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 A 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.
Anderson
A C
AC
Committee on Biophysics, Harvard University and Dana-Farber Cancer Institute, 44 Binney Street, S1036, Boston, Massachusetts 02115, USA.
O'Neil
R H
RH
Filman
D J
DJ
Frederick
C A
CA
D020137:Base Pair Mismatch; D001483:Base Sequence; D001966:Bromine / Q000737:chemistry*; D018360:Crystallography, X-Ray; D017931:DNA Primers; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
D017931:DNA Primers; D012313:RNA; D001966:Bromine