Two RNA duplexes, 5'(GAUCACCUG)/ 3'(CUUGUGGAC) and 5'(GACCUAUCG)/ 3'(CUGGAUUGC), were previously characterized thermodynamically.  Both duplexes contain the same 5'(AUC)/3'(GUU) motif; however, the mismatch contribution at the 5'-shifted position is 0.85 kcal/mol more stable than the 3'-shifted position.  In order to determine if a structural difference is responsible for this stability difference, both duplexes were studied by 2D NMR.  The NMR data suggests that the duplex containing the 5'-shifted mismatch adopts a standard A-form conformation that is not significantly dynamic.  The duplex containing the 3'-shifted mismatch also adopts a standard A-form conformation; however, missing cross-peaks suggest that the structure is dynamic.  The resulting NMR-derived distance restraints were utilized with molecular dynamics and energy minimization in order to generate three-dimensional structures consistent with the NMR data.  The two structures are being compared to determine if the structural features are consistent with the thermodynamic results.

NMR structures of U-U mismatches in RNA

246th National Meeting (2013)

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