A Kissing Complex Together with a Stable Dimer Is Involved in the HIV-1<sub>Lai</sub> RNA Dimerization Process <i>in Vitro</i>

Muriaux, Delphine; Fossé, Philippe; Paoletti, Jacques

doi:10.1021/bi952822s

Cited by 150 publications

(171 citation statements)

References 41 publications

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“…These tight dimers are defined by their resistance to dissociation during electrophoresis at room temperature and in the presence of EDTA. The tight dimer behavior of small HIV-1 or HIV-2 RNAs is thought to be caused by an extended base pairing arrangement of SL1 (first proposed in (6,33,34) and further analyzed in (10,11,15)). The 1-444 RNA is well suited to forming a tight dimer probably because the SL1 dimer-inducing element is located at the very 3′ end of this fragment ( Figure 1).…”

Section: Discussionmentioning

confidence: 99%

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

et al. 2003

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An essential step in the replication cycle of all retroviruses is the dimerization of genomic RNA prior to or during budding and maturation of the viral particle. In HIV-1 a 5′ leader region site referred to as stem-loop1 (SL1) promotes RNA dimerization in vitro and influences dimerization in vivo. In HIV-2, two sequences promote dimerization of RNA fragments in vitro: the 5′-end of the primerbinding site (PBS) and a stem loop homologous to the HIV-1 SL1 sequence. Because HIV-2 RNA constructs of different lengths use these two dimerization signals disproportionately, we hypothesized that other sequences could modulate their relative utilization. Here, we characterized the influence of sequences upstream and downstream of the major splice donor site on the formation of HIV-2 RNA dimers in vitro using a variety of RNA constructs and dimerization/electrophoresis protocols. We first assayed the formation of loose or tight dimers for 1-444 and 1-561 model RNAs. Although both RNAs could form PBS-dependent loose dimers, the 1-561 RNA was unable to make SL1-dependent tight dimers. Using RNAs truncated at their 5′ and/or 3′ ends and by making compensatory base substitutions we found that two elements interfere with the formation of SL1-dependent tight dimers. The cores of these elements are located at nucleotides 189-196 and 543-550. Our results suggest that base pairing between these sequences prevents the formation of SL1- † This research was supported by the National Institutes of Health grant number AI45388 to J.S.L.

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Section: Discussionmentioning

confidence: 99%

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

et al. 2003

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“…2; 3; 7; 18-20 Experiments performed in vitro have shown that the metastable KL complex can subsequently isomerize into a more stable extended duplex (ED) that involves extensive intermolecular base-pairing along the entire SL1 sequence (Scheme 1). [21][22][23][24][25] The transition between KL and ED forms is catalyzed in vitro by NC, 23; 26-29 in a process that could explain the increased thermal stability observed for genomic RNA of HIV-1 and Moloney murine leukemia virus upon protease-dependent viral maturation. 30-32 The 3D structures of SL1 constructs in monomeric, 33-35 KL, 36-40 and ED form 38; 41-43 support the two-step dimerization model.…”

Section: Introductionmentioning

confidence: 99%

Dissecting the Protein–RNA and RNA–RNA Interactions in the Nucleocapsid-mediated Dimerization and Isomerization of HIV-1 Stemloop 1

Hagan¹,

Fabris²

2007

Journal of Molecular Biology

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The specific binding of HIV-1 nucleocapsid protein (NC) to the different forms assumed in vitro by the stemloop 1 (Lai variant) of the genome's packaging signal has been investigated using electrospray ionization-Fourier transform mass spectrometry (ESI-FTMS). The simultaneous observation of protein-RNA and RNA-RNA interactions in solution has provided direct information about the role of NC in the two-step model of RNA dimerization and isomerization. In particular, two distinct binding sites have been identified on the monomeric stemloop structure, corresponding to the apical loop and stem-bulge motifs. These sites share similar binding affinities that are intermediate between those of stemloop 3 (SL3) and the putative stemloop 4 (SL4) of the packaging signal. Binding to the apical loop, which contains the dimerization initiation site (DIS), competes directly with the annealing of self-complementary sequences to form a metastable kissing-loop (KL) dimer. In contrast, binding to the stem-bulge affects indirectly the monomer-dimer equilibrium by promoting the rearrangement of KL into the more stable extended duplex (ED) conformer. This process is mediated by the duplex-melting activity of NC, which destabilizes the intramolecular base pairs surrounding the KL stem-bulges and enables their exchange to form the inter-strand pairs that define the ED structure. In this conformer, high-affinity binding takes place at stem-bulge sites that are identical to those present in the monomeric and KL forms. In this case, however, the NC-induced 'breathing' does not result in dissociation of the double-stranded structure because of the large number of intermolecular base pairs. The different binding modes manifested by conformer-specific mutants have shown that NC can also provide low affinity interactions with the bulged-out adenines flanking the DIS region of the ED conformer, thus supporting the hypothesis that these exposed nucleotides may constitute 'base-grips' for protein contacts during the late stages of the viral lifecycle.

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“…The transient formation of an intermolecular kissing complex is required for RNA dimerization during the life cycle of retroviruses (11)(12)(13)(14)(15), and for the formation of some antisensetarget complexes (16,17). Kissing complexes in which the loop nucleotides are complementary can form stable dimers that contain intermolecular base pairs between the loop nucleotides only.…”

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confidence: 99%

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Andersen

Collins

2001

Proc. Natl. Acad. Sci. U.S.A.

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Kissing interactions in RNA are formed when bases between two hairpin loops pair. Intra-and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs. Self-cleavage of the wild-type Varkud satellite (VS) ribozyme requires a kissing interaction between the hairpin loops of stemloops I and V. In addition, self-cleavage requires a rearrangement of several base pairs at the base of stem I. We show that the kissing interaction is necessary for the secondary structure rearrangement of wild-type stem-loop I. Surprisingly, isolated stem-loop V in the absence of the rest of the ribozyme is sufficient to rearrange the secondary structure of isolated stem-loop I. In contrast to kissing interactions in other RNAs that are either confined to the loops or culminate in an extended intermolecular duplex, the VS kissing interaction causes changes in intramolecular base pairs within the target stem-loop.R NA kissing interactions, also called loop-loop pseudoknots, occur when the unpaired nucleotides in one hairpin loop base pair with the unpaired nucleotides in another hairpin loop (1). When the hairpin loops are located on separate RNA molecules, their intermolecular interaction is called a kissing complex. These interactions generally form between stem-loops containing extensive complementarity; however, stable complexes have been observed containing only two intermolecular Watson-Crick base pairs (2).Intramolecular kissing interactions are observed in the native structures of a variety of RNAs including Varkud satellite (VS) RNA, tRNA, and group I introns (3-6). These kissing interactions contribute to the assembly and stabilization of their respective RNA structures by joining and orienting helices. Kissing interactions may stabilize both native and nonnative interactions during tertiary folding, which can affect the rate at which the native structure is formed (7). Kissing interactions often form distorted structures that can serve as recognition sites for proteins, RNAs, metal ions, or other ligands (8-10). As a result, kissing interactions contribute to the stability of an RNA structure by affecting both global and local RNA interactions.The transient formation of an intermolecular kissing complex is required for RNA dimerization during the life cycle of retroviruses (11-15), and for the formation of some antisensetarget complexes (16,17). Kissing complexes in which the loop nucleotides are complementary can form stable dimers that contain intermolecular base pairs between the loop nucleotides only. Other stem-loops with more extensive complementarity sometimes form unstable kissing complexes, which are quickly remodeled into stable duplex or cruciform isoforms (18)(19)(20). Secondary structure remodeling involves breaking intramolecular base pairs in each hairpin and using the bases to form intermolecular helices.The VS ribozyme contains a kissing interaction that is required for self-cleavage of the wild-type RNA in vitro (6). This interaction involves Watson-Crick bas...

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A Kissing Complex Together with a Stable Dimer Is Involved in the HIV-1_Lai RNA Dimerization Process in Vitro

Cited by 150 publications

References 41 publications

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

Dissecting the Protein–RNA and RNA–RNA Interactions in the Nucleocapsid-mediated Dimerization and Isomerization of HIV-1 Stemloop 1

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

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A Kissing Complex Together with a Stable Dimer Is Involved in the HIV-1Lai RNA Dimerization Process in Vitro

Cited by 150 publications

References 41 publications

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

Elements Located Upstream and Downstream of the Major Splice Donor Site Influence the Ability of HIV-2 Leader RNA To Dimerize in Vitro

Dissecting the Protein–RNA and RNA–RNA Interactions in the Nucleocapsid-mediated Dimerization and Isomerization of HIV-1 Stemloop 1

Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

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A Kissing Complex Together with a Stable Dimer Is Involved in the HIV-1_Lai RNA Dimerization Process in Vitro