Spontaneous rearrangements in RNA sequences

Chetverina, Helena V.; Demidenko, Alexander A.; Ugarov, Victor I.; Chetverin, Alexander B.

doi:10.1016/s0014-5793(99)00469-x

Cited by 71 publications

(78 citation statements)

References 24 publications

(44 reference statements)

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“…The emergence of longer RNA strings could have proceeded not only via polymerization but also through spontaneous rearrangements of RNA sequences that may progress in the absence of any enzymes or ribozymes [351][352][353]; such rearrangements may have dramatically accelerated evolution [57,354].…”

Section: First Settlers In the Zns Worldmentioning

confidence: 99%

Inorganic Polyphosphate Modulates TRPM8 Channels

Trimm¹

2011

Inorganic Chemistry

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Section: First Settlers In the Zns Worldmentioning

confidence: 99%

Inorganic Polyphosphate Modulates TRPM8 Channels

Trimm¹

2011

Inorganic Chemistry

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“…RNA provides, for the time being, the only plausible solution to self-generation, as allowed by self-polymerization and by a variety of self-catalytic processes. Pioneering reports of RNA recombination have appeared [7][8][9][10][11][12]. With the possible exception of the systems described in [13][14][15], the reactions reported so far are not simple and robust enough to be of likely prebiotic relevance.…”

Section: Introductionmentioning

confidence: 99%

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

Pino

Costanzo

Giorgi

et al. 2013

Entropy

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3′,5′-Cyclic GMP spontaneously nonenzymatically polymerizes in a base-catalyzed reaction affording G oligonucleotides. When reacted with fully or partially sequence-complementary RNA (oligo C), the abiotically generated oligo G RNA displays a typical ribozyme activity consisting of terminal ligation accompanied by cleavage of an internal phosphate site of the donor oligonucleotide stem upon attack of the acceptor 3′ terminal OH. This reaction is dubbed Ligation following Intermolecular Cleavage (LIC). In a prebiotic perspective, the ability of oligo G polynucleotides to react with other sequences outlines a simple and possible evolutionary scenario based on the autocatalytic properties of RNA.

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“…Important structural factors of the template or nascent strand that are used for classification have been identified in these model viruses and can be subdivided into primary factors, such as sequence similarity, AU-rich motifs, sequence complementarity and replicative cis elements, and secondary structures, such as stem-loops (Bruyere et al, 2000;Nagy & Bujarski, 1993Olsthoorn et al, 2002;Shapka & Nagy, 2004). So far, nonreplicative RNA recombination, possibly based on RNA breakage and ligation, has only been detected in bacteriophage Qb and polioviruses (Chetverin et al, 1997;Chetverina et al, 1999;Gallei et al, 2004;Gmyl et al, 1999Gmyl et al, , 2003, but not yet in plant viruses.…”

Section: Introductionmentioning

confidence: 99%

Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus X RNA recombination

Draghici

Varrelmann

2009

Journal of General Virology

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Virus RNA recombination, one of the main factors for genetic variability and evolution, is thought to be based on different mechanisms. Here, the recently described in vivo potato virus X (PVX) recombination assay . J Virol 83, 7761-7769] was applied to characterize structural parameters of recombination. The assay uses an Agrobacterium-mediated expression system incorporating a PVX green fluorescent protein (GFP)-labelled full-length clone. The clone contains a partial coat protein (CP) deletion that causes defectiveness in cell-to-cell movement, together with a functional CP+39 non-translated region (ntr) transcript, in Nicotiana benthamiana leaf tissue. The structural parameters assessed were the length of sequence overlap, the distance between mutations and the degree of sequence similarity. The effects on the observed frequency of reconstitution and the composition of the recombination products were characterized. Application of four different type X intact PVX CP genes with variable composition allowed the estimation of the junction sites of precise homologous recombination. Although one template switch would have been sufficient for functional reconstitution, between one and seven template switches were observed. Use of PVX-GFP mutants with CP deletions of variable length resulted in a linear decrease of the reconstitution frequency. The critical length observed for homologous recombination was 20-50 nt. Reduction of the reconstitution frequency was obtained when a phylogenetically distant PVX type Bi CP gene was used. Finally, the prediction of CP and 39-ntr RNA secondary structure demonstrated that recombination-junction sites were located mainly in regions of stem-loop structures, allowing the recombination observed to be categorized as similarity-assisted.

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Spontaneous rearrangements in RNA sequences

Cited by 71 publications

References 24 publications

Inorganic Polyphosphate Modulates TRPM8 Channels

Inorganic Polyphosphate Modulates TRPM8 Channels

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

Evidence for similarity-assisted recombination and predicted stem-loop structure determinant in potato virus X RNA recombination

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