The secondary structure of a fourteen-nucleotide fragment of the hairpin ribozyme.
A fourteen nucleotide RNA has been synthesized and its secondary structure investigated by non-denaturing polyacrylamide gel electrophoresis and 1H nuclear magnetic resonance spectroscopy. This fourteen nucleotide RNA corresponds to the hairpin loop end of the proposed secondary structure of the (-)sTRSV hairpin ribozyme. Non-denaturing polyacrylamide gel electrophoresis indicates that the fourteen nucleotide RNA exists predominantly as a monomer at a 1 mM strand concentration. Four peaks are found in the imino hydrogen region of the 1H NMR spectrum of the fourteen nucleotide RNA at this concentration. One-dimensional nuclear Overhauser effect spectroscopy of the imino hydrogen region of the 1H NMR spectrum gives results consistent with a model of the secondary structure of the fourteen nucleotide RNA having a three nucleotide hairpin loop and two double-stranded stems separated by a single bulged adenosine.
Brinegar
J D
JD
Department of Biochemistry and Molecular Biology, Kettering Medical Center, Wright State University, Dayton, Ohio 45435, USA.
Hampel
A
A
Alter
G M
GM
Cruz
P
P
D001482:Base Composition; D001483:Base Sequence; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D017860:Nepovirus / Q000737:chemistry / Q000235:genetics; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry*
D016337:RNA, Catalytic