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Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns.

Petzold, Katja; Duchardt, Elke; Flodell, Sara; Larsson, Göran; Kidd-Ljunggren, Karin LU ; Wijmenga, Sybren and Schleucher, Jürgen (2007) In Nucleic Acids Research 35(20). p.6854-6861
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... (More)
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. (Less)
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Contribution to journal
publication status
published
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in
Nucleic Acids Research
volume
35
issue
20
pages
6854 - 6861
publisher
Oxford University Press
external identifiers
  • wos:000251336000020
  • scopus:36749029316
ISSN
1362-4962
DOI
10.1093/nar/gkm774
language
English
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yes
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b37023be-2344-44be-ac01-bb9627f599ed (old id 608630)
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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=17933777&dopt=Abstract
date added to LUP
2008-07-31 13:06:17
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2017-01-01 04:42:47
@article{b37023be-2344-44be-ac01-bb9627f599ed,
  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.},
  author       = {Petzold, Katja and Duchardt, Elke and Flodell, Sara and Larsson, Göran and Kidd-Ljunggren, Karin and Wijmenga, Sybren and Schleucher, Jürgen},
  issn         = {1362-4962},
  language     = {eng},
  number       = {20},
  pages        = {6854--6861},
  publisher    = {Oxford University Press},
  series       = {Nucleic Acids Research},
  title        = {Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns.},
  url          = {http://dx.doi.org/10.1093/nar/gkm774},
  volume       = {35},
  year         = {2007},
}