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Nucleic Acids Research Advance Access published online on April 11, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm131
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© 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

Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals

Frederic C. Girard, Otmar M. Ottink, Kirsten A.M. Ampt, Marco Tessari and Sybren S. Wijmenga*

Department of Physical Chemistry/Biophysical Chemistry, Radboud University, Toernooiveld 1 6525 ED Nijmegen, The Netherlands

*To whom correspondence should be addressed. Tel: +31 24 3653384/2678; Fax: +31 24 3652112; Email: s.wijmenga{at}nmr.ru.nl

Received January 15, 2007. Revised February 19, 2007. Accepted February 19, 2007.

Hepatitis B virus (HBV) replication is initiated by binding of its reverse transcriptase (P) to the apical stem-loop (AL) and primer loop (PL) of epsilon, a highly conserved RNA element at the 5'-end of the RNA pregenome. Mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their P–epsilon interaction. Here, NMR and UV thermodynamic data on AL (and PL) from these three species are presented. The stabilities of the duck and heron ALs were found to be similar, and much lower than that of human. NMR data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron AL. In duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 35°C well below the overall AL melting temperature. Surprisingly, the duck- and heron ALs were both found to be capped by a stable well-structured UGUU tetraloop. All avian ALs are expected to adhere to this because of their conserved sequence. Duck PL is stable and structured and, in view of sequence similarities, the same is expected for heron - and human PL.


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