Dimerization begins when the stem-loops
(SL1) of two genomic strands associate by Watson-Crick base-pairing
of their loops (a and b
forming a transient kissing-loop
complex. This complex is then believed to isomerize into a
duplex, sometimes referred to as the mature SL1 dimer initiation
complex. Within this complex the intrastrand base pairs of the stems
have melted and reformed as interstrand pairs, creating a more stable linkage
between the two strands2.
The SL1 stems form canonical A-type helices <right-handed helix <
The flanking adenines remain unbound,
instead, through stacking interactions they help to partially stabilize
the kissing-loop form. To form the kissing-loop, each A9
/ A9 base
rotate around the backbone to stack against bases of the opposite strand.
This angle allows for only partial stacking of A9, A8, A16 and G7.
Despite their divergent overall structures, the NMR spectum of the linear duplex and the kissing-loop are remarkably similar. This is due to the fact that the local environment and bonding interactions are the same in both structures, except that all intramolecular base pairs of the kissing-loop are converted to intermolecular base pairs in the linear duplex. One difference is the presence of the G7-C17 <base pair, absent in the kissing-loop, in the mature dimer. This reformed base pair normalizes the A-helices conformation in the linear form, thus increasing stacking, relieving strain on the helix, and granting favorable thermodynamic effects. These benefits likely account for the tendency of the kissing-loop complex to spontaneously convert to the linear form.
polypeptide is derived from the N-terminal end of the Gag gene, and facilitates
the nuclear transport of the viral genome, which in turn allows HIV-1
to infect nondividing cells. The capsid protein forms the conical
core of viral particles. Cyclophilin A interacts with the p24 region
of the Gag gene, resulting in its incorporation into HIV-1
particles. The nucleocapsid recognizes the packaging signal of
HIV-1, which consists of four stem loop structures
at the 5' end of the viral RNA, and mediates the incorporation of a heterologous
RNA into HIV-1
(www.columbia.edu/cu/cie/techlists/ patents/5773225.htm, 12/7/00).
Studies have shown that deletion mutations introduced into the kissing-loop decreased the infectivity of the resulting viruses, reduced the amount of genomic RNA packaged per virus, and the proportion of dimeric genomic RNA was reduced4. However, long-term culture of the mutated RNAs in MT-2 cells resulted in a restoration of infectiousness, due to a series of compensatory point mutations5.
al.6 found that destroying the stem-loop
1. Laughrea M, Jette L. 1996. Kissing-Loop Model of HIV-1 Genome Dimerization: HIV-1 RNAs Can Assume Alternative Dimeric Forms, and All Sequences Upstream or Downstream of Hairpin 248-271 are Dispensable for Dimer Formation. Biochemistry 35:1589-1598.
2. Mujeeb A, Parslow TG, Zarrinpar A, Das C, James TL. 1999. NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA. Federation of European Biochemical Societies 458:387-392.
Mujeeb A, Clever JL, Billeci TM, James TL, Parslow TG. 1998. Structure
of the dimer initiation complex of HIV-1 genomic RNA. Nature Structural Biology 5:432-436.
4. Laughrea M, Jette L, Mak J, Kleinman L, Liang C, Wainberg MA. 1997. Mutations in the kissing-loop hairpin of human inmmunodeficiency virus type-1 reduce viral infectivity as well as genomic RNA packaging and dimerization. Journal of Virology 71: 3397-406.
5. Liang C, Rong L, Quan Y, Laughrea M, Kleiman L, Wainberg MA. 1999. Mutations within four distinct gag proteins are required to restore replication of human immunodeficiency virus type-1 after deletion mutagenesis within the dimerization initiation site. Journal of Virology 73: 7014-20.
6. Shen N, Jette L, Liang C, Wainberg MA, Laughrea M. 2000. Impact of human immunodeficiency virus type-1 RNA dimerization on viral infectivity and of stem-loop B on RNA dimerization and reverse transcription and dissociation of dimerization form packaging. Journal of Virology 74: 5729-35.
Human Immunodeficiency Virus: An Interactive Exploration of Recent Literature.
Judith Kandel, Biology 302, Department of Biological Science, California
State University at Fullerton. http://biology.fullerton.edu/biol302/Browser/moreabout.html.