Structural consensus of RNA templates replicated by Qβ replicase

Voronin, L.A.

doi:10.1016/0300-9084(92)90090-2

Cited by 12 publications

(16 citation statements)

References 7 publications

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“…The conditions listed do not suffice for replication; another condition, the presence of both a 3'-terminal and an interior C-cluster (or pyrimidine cluster; Kiippers & Sumper, 1975), is also fulfilled. Other structural similarities among RNA species replicated by Qp replicase found (Voronin, 1992) are not present but may be required for higher replication efficiencies.…”

Section: Discussionmentioning

confidence: 96%

Sequence analysis of RNA species synthesized by Q.beta. replicase without template

Biebricher¹,

Luce²

1993

Biochemistry

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Q beta replicase amplifies certain short-chained RNA templates autocatalytically with high efficiency. In the absence of extraneously added template, synthesis of new RNA species by Q beta replicase is observed under conditions of high enzyme and substrate concentrations and after long lag times. Even under identical conditions, different RNA species are produced in different experiments. The sequences of several independent template-free products have been determined by cloning their cDNAs into plasmids by a novel cloning procedure. Their nucleotide chain lengths are small, ranging from 25 to about 50 nucleotides. While their primary sequences are unrelated except for the invariant 5'-terminal G and 3'-terminal C clusters, their tentative secondary structures show a common principle: both their plus and minus strands have a stem at the 5' terminus, while the 3' terminus is unpaired. Direct accumulation of sufficient quantities of early template-free synthesis products by Q beta replicase is prevented by the inherent irreproducibility of the synthesis process and by the rapid change of the products during amplification by evolution processes, but large amounts of such RNA can be synthesized in vitro by transcription from the cDNA clones. RNA species produced in template-free reactions replicate much more slowly than the optimized RNA species characterized previously. These experimental results illustrate how biological information can be gained in small bits by trial and error.

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Section: Discussionmentioning

confidence: 96%

Sequence analysis of RNA species synthesized by Q.beta. replicase without template

Biebricher¹,

Luce²

1993

Biochemistry

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“…Similarly, in vitro amplification methods, such as PCR and isothermal amplification, have also spawned molecular parasites. The oldest and by far the best known are the bestiary of "monsters" that arose during in vitro RNA replication by Q ␤ replicase (Kacian et al 1972;Mills et al 1975;Biebricher et al 1986;Chetverin et al 1991;Voronin 1992;Biebricher and Luce 1993), but parasites of in vitro, T7 RNA polymerase transcription Sharp 1989, 1990;Biebricher and Luce 1996), or isothermal amplification methods (Breaker and Joyce 1994) have also been discovered.…”

Section: Introductionmentioning

confidence: 99%

“…Viruses are thought to have been derived from larger, organismal genomes (Becker 1995a(Becker ,b, 1998. The Q␤ "midivariants" and "minivariants" were originally derived from a full-length Q ␤ genome (Voronin 1992). The short "RNA Z" isothermal amplification parasite was derived from a full-length Group II self-splicing intron (Breaker and Joyce 1994).…”

Section: Introductionmentioning

confidence: 99%

Molecular Parasites That Evolve Longer Genomes

Marshall

Ellington

1999

J Mol Evol

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Molecular parasites that utilize the replication machinery of cells or of in vitro amplification reactions have previously been characterized. By and large, these parasites have been smaller than the viruses or amplicons that gave rise to them. This is likely because shorter genomes can be replicated more quickly. In contrast, we have identified and characterized parasites of an isothermal amplification reaction that are longer than their parental molecules yet replicate much more efficiently. These results raise interesting questions regarding whether the optimal size of replicators reflects a trade-off between the information encoded in a parasite and the information encoded in the machinery replicating that parasite.

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“…The replicative form of various small RNA molecules copied by QP replicase consists of a single strand selfannealed into a series of hairpin loops (Schaffner et al 1977;Mills et a l . 1978;Priano 1987;Munishkin et al 1988Munishkin et al , 1991Biebricher & Luce 1992;Voronin 1992). A shared generic folding pattern in this heterogeneous set of RNA molecules suggests that replicative fitness depends on molecular shape, in dependent of most of the underlying base sequence.…”

Section: Introductionmentioning

confidence: 99%

“…A shared generic folding pattern in this heterogeneous set of RNA molecules suggests that replicative fitness depends on molecular shape, in dependent of most of the underlying base sequence. There is evidence that they require a minimum of one hairpin loop at the 5'-end for template competence (Schafiner et al 1977;Biebricher & Luce 1993), with the preferred configuration including a second at the 3r-end (Voronin 1992), giving the transcription in itiation site a tRNA-like structure (Adhin et al 1990). Quasispecies-forming RNA variants are highly folded, however.…”

Section: Introductionmentioning

confidence: 99%

Significance of strand configuration in self-replicating RNA molecules

Davis

1995

Phil. Trans. R. Soc. Lond. B

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The kinetic theory of replication has been extended to include dual mechanisms for conversion of self-annealed single-strand RNA to double-strand molecules, which do not replicate. An analysis of experimental results established that the replicate-template annealing reaction during transcription significantly retarded replication in vitro among three RNA variants copied by Q beta replicase. Annealing between complementary RNA strands free in solution had far less significance. The finding that an RNA variant can be replicated in a multiple hairpin configuration, but not as its single, long hairpin conformer, the correlation between stability of strand secondary structure and replicative fitness, and a lack of homology in the internal sequence of RNA variants copied by Q beta replicase support the conclusion that template competence depends on strand configuration, independent of most of the underlying base sequence. Occurrence of self-annealed strands in the Q beta replicase system was attributed to its reliance on RNA-driven strand separation, in the absence of enzyme catalysed strand unwinding. A 'configuration before sequence' path to self-replication exhibited a substantially lower combinatorial barrier than standard sequence-dependent evolution. RNA-dependent RNA synthesis in the Q beta system thus displays features of an RNA World and, interestingly, they reveal a rapid path for evolution of the first self-replicating molecule on Earth.

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Structural consensus of RNA templates replicated by Qβ replicase

Cited by 12 publications

References 7 publications

Sequence analysis of RNA species synthesized by Q.beta. replicase without template

Sequence analysis of RNA species synthesized by Q.beta. replicase without template

Molecular Parasites That Evolve Longer Genomes

Significance of strand configuration in self-replicating RNA molecules

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