Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings
Language English Country Netherlands Media print
Document type Journal Article, Research Support, Non-U.S. Gov't
- MeSH
- DNA, Single-Stranded chemistry genetics MeSH
- Nucleic Acid Conformation * MeSH
- Magnetic Resonance Spectroscopy methods MeSH
- Models, Molecular MeSH
- Carbohydrates chemistry MeSH
- Base Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- DNA, Single-Stranded MeSH
- Carbohydrates MeSH
The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.
References provided by Crossref.org
Experiments for correlating quaternary carbons in RNA bases
DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum
Program MULDER -- a tool for extracting torsion angles from NMR data
