scholarly journals Solvation and Stabilization of Single Strand RNA at the Air/ice Interface Support a Primordial RNA World on Ice

2020 ◽  
Author(s):  
Ivan Gladich ◽  
Margaret Berrens ◽  
Penny Rowe ◽  
Rodolfo Pereyra ◽  
Steven Neshyba
Keyword(s):  
Rna World ◽  
Nucleophilic Attack ◽  
Oh Groups ◽  
Phosphate Diester ◽  
Quasi Liquid Layer ◽  
The Stability ◽  
World Hypothesis ◽  
Dynamics Simulations ◽  
Recent Experimental Work ◽  
Rna World Hypothesis

<div>Outstanding questions about the RNA world hypothesis for the emergence of life</div><div>on Earth concern the stability and self-replication of prebiotic aqueous RNA.</div><div>Recent experimental work has suggested that solid substrates and low</div><div>temperatures could help resolve these issues. Here, we use classical molecular</div><div>dynamics simulations to explore the possibility that the substrate is ice itself. We</div><div>find that at -20 C, a quasi-liquid layer at the air/ice interface solvates a short (8-</div><div>nucleotide) RNA strand such that phosphate groups tend to anchor to specific</div><div>points of the underlying crystal lattice, lengthening the strand. Hydrophobic bases,</div><div>meanwhile, tend to migrate to the air/ice interface. Further, contacts between</div><div>solvent water and ribose 2-OH’ groups are found to occur less frequently for RNA</div><div>on ice than for aqueous RNA at the same temperature; this reduces the likelihood</div><div>of deprotonation of the 2-OH’ and its subsequent nucleophilic attack on the</div><div>phosphate diester. The implied enhanced resistance to hydrolysis, in turn, could</div><div>increase opportunities for polymerization and self-copying. These findings thus</div><div>offer the possibility of a role for an ancient RNA world on ice distinct from that</div><div>considered in extant elaborations of the RNA world hypothesis. This work is, to the</div><div>best of our knowledge, the first molecular dynamics study of RNA on ice</div>

scholarly journals Solvation and Stabilization of Single Strand RNA at the Air/ice Interface Support a Primordial RNA World on Ice

2020 ◽  
Author(s):  
Ivan Gladich ◽  
Margaret Berrens ◽  
Penny Rowe ◽  
Rodolfo Pereyra ◽  
Steven Neshyba
Keyword(s):  
Rna World ◽  
Nucleophilic Attack ◽  
Oh Groups ◽  
Phosphate Diester ◽  
Quasi Liquid Layer ◽  
The Stability ◽  
World Hypothesis ◽  
Dynamics Simulations ◽  
Recent Experimental Work ◽  
Rna World Hypothesis

<div>Outstanding questions about the RNA world hypothesis for the emergence of life</div><div>on Earth concern the stability and self-replication of prebiotic aqueous RNA.</div><div>Recent experimental work has suggested that solid substrates and low</div><div>temperatures could help resolve these issues. Here, we use classical molecular</div><div>dynamics simulations to explore the possibility that the substrate is ice itself. We</div><div>find that at -20 C, a quasi-liquid layer at the air/ice interface solvates a short (8-</div><div>nucleotide) RNA strand such that phosphate groups tend to anchor to specific</div><div>points of the underlying crystal lattice, lengthening the strand. Hydrophobic bases,</div><div>meanwhile, tend to migrate to the air/ice interface. Further, contacts between</div><div>solvent water and ribose 2-OH’ groups are found to occur less frequently for RNA</div><div>on ice than for aqueous RNA at the same temperature; this reduces the likelihood</div><div>of deprotonation of the 2-OH’ and its subsequent nucleophilic attack on the</div><div>phosphate diester. The implied enhanced resistance to hydrolysis, in turn, could</div><div>increase opportunities for polymerization and self-copying. These findings thus</div><div>offer the possibility of a role for an ancient RNA world on ice distinct from that</div><div>considered in extant elaborations of the RNA world hypothesis. This work is, to the</div><div>best of our knowledge, the first molecular dynamics study of RNA on ice</div>

Molecular Dynamics simulations indicate solvation and stability of single-strand RNA at the air/ice interface, supporting a primordial RNA world on Ice

2020 ◽  
Author(s):  
Steven Neshyba ◽  
Ivan Gladich ◽  
Penny Rowe ◽  
Maggie Berrens ◽  
Rodolfo Pereyra
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Rna World ◽  
Nucleophilic Attack ◽  
Solvent Water ◽  
Phosphate Diester ◽  
World Hypothesis ◽  
Dynamics Simulations ◽  
Rna World Hypothesis

&lt;p&gt;Outstanding questions about the RNA world hypothesis for the emergence of life on Earth concern the stability and self-replication of prebiotic aqueous RNA. Recent experimental work has suggested that solid substrates and low temperatures could help resolve these issues. Here, we use classical molecular dynamics simulations to explore the possibility that the substrate is ice itself. We find that at -20 C, a quasi-liquid layer at the air/ice interface partially solvates a short (8-nucleotide) RNA strand such that the phosphate backbone anchors to the underlying crystalline ice structure though long-lived hydrogen bonds. The hydrophobic bases, meanwhile, are seen to migrate toward the outermost layer, exposed to air. Our simulations also reveal two key kinetic differences with respect to aqueous RNA. First, hydrogen bonds between solvent water molecules and phosphate diester moieties, believed to shield the RNA from hydrolysis, are much longer-lived for RNA on ice, compared to aqueous RNA at the same temperature. Second, contact between solvent water and ribose 2-OH&amp;#8217; groups, considered a precursor to nucleophilic attack by deprotonated 2-OH&amp;#8217; on the phosphate diester, is significantly less frequent for RNA on ice. Both differences point to lower susceptibility to hydrolysis of RNA on ice, and therefore increased opportunities for polymerization and self-copying compared to aqueous RNA. Moreover, exposure of hydrophobic bases at the air/ice interface offers opportunities for reaction that are not readily available to aqueous RNA (e.g., base-pairing reaction with free nucleotides diffusing across the air/ice interface). These findings thus offer the possibility of a role for an ancient RNA world on ice distinct from that considered in extant elaborations of the RNA world hypothesis. This work is, to the best of our knowledge, the first molecular dynamics study of RNA on ice.&lt;/p&gt;

Randomness and Complexity

2018 ◽  
Author(s):  
Steven E. Vigdor
Keyword(s):  
Quantum Mechanics ◽  
Natural Selection ◽  
Rna World ◽  
Biological Evolution ◽  
Variable Theory ◽  
Cosmological Natural Selection ◽  
Einstein Podolsky Rosen ◽  
World Hypothesis ◽  
Rna World Hypothesis

Chapter 7 describes the fundamental role of randomness in quantum mechanics, in generating the first biomolecules, and in biological evolution. Experiments testing the Einstein–Podolsky–Rosen paradox have demonstrated, via Bell’s inequalities, that no local hidden variable theory can provide a viable alternative to quantum mechanics, with its fundamental randomness built in. Randomness presumably plays an equally important role in the chemical assembly of a wide array of polymer molecules to be sampled for their ability to store genetic information and self-replicate, fueling the sort of abiogenesis assumed in the RNA world hypothesis of life’s beginnings. Evidence for random mutations in biological evolution, microevolution of both bacteria and antibodies and macroevolution of the species, is briefly reviewed. The importance of natural selection in guiding the adaptation of species to changing environments is emphasized. A speculative role of cosmological natural selection for black-hole fecundity in the evolution of universes is discussed.

scholarly journals Transcription and translation in an RNA world

2006 ◽  
Vol 361 (1474) ◽  
pp. 1751-1760 ◽  
Author(s):  
William R Taylor
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Rna World ◽  
Large Subunit ◽  
Trna Synthetase ◽  
Nucleoside Triphosphate ◽  
Amino Acid Binding ◽  
World Hypothesis ◽  
Protein Elongation ◽  
Rna World Hypothesis

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90°C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have ‘poisoned’ the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors.

scholarly journals RNA Back and Forth: Looking through Ribozyme and Viroid Motifs

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 283 ◽  
Author(s):  
Marie-Christine Maurel ◽  
Fabrice Leclerc ◽  
Jacques Vergne ◽  
Giuseppe Zaccai
Keyword(s):  
Rna World ◽  
Hammerhead Ribozyme ◽  
Intramolecular Interactions ◽  
Modern World ◽  
Widespread Occurrence ◽  
Living Fossils ◽  
Evolution Of Life ◽  
Catalytically Active ◽  
World Hypothesis ◽  
Rna World Hypothesis

Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the “RNA world” hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the widespread occurrence of HHRs in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitous features of life. Those are the structural and functional versatility of small RNAs, ribozymes, and viroids, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.

The “Strong” RNA World Hypothesis: Fifty Years Old

Astrobiology ◽  
2013 ◽  
Vol 13 (4) ◽  
pp. 391-403 ◽  
Author(s):  
Marc Neveu ◽  
Hyo-Joong Kim ◽  
Steven A. Benner
Keyword(s):  
Rna World ◽  
World Hypothesis ◽  
Rna World Hypothesis

scholarly journals Solvent viscosity facilitates replication and ribozyme catalysis from an RNA duplex in a model prebiotic process

2019 ◽  
Vol 47 (13) ◽  
pp. 6569-6577 ◽  
Author(s):  
Christine He ◽  
Adriana Lozoya-Colinas ◽  
Isaac Gállego ◽  
Martha A Grover ◽  
Nicholas V Hud
Keyword(s):  
Information Transfer ◽  
Rna World ◽  
Hammerhead Ribozyme ◽  
Information Storage ◽  
Additional Challenge ◽  
The Origin Of Life ◽  
World Hypothesis ◽  
Synthesis Reactions ◽  
Rna World Hypothesis ◽  
Single Sequence

Abstract The RNA World hypothesis posits that RNA was once responsible for genetic information storage and catalysis. However, a prebiotic mechanism has yet to be reported for the replication of duplex RNA that could have operated before the emergence of polymerase ribozymes. Previously, we showed that a viscous solvent enables information transfer from one strand of long RNA duplex templates, overcoming ‘the strand inhibition problem'. Here, we demonstrate that the same approach allows simultaneous information transfer from both strands of long duplex templates. An additional challenge for the RNA World is that structured RNAs (like those with catalytic activity) function poorly as templates in model prebiotic RNA synthesis reactions, raising the question of how a single sequence could serve as both a catalyst and as a replication template. Here, we show that a viscous solvent also facilitates the transition of a newly synthesized hammerhead ribozyme sequence from its inactive, duplex state to its active, folded state. These results demonstrate how fluctuating environmental conditions can allow a ribozyme sequence to alternate between acting as a template for replication and functioning as a catalyst, and illustrate the potential for temporally changing environments to enable molecular processes necessary for the origin of life.

scholarly journals Expanding the informational chemistries of life: peptide/RNA networks

2017 ◽  
Vol 375 (2109) ◽  
pp. 20160356 ◽  
Author(s):  
Olga Taran ◽  
Chenrui Chen ◽  
Tolulope O. Omosun ◽  
Ming-Chien Hsieh ◽  
Allisandra Rha ◽  
...  
Keyword(s):  
Rna World ◽  
Chemical Information ◽  
Disease States ◽  
Complementary Approach ◽  
The Subject ◽  
Active Research ◽  
World Hypothesis ◽  
Reaction Cascades ◽  
Rna World Hypothesis ◽  
Emergent Behaviours

The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond. This article is part of the themed issue ‘Reconceptualizing the origins of life’.

scholarly journals Depsipeptide nucleic acids: prebiotic formation, oligomerization, and self-assembly of a new candidate proto-nucleic acid

2020 ◽  
Author(s):  
David M. Fialho ◽  
Suneesh C. Karunakaran ◽  
Katherine W. Greeson ◽  
Isaac Martínez ◽  
Gary B. Schuster ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Self Assembly ◽  
Rna World ◽  
Chemical Components ◽  
Early Earth ◽  
New Class ◽  
Self Assembling ◽  
World Hypothesis ◽  
Rna World Hypothesis

AbstractThe mechanism by which genetic polymers spontaneously formed on the early Earth is currently unknown. The RNA World hypothesis implies that RNA oligomers were produced prebiotically, but the demonstration of this process has proven challenging. Alternatively, RNA may be the product of evolution and some, or all, of its chemical components may have been preceded by functionally analogous moieties that were more readily accessible under plausible early-Earth conditions. We report a new class of nucleic acid analog, depsipeptide nucleic acid, which displays several properties that make it an attractive candidate for the first informational polymer to arise on the Earth. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these depsipeptide nucleic acid oligomers are capable of complementary self-assembly, and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers may have been relatively facile.

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