RESONANCE
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