Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

Modeling the Maturation Pathway of the HIV-1 5’-UTR RNA Dimer

HIV-1 genomic RNA is packaged as a dimer into the virions. The initial metastable RNA dimer is believed to be formed by virtue of “kissing interactions” between two copies of the palindromic apical loops of stem-loop SL1 of the 5’-untranslated region (5’-UTR) of the genomic RNA. Viral nucleocapsid protein NCp7 promotes maturation of the RNA dimer into more stable form, which involves extended or linear form of SL1 dimer (reviewed in Paillart et al. 2004; Moore & Hu 2009; Lu et al. 2011). In vitro experiments have shown that this conversion occurs at stoichiometric amounts of NCp7 without breaking interactions between the two copies of the SL1 apical loops (Mujeeb et al. 2007). We have proposed a hypothetical pathway and calculated models of the intermediate structures for the SL1 stem-loop dimer maturation that does not require simultaneous dissociation of all base pairs in SL1 stems; this pathway involves formation of an RNA analog of the Holliday junction intermediate between the two stems of the SL1 dimer and a following branch migration towards the palindromic duplex (Ulyanov et al. 2011). Here we extend these models to the dimer of the 1-344 fragment of HIV-1 RNA, which includes all of the 5’-UTR and the gag start AUG codon region, and show that the branch migration mechanism of the dimer maturation is also feasible for the full 5’-UTR RNA. All RNA models have been calculated with the miniCarlo program (Zhurkin et al. 1991).

This research was supported in part by the California HIV/AIDS Research Program award ID09-SF-030.


    K. Lu, X. Heng, & M.F. Summers. J Mol Biol 410, 609-33 (2011).

    M.D. Moore & W.-S. Hu. AIDS Rev 11, 91-102 (2009).

    A. Mujeeb, N.B. Ulyanov, S. Georgantis, I. Smirnov, J. Chung, T.G. Parslow & T.L. James. Nucl Acids Res 35, 2026-34 (2007).

    J.-C. Paillart, M. Shehu-Xhilaga, R. Marquet & J. Mak. Nat Rev Microbiol 2, 461-72 (2004).

    N.B. Ulyanov, R. Tjhen, C. Guilbert & T.L. James. J Biomol Struct Dyn 28, 1082-83 (2011).

    V.B. Zhurkin, N.B. Ulyanov, A.A. Gorin & R.L. Jernigan. Proc Natl Acad Sci USA 88, 7046-50 (1991).

Nikolai B. Ulyanov1
Christophe Guilbert
Richard Tjhen
Thomas L. James

Department of Pharmaceutical Chemistry
University of California
San Francisco, CA 94158-2517, U.S.A.
1 Current address: Laboratory of Cell Biology
NCI, NIH, Bethesda, MD 20892

Ph: (650)872-9107