Crystal Structure of a Brominated RNA Helix with Four Mismatched Base Pairs: An Investigation into RNA Conformational Variability

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Abstract
The X-ray crystal structure of a brominated RNA helix with four mismatched base pairs and sequence r(UGBrCBrCAGUUCGCUGGC)2 was determined to 2.1 Å 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 conformational variability at high resolution for this sequence. The structure shows that the sequence itself does not define a consistent pattern of solvent molecules, with the exception of the mismatched base pairs, implying that specific RNA−protein interactions would occur only with the nucleotides. There are a number of significant tertiary interactions, some of which are a result of the brominated base pairs and others that are directly mediated by the RNA 2‘ hydroxyl groups. The mismatched base pairs exhibit a solvent network as well as a stacking pattern with their nearest neighbors that validate previous thermodynamic analysis.