Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing.
The duplex (rGAGGUCUC)2 contains the motif [sequence: see text] which is unusually stable compared with other symmetric tandem GU mismatches and occurs in the P5 helix of the group I intron of Tetrahymena thermophila. The three-dimensional solution structure of (rGAGGUCUC)2 was determined using two-dimensional NMR and a simulated annealing protocol. The structure is remarkably similar to the A-DNA crystal structure of (dGGGGTCCC)2 [Kneale, G., Brown, T., & Kennard, O. (1985) J. Mol. Biol. 186, 805-814] which contains the analogous motif [sequence: see text]. Incorporation of the [sequence: see text] motif has little effect on backbone torsion angles and helical parameters compared with standard A-form. The only significant departure from A-form is a slight overtwisting 5' of the G in the GU mismatch and a displacement of the mismatches toward the minor groove. Inspection of stacking patterns of this structure and comparison with symmetric tandem GT mismatches in A-DNA oligonucleotides from crystal structure data suggest that electrostatics are important in determining motif stability.
McDowell
J A
JA
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
Turner
D H
DH
D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry*; D013816:Thermodynamics
D009841:Oligonucleotides