The catalytic domain of human hepatitis delta virus RNA. A proton nuclear magnetic resonance study.
We have obtained and analyzed the 600 MHz proton NMR spectra of a 74-mer RNA derived from the catalytic domain of hepatitis delta virus genomic RNA (HDV RNA) to determine its secondary structure. Deconvolution of the NMR spectrum obtained at 32 degrees C indicates that part of the 74-mer RNA molecule may exist in multiple conformations in equilibrium. The major conformer contains two A-U base pairs and 14 +/- 2 G-C base pairs. It appears to contain no standard G-U base pairs. Our NMR melting study suggests that this conformer has at least two stem-loop regions. One of the regions has been identified to be a tetra-loop. We have assigned five imino proton resonances of the tetra-loop stem. Our data is consistent with the pseudoknot model of Perrotta and Been.
Lee
B S
BS
Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan, ROC.
Wu
H N
HN
Huang
T H
TH
D001483:Base Sequence; D003698:Hepatitis Delta Virus / Q000737:chemistry*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D016337:RNA, Catalytic / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry / Q000648:ultrastructure*
D016337:RNA, Catalytic; D012367:RNA, Viral