title: The 5' stem-loop from human U4 snRNA adopts a novel conformation stabilized by G-C and G-U base pairs.
abstract: 1H NMR and molecular modeling studies of the 5' stem-loop from human U4 snRNA were undertaken to determine the conformation of this stem-loop that is essential for spliceosome formation and pre-mRNA splicing. Sixteen of the 35 nucleotides of this stem-loop are in the loop region and inspection of the loop sequence revealed no decomposition into elements of secondary structure commonly found in other RNA stem-loops. An analysis of possible base pairing interactions for this stem-loop using the methods of Zuker revealed the lowest energy secondary structure for the 16 nucleotide loop consisted of four base pairs at the base of a non-canonical tetraloop (UUUA). This shorter stem-loop was joined to the nine base pair stem by two A residues on the 5' side and a single bulged A on the 3' side. Both stems also had bulged A residues. 1H NMR experiments performed on solutions of the 35 mer stem-loop, the stem region, and the loop region confirmed the 35 mer adopted this secondary structure in solution. A 3D molecular model of this structure consistent with the NMR data was generated to assist in visualization of this novel structure.
authors.affiliation: Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha 68198-6805, USA.
authors.forename: P V
authors.initials: PV
authors.lastname: Sahasrabudhe
authors.forename: J
authors.initials: J
authors.lastname: Sun
authors.forename: W H
authors.initials: WH
authors.lastname: Gmeiner
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D003596:Cytosine; D006147:Guanine; D006801:Humans; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000737:chemistry; D012342:RNA, Small Nuclear / Q000737:chemistry*; D013816:Thermodynamics; D014498:Uracil
chemical_list: D009843:Oligoribonucleotides; D012342:RNA, Small Nuclear; D014498:Uracil; D006147:Guanine; D003596:Cytosine