The eightfold path to non-enzymatic RNA replication

Szostak, Jack W.

doi:10.1186/1759-2208-3-2

Cited by 308 publications

(387 citation statements)

References 68 publications

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“…Given the wide interest in simple autocatalytic molecules 14,15 and the significant influence of the RNA world hypothesis 16 , molecules capable of template-based self-replication have been studied for many years. This field has advanced to the point that there now exist candidate substrates for the genetic material of a protocell 17 , and it has been proposed that non-enzymatic chemical replication of RNA may even be possible 18 .…”

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confidence: 99%

Physical autocatalysis driven by a bond-forming thiol–ene reaction

2014

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Autocatalysis has been extensively studied because it is central to the propagation of living systems. Chemical systems which self-reproduce like living cells would offer insight into principles underlying biology and its emergence from inanimate matter. Protocellular models feature a surfactant boundary, providing compartmentalization in the form of a micelle or vesicle and any model of the emergence of cellular life must account for the appearance, and evolution of, such boundaries. Here, we describe an autocatalytic system where two relatively simple components combine to form a more complex product. The reaction products aggregate into micelles that catalyse molecular self-reproduction. Study of the reaction kinetics and aggregation behaviour suggests a mechanism involving micelle-mediated physical autocatalysis and led to the rational design of a second-generation system. These reactions are driven by irreversible bond formation and provide a working model for the autocatalytic formation of protocells from the coupling of two simple molecular components.

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confidence: 99%

Physical autocatalysis driven by a bond-forming thiol–ene reaction

2014

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“…The nonenzymatic RNA-templated polymerization of activated nucleotides or oligonucleotides has been extensively studied, with the intent of optimizing the rate, extent, and fidelity of nonenzymatic RNA/DNA polymerization (3,4). Numerous phosphate-activating groups have been studied in the context of nonenzymatic RNA replication.…”

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confidence: 99%

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Zhang

Tam

Walton

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The nonenzymatic copying of RNA templates with imidazoleactivated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3ʹ-hydroxyl oriented to attack the 5ʹ-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazoliumbridged dinucleotide intermediate would be preorganized to react with the primer by in-line S N 2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5ʹ-5ʹ linkage are important for optimal preorganization of the complex, whereas the position of the 5ʹ-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.RNA self-replication | diguanosine dinucleotide | crystal structure | origin of life I n the RNA world hypothesis, the emergence of RNA-catalyzed RNA replication is thought to have been preceded by a stage in which RNA replication was driven purely through chemical processes (1, 2). The nonenzymatic RNA-templated polymerization of activated nucleotides or oligonucleotides has been extensively studied, with the intent of optimizing the rate, extent, and fidelity of nonenzymatic RNA/DNA polymerization (3, 4). Numerous phosphate-activating groups have been studied in the context of nonenzymatic RNA replication. For example, imidazoles such as 2-methylimidazole (5) and, more recently, 2-aminoimidazole (6), have been found to be useful phosphate activators. The potentially prebiotic synthesis of imidazoles under primitive Earth conditions has been investigated (7). On the other hand, Richert and coworkers reported the use of benzotriazole-activated monomers to improve the rate of primer extension (8). In an alternative approach, the in situ activation of monoribonucleotides, and subsequent template-guided polymerization, has been achieved by Richert and coworkers (9), using a carbodiimide reagent together with N-alkyl-imidazole catalysts.Many of the thermodynamic and kinetic parameters associated with nonenzymatic RNA replication have been quantitatively determined (10-14). Until recently, the general assumption has been that nonenzymatic primer extension with activated mononucleotides involves classical S N 2 nucleophilic substitution, in which the nucleophilic 3ʹ-hydroxyl group of the primer attack...

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“…The modulation of base-pair affinity and specificity by simple chemical modifications may have been particularly important during the emergence of the RNA world, before the evolution of polymerase-catalyzed replication. It is an intriguing speculation that the continued use of these modifications in extant biochemistry may be a relic of the chemical origins of life (23).…”

Section: Discussionmentioning

confidence: 99%

Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer

Zhang

Blain

Zielińska

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Recent advances suggest that it may be possible to construct simple artificial cells from two subsystems: a self-replicating cell membrane and a self-replicating genetic polymer. Although multiple pathways for the growth and division of model protocell membranes have been characterized, no self-replicating genetic material is yet available. Nonenzymatic template-directed synthesis of RNA with activated ribonucleotide monomers has led to the copying of short RNA templates; however, these reactions are generally slow (taking days to weeks) and highly error prone. N 3′ -P 5′ -linked phosphoramidate DNA (3′-NP-DNA) is similar to RNA in its overall duplex structure, and is attractive as an alternative to RNA because the high reactivity of its corresponding monomers allows rapid and efficient copying of all four nucleobases on homopolymeric RNA and DNA templates. Here we show that both homopolymeric and mixed-sequence 3′-NP-DNA templates can be copied into complementary 3′-NP-DNA sequences. G:T and A:C wobble pairing leads to a high error rate, but the modified nucleoside 2-thiothymidine suppresses wobble pairing. We show that the 2-thiothymidine modification increases both polymerization rate and fidelity in the copying of a 3′-NP-DNA template into a complementary strand of 3′-NP-DNA. Our results suggest that 3′-NP-DNA has the potential to serve as the genetic material of artificial biological systems.origin of life | nonenzymatic primer extension | artificial genetic systems | nucleotide modifications | mismatch T he phosphoramidate nucleic acids are of particular interest as potential genetic materials for artificial life-forms because of their potential for replication by the nonenzymatic polymerization of amino-sugar nucleotides. Because of the greater nucleophilicity of the amino group relative to the 3′-hydroxyl group of ribo-and deoxyribo-nucleotides, amino-sugar nucleotides exhibit more rapid spontaneous polymerization. Obviating the requirement for a polymerase greatly simplifies the task of creating and assembling the components of an artificial cell, and thus of constructing simple living systems from inanimate materials. We and others have therefore explored the synthesis of a variety of phosphoramidatelinked nucleic acids, their corresponding amino-sugar monomers, and the characterization of nonenzymatic template-directed primer extension reactions in these systems (1-11). Among these systems, we have examined 2′-amino versions of the acyclic glycerol nucleic acid (5), 2′-amino-2′,3′-dideoxyribonucleic acid (4, 6), and 3′-amino-2′,3′-dideoxyribonucleic acid (7).The structural simplicity of the acyclic sugar-phosphate nucleic acid backbones has made them attractive targets for study. Indeed, an acyclic nucleotide consisting of a glycerol-phosphate backbone linked to a formylated nucleobase (12) was among the first of such nucleic acids to be chemically synthesized, but incorporation of this nucleotide into oligomers caused a severe loss of duplex stability. Much later, the glycerol nucleic acids, in which...

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The eightfold path to non-enzymatic RNA replication

Cited by 308 publications

References 68 publications

Physical autocatalysis driven by a bond-forming thiol–ene reaction

Physical autocatalysis driven by a bond-forming thiol–ene reaction

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer

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