Crystal structure of a brominated RNA helix with four mismatched base pairs: An investigation into RNA conformational variability

The X-ray crystal structure of a brominated RNA helix with four mismatched base pairs and sequence r(UG(Br)C(Br)CAGUUCGCUGGC)(2) was determined to 2.1 Angstrom using the methods of multiwavelength anomalous diffraction (MAD) applied to the bromine K-absorption edge. There are three molecules in the asymmetric unit with unique crystal-packing environments, revealing true co nformational variability at high resolution for this sequence. The structur e shows that the sequence itself does not define a consistent pattern of so lvent molecules, with the exception of the mismatched base pairs, implying that specific RNA-protein interactions would occur only with the nucleotide s. There are a number of significant tertiary interactions, some of which a re a result of the brominated base pairs and others that are directly media ted by the RNA 2' hydroxyl groups. The mismatched base pairs exhibit a solv ent network as well as a stacking pattern with their nearest neighbors that validate previous thermodynamic analysis.