Solution Structure of Poly(UG) RNA. J Mol Biol 2023 Dec 15;435(24):168340
Date
11/05/2023Pubmed ID
37924862Pubmed Central ID
PMC10841838DOI
10.1016/j.jmb.2023.168340Scopus ID
2-s2.0-85176335943 (requires institutional sign-in at Scopus site) 8 CitationsAbstract
Poly(UG) or "pUG" RNAs are UG or GU dinucleotide repeat sequences which are highly abundant in eukaryotes. Post-transcriptional addition of pUGs to RNA 3' ends marks mRNAs as vectors for gene silencing in C. elegans. We previously determined the crystal structure of pUG RNA bound to the ligand N-methyl mesoporphyrin IX (NMM), but the structure of free pUG RNA is unknown. Here we report the solution structure of the free pUG RNA (GU)12, as determined by nuclear magnetic resonance spectroscopy and small and wide-angle x-ray scattering (NMR-SAXS-WAXS). The low complexity sequence and 4-fold symmetry of the structure result in overlapped NMR signals that complicate chemical shift assignment. We therefore utilized single site-specific deoxyribose modifications which did not perturb the structure and introduced well-resolved methylene signals that are easily identified in NMR spectra. The solution structure ensemble has a root mean squared deviation (RMSD) of 0.62 Å and is a compact, left-handed quadruplex with a Z-form backbone, or "pUG fold." Overall, the structure agrees with the crystal structure of (GU)12 bound to NMM, indicating the pUG fold is unaltered by docking of the NMM ligand. The solution structure reveals conformational details that could not be resolved by x-ray crystallography, which explain how the pUG fold can form within longer RNAs.
Author List
Escobar CA, Petersen RJ, Tonelli M, Fan L, Henzler-Wildman KA, Butcher SEAuthor
Riley J. Petersen PhD, BA Postdoctoral Researcher in the Biophysics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AnimalsCaenorhabditis elegans
Crystallography, X-Ray
Ligands
Models, Molecular
Nucleic Acid Conformation
Poly G
Poly U
RNA
Scattering, Small Angle
X-Ray Diffraction
