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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2007 35(20):6854-6861; doi:10.1093/nar/gkm774
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Nucleic Acids Research, 2007, Vol. 35, No. 20 6854-6861
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

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

Katja Petzold1, Elke Duchardt1, Sara Flodell1, Göran Larsson1, Karin Kidd-Ljunggren2, Sybren Wijmenga3 and Jürgen Schleucher1,*

1Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, 2Department of Infectious Diseases, Lund University, SE-221 85 Lund, Sweden and 3Department of Biophysical Chemistry, Radboud University Nijmegen, Toernooiveld 1, 6225ED Nijmegen, The Netherlands

* To whom correspondence should be addressed. Tel: +46-90-7865388; Fax: +46-90-7869795; Email: jurgen.schleucher{at}chem.umu.se

Received June 14, 2007. Revised September 17, 2007. Accepted September 17, 2007.

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.


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