title: Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns.
abstract: The number of regulatory RNAs with identified non-canonical structures is increasing, and structural transitions often play a role in their biological function. This stimulates interest in internal motions of RNA, which can underlie structural transitions. Heteronuclear NMR relaxation measurements, which are commonly used to study internal motion, only report on local motions of few sites within the molecule. Here we have studied a 27-nt segment of the human hepatitis B virus (HBV) pregenomic RNA, which is essential for viral replication. We combined heteronuclear relaxation with the new off-resonance ROESY technique, which reports on internal motions of H,H contacts. Using off-resonance ROESY, we could for the first time detect motion of through-space H,H contacts, such as in intra-residue base-ribose contacts or inter-nucleotide contacts, both essential for NMR structure determination. Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale. Different patterns of mobility were observed among several mobile nucleotides. The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA's biological function.
authors.affiliation: Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.
authors.forename: Katja
authors.initials: K
authors.lastname: Petzold
authors.forename: Elke
authors.initials: E
authors.lastname: Duchardt
authors.forename: Sara
authors.initials: S
authors.lastname: Flodell
authors.forename: Göran
authors.initials: G
authors.lastname: Larsson
authors.forename: Karin
authors.initials: K
authors.lastname: Kidd-Ljunggren
authors.forename: Sybren
authors.initials: S
authors.lastname: Wijmenga
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schleucher
mesh_terms: D001483:Base Sequence; D006515:Hepatitis B virus / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D022661:RNA, Untranslated / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D014779:Virus Replication
chemical_list: D022661:RNA, Untranslated; D012367:RNA, Viral