Structure and dynamics of DNA and RNA oligonucleotides as studied using solution and solid state NMR. [NMR (nuclear magnetic resonance)]
NMR experiments reveal that the base H8/H6 and H1[prime] protons of RNA have T[sub 1] relaxation times that are distinctly longer than those of DNA. NMR and circular dichroism experiments indicate that the segments of RNA maintain their A-form geometry even in the interior of DNA-RNA-DNA chimeric duplexes, suggesting that the relaxation times are correlated with the type of helix topology. Results from solid state [sup 2]H NMR experiments on the purine C-8 deuterium-labeled 12 base pair RNA duplex [r(CG*CG*A*A*UUGG*CG*)][sub 2] were compared with results obtained by other investigators on the 12 base pair DNA duplex [d(CG*CG*A*A*TTCG*CG*)][sub 2]. The motional amplitudes of DNA and RNA purines are similar at 0%-88% RH and their internal rates of motion are different at 0%-80% RH. The assumption that dodecameric oligonucleotides (12-mers) tumble isotropically in solution is often used when calculating proton-proton distances from NOE data. The authors have undertaken the task of testing the isotropic assumption using experimental NMR data. The authors have calculated the structure of [d(GCGTTTAAACGC)][sub 2] using both the isotropic assumption and the assumption that the duplex tumbles anisotropically in solution like a perfect cylinder. The resulting structures from both approaches are virtually indistinguishable. The isotropic assumption is valid for oligonucleotides 12 base pairs and shorter. The solution structure of the 12 base pair hybrid chimeric duplex [r(gcg)d(TATATACGC)][sub 2] has been solved using NMR techniques combined with distance geometry and NOE back-calculation methods. The structure is characterized by a dramatic bend of 52[degrees] in the helix axis. The location of the bend is not at the RNA-DNA step but occurs between the first and second residues of the DNA segment. The center of the DNA TATATA segment has a remarkably narrow minor groove that becomes very wide in the hybrid portions of the duplex.
- Research Organization:
- Washington Univ., Seattle, WA (United States)
- OSTI ID:
- 7296690
- Resource Relation:
- Other Information: Thesis (Ph.D.)
- Country of Publication:
- United States
- Language:
- English
Similar Records
High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions
Solution structure of nucleic acids by nuclear magnetic resonance (NMR) spectroscopy