HIV-1 Genome Dimerization: Kissing-Loop Hairpin Dictates Whether Nucleotides Downstream of the 5‘ Splice Junction Contribute to Loose and Tight Dimerization of Human Immunodeficiency Virus RNA

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Abstract
The genome of all retroviruses consists of two identical RNAs noncovalently linked near their 5' end. Adjacent genomic RNAs from human immunodeficiency virus type 1 (HIV-1) can form loose or tight dimers depending on whether their respective kissing-loop hairpins (nts 248-270 in HIV-1Lai) bond via their autocomplementary sequences (ACS) or via the ACS and stem sequences [Laughrea, M., & Jetté, L. (1996a) Biochemistry 35, 1589-1598]. Loose dimers from HIV-1Mal, but not HIV-1Lai, are stabilized by a sequence (3'DLS) located downstream of the 5' splice junction [Laughrea, M., & Jetté, L. (1996b) Biochemistry 35; 9366-9374]. To understand the ACS-3'DLS interplay in the formation and stability of loose and tight HIV-1 RNA dimers, we replaced the ACS of HIV-1Lai (GCGCGC262) by GUGCAC, GUGCGC (two alternative HIV-1 ACS), or GAGCUC (a non-HIV ACS). For each mutant, RNAs truncated immediately upstream or downstream of the 3'DLS were prepared; their ability to dimerize and their thermal stabilities were compared. The results suggest that the ACS determines whether the 3'DLS participates in RNA dimerization: (1) GAGCUC262 led to poorly stable loose dimers due to the inability of the 3'DLS to stabilize them (the 3'DLS stabilized the GUGCAC and GUGCGC RNAs); (2) GAGCUC262 led to poor formation of tight dimers, due to an inhibitory effect of the 3'DLS (the 3'DLS had little effect on the tight dimerization of the GUGCAC, GUGCGC and GCGCGC RNAs). The results indicate that communication exists between HIV-1 RNA sequences respectively located upstream and downstream of the 5' splice junction; they are consistent with the idea that the 3'DLS plays two ACS-dependent roles in the dimerization process: loose dimer stabilization in HIV-1 RNAs bearing an HIV ACS (unless the ACS already conferred a thermostability equal or superior to that offered by the 3'DLS), and inhibition of tight dimer formation in an HIV-1 RNA bearing a non-HIV ACS.