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 (5'-GGUC-3')(3'-CUGG-5), 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 (5'GGUC-3')(3'-CTGG-5'), 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.