Structure determination of a DNA octamer in solution by NMR spectroscopy. Effect of fast local motions

Journal Article · Tue Apr 16 04:00:00 EDT 1991 · Biochemistry; (United States)

DOI:https://doi.org/10.1021/bi00229a028· OSTI ID:5595043

Koning, T M.G.; Boelens, R; Kaptein, R ^[1]; van der Marel, G A; van Boom, J H ^[2]

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1. Univ. of Utrecht (Netherlands)
2. 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), Journal Name: Biochemistry; (United States) Vol. 30:15; ISSN 0006-2960; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550601* -- Medicine-- Unsealed Radionuclides in Diagnostics
62 RADIOLOGY AND NUCLEAR MEDICINE
BARYONS
DNA
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC RESONANCE
MOLECULAR STRUCTURE
NMR SPECTRA
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
OLIGONUCLEOTIDES
ORGANIC COMPOUNDS
OVERHAUSER EFFECT
PROTONS
RESONANCE
SPECTRA