title: NMR structure of a bacteriophage T4 RNA hairpin involved in translational repression.
abstract: A high-resolution structure of a 16-nucleotide bacteriophage T4 RNA hairpin, 5'-GCCU[AAUAACUC]GGGC (loop bases in square brackets), has been determined in solution by proton, phosphorus, and carbon (natural abundance) NMR spectroscopy. This RNA hairpin is known to play a crucial role in the translational repression of bacteriophage T4 DNA polymerase. Ultraviolet absorbance melting curves indicate that the structure formed is unimolecular. The NMR spectra indicate that a single conformation consistent with a hairpin structure is formed. Strong imino-imino NOEs confirm the formation of the G.U base pair at the stem-loop junction. There is no evidence that A5 is protonated (at pH 6.0) and involved in an A+.C pair. However, the NMR data indicate that the stem is extended beyond the G.U pair and that A-form stacking continues for three nucleotides on the 5' side and one nucleotide on the 3' side. Structure calculations using restraints obtained from NMR data give a precisely defined structure with an average root mean square deviation (RMSD) of approximately 1.2 A for the entire molecule. The assignment of all the protons and most of the 31P resonances in the loop yielded a large number of distance and torsion angle restraints for these nucleotides. These helped obtain a well-defined loop with an average RMSD of 1.1 A for the loop nucleotides of 11 converged structures.
authors.affiliation: Department of Chemistry, University of California, Berkeley, USA.
authors.forename: S R
authors.initials: SR
authors.lastname: Mirmira
authors.forename: I
authors.initials: I
authors.lastname: Tinoco
mesh_terms: D017122:Bacteriophage T4 / Q000378:metabolism; D001483:Base Sequence; D016384:Consensus Sequence; D006860:Hydrogen Bonding; D007202:Indicators and Reagents; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D010758:Phosphorus; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D007202:Indicators and Reagents; D009843:Oligoribonucleotides; D012367:RNA, Viral; D010758:Phosphorus