Self-sustained replication of an RNA enzyme.
Ontology highlight
ABSTRACT:
SUBMITTER: Lincoln TA
PROVIDER: S-EPMC2652413 | biostudies-literature | 2009 Feb
REPOSITORIES: biostudies-literature
Publications
Self-sustained replication of an RNA enzyme.
Lincoln Tracey A TA Joyce Gerald F GF
Science (New York, N.Y.) 20090108 5918
An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allow ...[more]
Similar Datasets
Project description:ImportanceMultiple pattern recognition receptors sense vRNAs and initiate downstream innate signaling: endosomal Toll-like receptors (TLRs) 3, 7, and 8 and cytoplasmic RIG-I-like receptors (RLRs) RIG-I, and MDA5. They engage distinct signaling scaffolds: mitochondrial antiviral signaling protein (RLR), MyD88, and TLR-adaptor interacting with SLC15A4 on the lysosome (TLR7 and TLR8) and toll/IL-1R domain-containing adaptor inducing IFN (TLR3). By virtue of their unusual vRNA structure and direct host cell entry path, the innate response to EVs uniquely is orchestrated by MDA5. We reported that PVSRIPO's profound attenuation and loss of cytopathogenicity triggers MDA5-directed polar TBK1-IRF3 signaling that generates priming of polyfunctional antitumor CD8+ T-cell responses and durable antitumor surveillance in vivo. Here we unraveled EV-host relations that control suppression of host type-I IFN responses and show that PVSRIPO's deficient immediate host eIF4G cleavage generates unopposed MDA5-directed downstream signaling cascades resulting in sustained type-I IFN release.
| S-EPMC10746184 | biostudies-literature
Project description:A nuclease-resistant RNA enzyme, constructed entirely from L-ribonucleotides, was shown to undergo ligand-dependent, self-sustained replication with exponential growth. The catalytic motif is based on a previously described RNA ligase that can undergo either self- or cross-replication but had been limited in its application to ligand sensing due to its susceptibility to degradation by ribonucleases. The self-replicating RNA enzyme and its RNA substrates were prepared synthetically from either D- or L-nucleoside phosphoramidites. The D and L reaction systems undergo isothermal, ligand-dependent exponential amplification in the same manner, but only the l system is impervious to ribonucleases and can operate, for example, in the presence of human serum. This system has potential for the quantitative detection of various ligands that are present within biological or environmental samples. In addition, this work provides the first demonstration of the self-sustained exponential amplification of nonbiological molecules.
| S-EPMC3357125 | biostudies-literature
Project description:The larger segment (RNA 1) of the bipartite, positive-sense RNA genome of the nodavirus flock house virus encodes the viral RNA-dependent RNA polymerase. Two nonstructural viral proteins are made during the self-directed replication of this RNA: protein A (110 kDa), the translation product of RNA 1 itself, and protein B (11 kDa), the translation product of a subgenomic RNA (RNA 3) that is produced from RNA 1 during replication. To examine the roles of these proteins in RNA replication, specialized T7 transcription plasmids that contained wild-type or mutant copies of flock house virus RNA 1 cDNA were constructed and used in cells infected with the vaccinia virus-T7 RNA polymerase recombinant to make full-length transcripts that directed their own replication. Sequences in the primary transcripts that extended beyond the ends of the authentic RNA 1 sequence inhibited self-directed RNA replication, but plasmids that were constructed to minimize these terminal extensions produced primary transcripts that replicated as abundantly as authentic RNA 1. Truncation or mutation of the open reading frame for protein A eliminated self-directed replication, although the mutant RNA 1 remained a competent template for replication by wild-type protein A supplied in trans. These results showed that protein A was essential for RNA replication and that the process was not inseparably coupled to complete translation of the template. In contrast, protein B could be eliminated without inhibiting replication by mutations that disrupted the second of the two overlapping open reading frames on RNA 3. Furthermore, a mutant of RNA 1 in which the first nucleotide of the RNA 3 region was changed from G to U replicated at levels as high as those of the wild type without making either RNA 3 or protein B. However, diminishing replication levels were observed during subsequent replicative passages of RNA from both the mutants that could not make protein B. Roles for this protein that could account for the subtle phenotype of these mutants are discussed.
| S-EPMC188634 | biostudies-other
Project description:Incorporating neuromorphic electronics in bioelectronic interfaces can provide intelligent responsiveness to environments. However, the signal mismatch between the environmental stimuli and driving amplitude in neuromorphic devices has limited the functional versatility and energy sustainability. Here we demonstrate multifunctional, self-sustained neuromorphic interfaces by achieving signal matching at the biological level. The advances rely on the unique properties of microbially produced protein nanowires, which enable both bio-amplitude (e.g., <100 mV) signal processing and energy harvesting from ambient humidity. Integrating protein nanowire-based sensors, energy devices and memristors of bio-amplitude functions yields flexible, self-powered neuromorphic interfaces that can intelligently interpret biologically relevant stimuli for smart responses. These features, coupled with the fact that protein nanowires are a green biomaterial of potential diverse functionalities, take the interfaces a step closer to biological integration.
| S-EPMC8184933 | biostudies-literature
Project description:Turbulence is known for its ability to vigorously mix fluid and transport heat. Despite over a century of research for enhancing heat transport, few have exceeded the inherent limits posed by turbulent-mixing. Here we have conceptualized a kind of "active particle" turbulence, which far exceeds the limits of classical thermal turbulence. By adding a minute concentration (?v???1%) of a heavy liquid (hydrofluoroether) to a water-based turbulent convection system, a remarkably efficient biphasic dynamics is born, which supersedes turbulent heat transport by up to 500%. The system operates on a self-sustained dynamically equilibrated cycle of a "catalyst-like" species, and exploits several heat-carrier agents including pseudo-turbulence, latent heat and bidirectional wake capture. We find that the heat transfer enhancement is dominated by the kinematics of the active elements and their induced-agitation. The present finding opens the door towards the establishment of tunable, ultra-high efficiency heat transfer/mixing systems.
| S-EPMC6659658 | biostudies-literature
Project description:Sustained dropwise condensation of water requires rapid shedding of condensed droplets from the surface. Here, we elucidate a microfluidic mechanism that spontaneously sweeps condensed microscale droplets without the need for the traditional droplet removal pathways such as use of superhydrophobicity for droplet rolling and jumping and utilization of wettability gradients for directional droplet transport among others. The mechanism involves self-generated, directional, cascading coalescence sequences of condensed microscale droplets along standard hydrophobic microgrooves. Each sequence appears like a spontaneous zipping process, can sweep droplets along the microgroove at speeds of up to ?1 m/s, and can extend for lengths more than 100 times the microgroove width. We investigate this phenomenon through high-speed in situ microscale condensation observations and demonstrate that it is enabled by rapid oscillations of a condensate meniscus formed locally in a filled microgroove and pinned on its edges. Such oscillations are in turn spontaneously initiated by coalescence of an individual droplet growing on the ridge with the microgroove meniscus. We quantify the coalescence cascades by characterizing the size distribution of the swept droplets and propose a simple analytical model to explain the results. We also demonstrate that, as condensation proceeds on the hydrophobic microgrooved surface, the coalescence cascades recur spontaneously through repetitive dewetting of the microgrooves. Lastly, we identify surface design rules for consistent realization of the cascades. The hydrophobic microgrooved textures required for the activation of this mechanism can be realized through conventional, scalable surface fabrication methods on a broad range of materials (we demonstrate with aluminum and silicon), thus promising direct application in a host of phase-change processes.
| S-EPMC6703749 | biostudies-literature
Project description:An impressive superlow coefficient of friction (CoF) as low as 0.004 (nearly equivalent to the rolling coefficient) was obtained by sliding a steel ball against a tetrahedral amorphous diamond-like carbon (ta-C) coating in glycerol under a boundary lubrication regime. X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) revealed substantial changes in the surface chemistry and topography in the friction track. As shown by XPS analysis, a transfer of iron atoms from the steel ball to the ta-C layer occurred, forming iron oxy-hydroxide (FeOOH) termination on both surfaces. Between them, theoretical calculations show that a nanometre-thick fluid film consisting of glycerol and its degradation products prevents direct contact between the solid surfaces by nm-thick film EHL lubrication and results in the superlow friction, in agreement with the experiment. Furthermore, molecular dynamics (MD) simulations reveal that hydrogen atoms act as "low-friction brushes" between sliding layers of crystalline FeOOH, resulting also in low friction. A new model of sustainable green superlubricity is proposed. The tribo-formation of FeOOH with glycerol leads to a unique polishing process, which in turn leads to a self-sustained Elasto-Hydrodynamic Lubrication (EHL) regime until the very thin fluid film is no more than a few nanometres thick. At lower thicknesses, the hydroxide layer takes over. Wear of the ta-C coating is negligible, while wear on the steel ball is very moderate and acceptable for many practical applications, such as bio-tribology and the food industry, in which green lubrication is especially needed.
| S-EPMC6472501 | biostudies-literature
Project description:Ubiquitination and deubiquitination processes are widely involved in modulating the function, activity, localization, and stability of multiple cellular proteins regulating almost every aspect of cellular function. Several virus families have been shown to exploit the cellular ubiquitin-conjugating system to achieve a productive infection: enter the cell, promote genome replication, or assemble and release viral progeny. In this study, we analyzed the role of deubiquitinating enzymes (DUBs) during chikungunya virus (CHIKV) infection. HEK293T, Vero-E6, and Huh-7 cells were treated with two DUB inhibitors (PR619 or WP1130). Then, infected cells were evaluated by flow cytometry, and viral progeny was quantified using the plaque assay method. The changes in viral proteins and viral RNA were analyzed using Western blotting and RT-qPCR, respectively. Results indicate that treatment with DUB inhibitors impairs CHIKV replication due to significant protein and viral RNA synthesis deregulation. Therefore, DUB activity may be a pharmacological target for blocking CHIKV infection.
| S-EPMC9966916 | biostudies-literature
Project description:The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium 'RNA reactor' enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.
| S-EPMC9032526 | biostudies-literature
Project description:Relative motion between soft wet solids arises in a number of applications in natural and artificial settings, and invariably couples elastic deformation fluid flow. We explore this in a minimal setting by considering a fluid-immersed negatively buoyant cylinder moving along a soft inclined wall. Our experiments show that there is an emergent robust steady-state sliding regime of the cylinder with an effective friction that is significantly reduced relative to that of rigid fluid-lubricated contacts. A simple scaling approach that couples the cylinder-induced flow to substrate deformation allows us to explain the elastohydrodynamic lift that underlies the self-sustained lubricated motion of the cylinder, consistent with recent theoretical predictions. Our results suggest an explanation for a range of effects such as reduced wear in animal joints and long-runout landslides, and can be couched as a design principle for low-friction interfaces.
| S-EPMC4889378 | biostudies-literature