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Nucleic Acids Research, 2003, Vol. 31, No. 15 4326-4331
© 2003 Oxford University Press

Solution structure of the HIV-1 frameshift inducing stem–loop RNA

David W. Staple and Samuel E. Butcher*

Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA

*To whom correspondence should be addressed. Tel: +1 608 263 3890; Fax: +1 608 262 3453; Email: butcher{at}nmrfam.wisc.edu

The translation of reverse transcriptase and other essential viral proteins from the HIV-1 Pol mRNA requires a programmed –1 ribosomal frameshift. This frameshift is induced by two highly conserved elements within the HIV-1 mRNA: a slippery sequence comprised of a UUUUUUA heptamer, and a downstream stem–loop structure. We have determined the structure of the HIV-1 frameshift inducing RNA stem–loop, using multidimensional heteronuclear nuclear magnetic resonance (NMR) methods. The 22 nucleotide RNA solution structure [root mean squared deviation (r.m.s.d.) = 1.2 Å] was determined from 475 nuclear Overhauser effect (NOE)-derived distance restrains, 20 residual dipolar couplings and direct detection of hydrogen bonds via scalar couplings. We find that the frameshift inducing stem–loop is an A-form helix capped by a structured ACAA tetraloop. The ACAA tetraloop is stabilized by an equilateral 5' and 3' stacking pattern, a sheared A–A pair and a cross-strand hydrogen bond. Unexpectedly, the ACAA tetraloop structure is nearly identical to a known tetraloop fold, previously identified in the RNase III recognition site from Saccharomyces cerevisiae.


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