Copying of RNA Sequences without Pre‐Activation

Jauker, Mario; Grießer, Helmut; Richert, Clemens

doi:10.1002/anie.201506592

Cited by 71 publications

(97 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As reported in Ref. 14, we have found that a combination of the water-soluble carbodiimide EDC and alkylated heterocycles, such as 1-ethylimidazole, induces copying processes in RNA via in situ activation of ribonucleotides, without the need for chemical pre-activation. Carbodiimide is a tautomer of cyanamide, a compound formed under presumed prebiotic conditions 15.…”

supporting

confidence: 60%

Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors

2015

Self Cite

View full text Add to dashboard Cite

How the biochemical machinery evolved from simple precursors is an open question. Here we show that ribonucleotides and amino acids condense to peptidyl RNAs in the absence of enzymes under conditions established for genetic copying. Untemplated formation of RNA strands that can encode genetic information, formation of peptidyl chains linked to RNA, and formation of the cofactors NAD+, FAD, and ATP all occur under the same conditions. In the peptidyl RNAs, the peptide chains are phosphoramidate-linked to a ribonucleotide. Peptidyl RNAs with long peptide chains were selected from an initial pool when a lipophilic phase simulating the interior of membranes was offered, and free peptides were released upon acidification. Our results show that key molecules of genetics, catalysis, and metabolism can emerge under the same conditions, without a mineral surface, without an enzyme, and without the need for chemical pre-activation.

show abstract

supporting

confidence: 60%

Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors

2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…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.…”

mentioning

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.

View full text Add to dashboard Cite

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...

show abstract

“…The drawback of this approach lies in the number of additional reaction components and the formation of side products that might interfere with the condensation reaction [23]. Water-soluble carbodiimides, like 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) [24] and hydroxy-7-azabenzotriazole (HOAt), have been used [25,26,27]. In the laboratory, 10 molar equivalents of EDC for guanine monomers and 50 molar equivalents for thymidine/uridine monomers are however required to yield an efficient coupling [23].…”

Section: Rna World Hypothesismentioning

confidence: 99%

“…The hybridization can force the template into an A-helix form for RNA that clearly enhances the rates [45], and the primer offers a base-stacking surface for the new approaching base, which will improve monomer association with the templating sequence. In a few studies [24,25,46], the interactions between the incoming monomer and template at the 3′ end of the primer were strengthened by the addition of short oligomers (4 to 6 nt) that hybridized downstream from the monomer insertion point (System (iii)): in such a system, the incoming monomer is associated more tightly with the template due to the increased stacking, hence increasing its probability to be linked to the primer. However, this last system should be viewed as a technological fix to improve sequence-specific monomer incorporation than a truly plausible prebiotic setup.…”

Section: Rna Polymerization In Bulk Aqueous Mediamentioning

confidence: 99%

“…Reactants are diluted very quickly, as diffusion rates are high, and water shifts the equilibrium towards hydrolysis. RNA polymerization reactions usually require critical concentrations of monomers [40] or of their precursors [24] in the range of several 10 s to 100 s mM [17] for an effective product synthesis (both in terms of numbers of molecules and their length). Such concentrations on the early Earth seem to be unrealistic in a bulk aqueous medium.…”

Section: Heterogeneous Media As Supporting Environments For Rna Pomentioning

confidence: 99%

See 1 more Smart Citation

Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

Monnard

2016

Life

View full text Add to dashboard Cite

Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.

show abstract

Copying of RNA Sequences without Pre‐Activation

Cited by 71 publications

References 47 publications

Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors

Spontaneous Formation of RNA Strands, Peptidyl RNA, and Cofactors

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

Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

Contact Info

Product

Resources

About