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Nucleic Acids Research Advance Access published online on October 7, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp779
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Interaction of the HIV-1 frameshift signal with the ribosome

Marie-Hélène Mazauric1, Yeonee Seol2, Satoko Yoshizawa1, Koen Visscher2,* and Dominique Fourmy1,*

1Laboratoire de Chimie et Biologie Structurales, FRC 3115 ICSN-CNRS 1 ave de la terrasse, 91190 Gif-sur-Yvette, France and 2Department of Physics, University of Arizona, AZ 85721, USA

*To whom correspondence should be addressed. Tel: 33 1 69 82 37 76; Fax: 33 1 69 82 37 84; Email: dominique.fourmy{at}icsn.cnrs-gif.fr Correspondence may also be addressed to Koen Visscher. Email: visscher{at}physics.arizona.edu

Received March 14, 2009. Revised September 1, 2009. Accepted September 2, 2009.

Ribosomal frameshifting on viral RNAs relies on the mechanical properties of structural elements, often pseudoknots and more rarely stem-loops, that are unfolded by the ribosome during translation. In human immunodeficiency virus (HIV)-1 type B a long hairpin containing a three-nucleotide bulge is responsible for efficient frameshifting. This three-nucleotide bulge separates the hairpin in two domains: an unstable lower stem followed by a GC-rich upper stem. Toeprinting and chemical probing assays suggest that a hairpin-like structure is retained when ribosomes, initially bound at the slippery sequence, were allowed multiple EF-G catalyzed translocation cycles. However, while the upper stem remains intact the lower stem readily melts. After the first, and single step of translocation of deacylated tRNA to the 30 S P site, movement of the mRNA stem-loop in the 5' direction is halted, which is consistent with the notion that the downstream secondary structure resists unfolding. Mechanical stretching of the hairpin using optical tweezers only allows clear identification of unfolding of the upper stem at a force of 12.8 ± 1.0 pN. This suggests that the lower stem is unstable and may indeed readily unfold in the presence of a translocating ribosome.

Present address: Yeonee Seol, NHLBI, National Institute of Health, Bethesda, MD, 20892, USA.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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