Replicable and recombinogenic RNAs

CHETVERIN, A

doi:10.1016/s0014-5793(04)00363-1

Cited by 4 publications

(4 citation statements)

References 41 publications

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“…Reviews of the replication of phages with DNA genomes focus on favourite model systems: λ (Campbell, 1994; Taylor & Wegrzyn, 1995), T4 (Mosig, 1998), φ29 (Meijer et al , 2001), f1/fd (Horiuchi, 1997), SPP1 (Alonso et al , 2005) and T7 (Richardson, 1983). Several recent research papers and reviews cover the field of RNA phages, which will not be discussed here (Bollback & Huelsenbeck, 2001; Chetverin, 2004; Makeyev & Grimes, 2004; Mindich, 2004; Poranen & Tuma, 2004).…”

Section: Introductionmentioning

confidence: 99%

Bacteriophage replication modules

2006

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Bacteriophages (prokaryotic viruses) are favourite model systems to study DNA replication in prokaryotes, and provide examples for every theoretically possible replication mechanism. In addition, the elucidation of the intricate interplay of phage-encoded replication factors with 'host' factors has always advanced the understanding of DNA replication in general. Here we review bacteriophage replication based on the long-standing observation that in most known phage genomes the replication genes are arranged as modules. This allows us to discuss established model systems--f1/fd, phiX174, P2, P4, lambda, SPP1, N15, phi29, T7 and T4--along with those numerous phages that have been sequenced but not studied experimentally. The review of bacteriophage replication mechanisms and modules is accompanied by a compendium of replication origins and replication/recombination proteins (available as supplementary material online).

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Section: Introductionmentioning

confidence: 99%

Bacteriophage replication modules

2006

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“…RQ RNAs were originally seen as spontaneously amplified RNA, without template RNA addition, in vitro by Qβ replicase and named “6S”, “variant”, or RQ RNA − , . Several origins for RQ RNAs are known, including contamination , , de novo synthesis from NTPs − , and recombination from several RNA origins − : Qβ genomic RNA , rRNA , and tRNA , . To avoid RQ RNA amplification, several experimental conditions are required depending on the origin of the RQ RNA.…”

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confidence: 99%

Compartmentalization in a Water-in-Oil Emulsion Repressed the Spontaneous Amplification of RNA by Qβ Replicase

et al. 2010

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During RNA replication mediated by Qbeta replicase, self-replicating RNAs (RQ RNAs) are amplified without the addition of template RNA. This undesired amplification makes the study of target RNA replication difficult, especially for long RNA such as genomic RNA of Qbeta phage. This perhaps is one of the reasons why the precise rate of genomic RNA replication in the presence of host factor Hfq has not been reported in vitro. Here, we report a method to repress RQ RNA amplification by compartmentalization of the reaction using a water-in-oil emulsion but maintaining the activity of Qbeta replicase. This method allowed us to amplify the phage Qbeta genome RNA exponentially without detectable amplification of RQ RNA. Furthermore, we found that the rate constant of genome RNA replication in the exponential phase at the optimum Hfq concentration was approximately 4.6 times larger than that of a previous report, close to in vivo data. This result indicates that the replication rate in vivo is largely explained by the presence of Hfq. This easy method paves the way for the study of genomic RNA replication without special care for the undesired RQ RNA amplification.

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“…To address these complications, the rapidly growing field of mRNA therapeutics can be a potent platform because of its safety, comparatively low-cost of production, capability of rapid development and higher efficacy. Except for a few rare cases of recombination between single-stranded RNA molecules [52,53], lack of genomic integration and replication makes mRNA vaccines a non-infectious agent [54,55]. On top of that, natural degradation and adjustable halflife provides a strong safety advantage [55].…”

Section: Introductionmentioning

confidence: 99%

Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach

Ahammad

Lira

2020

International Journal of Biological Macromolecules

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SARS-CoV-2 is the deadly virus behind COVID-19, the disease that went on to ravage the world and caused the biggest pandemic 21st century has witnessed so far. On the face of ongoing death and destruction, the urgent need for the discovery of a vaccine against the virus is paramount. This study resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. Various immunoinformatics tools were utilized to predict T and B lymphocyte epitopes. The epitopes were channeled through a filtering pipeline comprised of antigenicity, toxicity, allergenicity, and cytokine inducibility evaluation with the goal of selecting epitopes capable of generating both T and B cell-mediated immune responses. Molecular docking simulation between the epitopes and their corresponding MHC molecules was carried out. 13 epitopes, a highly immunogenic adjuvant, elements for proper sub-cellular trafficking, a secretion booster, and appropriate linkers were combined for constructing the vaccine. The vaccine was found to be antigenic, almost neutral at physiological pH, non-toxic, non-allergenic, capable of generating a robust immune response and had a decent worldwide population coverage. Based on these parameters, this design can be considered a promising choice for a vaccine against SARS-CoV-2.

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Replicable and recombinogenic RNAs

Cited by 4 publications

References 41 publications

Bacteriophage replication modules

Bacteriophage replication modules

Compartmentalization in a Water-in-Oil Emulsion Repressed the Spontaneous Amplification of RNA by Qβ Replicase

Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach

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