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Review
. 2004 Aug 18:1:22.
doi: 10.1186/1742-4690-1-22.

The retroviral RNA dimer linkage: different structures may reflect different roles

Jane Greatorex  1
Affiliations
Review

The retroviral RNA dimer linkage: different structures may reflect different roles

Jane Greatorex. Retrovirology. .

Abstract

Retroviruses are unique among virus families in having dimeric genomes. The RNA sequences and structures that link the two RNA molecules vary, and these differences provide clues as to the role of this feature in the viral lifecycles. This review draws upon examples from different retroviral families. Differences and similarities in both secondary and tertiary structure are discussed. The implication of varying roles for the dimer linkage in related viruses is considered.

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Figures

Figure 1
Figure 1
Structure of the HIV-2 leader region. 1a. Secondary structure model of the HIV-2 leader region based on mfold predictions. Indicated are the putative dimer linkage sites (in red). Also highlighted is the DM region defined as being critical for packaging [28], in blue). 1b. The effect of the DM deletion on the SL1/DIS stem loop. The stem is truncated and the internal bulge altered in approximately half the predicted structures.
Figure 2
Figure 2
Structure of the key elements involved in HIV-1 RNA dimerisation. 2a. Secondary structure model of the packaging signal of HIV-1Lai ([64] [65]), containing the principal DLS. 2b Proposed sequence of the RNA dimerisation process in HIV-1Lai. The initial kissing hairpin interaction (including loop B) followed by formation of the extended duplex ([1]). 2c. Loop B, one of the critical elements in the dimer interaction. The flexibility of this internal loop allows the duplex to form ([44]).
Figure 3
Figure 3
Dimer linkages of the retroviridae (excluding the lentiviruses). 3a. Loose and tight dimers ([51]). 3b. Imperfect repeats ([66]). 3c. Palindromes ([38]). 3d. GACG loops ([23]). 3e. CAG tri-loops (see Figure 4).
Figure 4
Figure 4
Proposed tertiary structure of the HTLV-1 dimer linkage. 4a Stereoview of 3D molecular modelling of a potential structure of the HTLV-1 DIS from nucleotide A730 to A744 using JUMNA ([61]). 4b. Close up of the terminal loop. Bases are coloured as follows: adenine, grey; cytosine, yellow; guanine, orange; and uracil, cyan.
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