title: Solution structure of the donor site of a trans-splicing RNA.
abstract: BACKGROUND
  RNA splicing is both ubiquitous and essential for the maturation of precursor mRNA molecules in eukaryotes. The process of trans-splicing involves the transfer of a short spliced leader (SL) RNA sequence to a consensus acceptor site on a separate pre-mRNA transcript. In Caenorhabditis elegans, a majority of pre-mRNA transcripts receive the 22-nucleotide SL from the SL1 RNA. Very little is known about the various roles that RNA structures play in the complex conformational rearrangements and reactions involved in premRNA splicing.
  
  
  RESULTS
  We have determined the solution structure of a domain of the first stem loop of the SL1 RNA of C. elegans, using homonuclear and heteronuclear NMR techniques; this domain contains the splice-donor site and a nine-nucleotide hairpin loop. In solution, the SL1 RNA fragment adopts a stem-loop structure: nucleotides in the stem region form a classical A-type helix while nucleotides in the hairpin loop specify a novel conformation that includes a helix, that extends for the first three residues; a syn guanosine nucleotide at the turn region; and an extrahelical adenine that defines a pocket with nucleotides at the base of the loop.
  
  
  CONCLUSIONS
  The proximity of this pocket to the splice donor site, combined with the observation that the nucleotides in this motif are conserved among all nematode SL RNAs, suggests that this pocket may provide a recognition site for a protein or RNA molecule in the trans-splicing process.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA. greenbau@cuhhca.hhmi.columbia.edu
authors.forename: N L
authors.initials: NL
authors.lastname: Greenbaum
authors.forename: I
authors.initials: I
authors.lastname: Radhakrishnan
authors.forename: D J
authors.initials: DJ
authors.lastname: Patel
authors.forename: D
authors.initials: D
authors.lastname: Hirsh
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000378:metabolism*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012322:RNA Precursors / Q000378:metabolism*; D012326:RNA Splicing / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D012322:RNA Precursors; D012313:RNA