Self-Assembly of Informational Polymers by Templated Ligation

Rosenberger, Joachim H.; Göppel, Tobias; Kudella, Patrick W.; Braun, Dieter; Gerland, Ulrich; Altaner, Bernhard

doi:10.1103/physrevx.11.031055

Cited by 22 publications

(44 citation statements)

References 78 publications

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“…Indeed, in Ref. 40 , in a bottom-up, coarse-grained model of a replicating system that obeyed similar dynamics to that described by the model in Fig. 2, the authors observed the formation of only long polymers that remained bound in complexes under isothermal conditions.…”

Section: Slow Cooperative Releasementioning

confidence: 73%

“…One could imagine, if the concentration of polymers in the bath grew to significant levels, that rebinding could occur. Indeed, the rebinding and subsequent elongation of prod-ucts was presented as a plausible pathway to the generation of longer RNA oligomers, bridging a portion of the gap between short RNA building blocks and the long RNA molecules that make up ribozymes in a pair of papers on templated ligation in an RNA world 39,40 . However, in our mechanism, polymerisation is coupled to the disruption of the copy-template bonds, reducing the interaction strength that most units in the polymer chain could rebind by.…”

Section: Discussionmentioning

confidence: 99%

“…In a recent theoretical and experimental work on non-enzymatic templated assembly, Rosenberger et al demonstrated that polymer aggregates with well-defined length-scales can be generated from short building blocks under isothermal conditions. However, these polymers were bound up in complexes, not separated from their templates 40 .…”

Section: Introductionmentioning

confidence: 99%

“…This disparity suggests a poor understanding of templating relative to self-assembly, and also represents a missed opportunity to harness biology's most important mechanism of producing complexity -both to generate synthetic sequence-controlled polymers 30 , and in the context of combinatorial molecular discovery 31,32 . Moreover, central questions in the RNA world hypothesis, and the origin of life itself, relate to the appearance of the first systems that could reliably copy sequence information encoded in templates [33][34][35][36][37][38][39][40] . Therefore, in this paper, we investigate minimal mechanisms for templated copying through a series of computational models that will guide the design of synthetic template copying systems.…”

Section: Introductionmentioning

confidence: 99%

“…Braun and colleagues have exploited the convective currents generated by thermal gradients, inspired by oceanic thermal vents 58 , with templating and polymerisation occurring in cool regions and separation in hot regions [53][54][55] . Environments with spatially and/or temporally varying conditions are thought to have been essential in the emergence of pre-biotic RNA-zymes from short building blocks under the RNA world hypothesis of the emergence of life [33][34][35][36][37][38][39][40] .…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions

Juritz,

Poulton,

Ouldridge

2021

Preprint

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Section: Slow Cooperative Releasementioning

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions

Juritz,

Poulton,

Ouldridge

2021

Preprint

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Abiogenesis through gradual evolution of autocatalysis into template‐based replication

et al. 2022

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How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.

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RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends

Todisco,

Radakovic,

Szostak

2024

J. Am. Chem. Soc.

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Multiple RNA strands can interact in solution and assume a large variety of configurations dictated by their potential for base pairing. Although duplex formation from two complementary oligonucleotides has been studied in detail, we still lack a systematic characterization of the behavior of higher order complexes. Here, we focus on the thermodynamic and kinetic effects of an upstream oligonucleotide on the binding of a downstream oligonucleotide to a common template, as we vary the sequence and structure of the contact interface. We show that coaxial stacking in RNA is well correlated with but much more stabilizing than helix propagation over an analogous intact double helix step (median ΔΔG°3 7 °C ≈ 1.7 kcal/mol). Consequently, approximating coaxial stacking in RNA with the helix propagation term leads to large discrepancies between predictions and our experimentally determined melting temperatures, with an offset of ≈10 °C. Our kinetic study reveals that the hybridization of the downstream probe oligonucleotide is impaired (lower k on ) by the presence of the upstream oligonucleotide, with the thermodynamic stabilization coming entirely from an extended lifetime (lower k off ) of the bound downstream oligonucleotide, which can increase from seconds to months. Surprisingly, we show that the effect of nicks is dependent on the length of the stacking oligonucleotides, and we discuss the binding of ultrashort (1−4 nt) oligonucleotides that are relevant in the context of the origin of life. The thermodynamic and kinetic data obtained in this work allow for the prediction of the formation and stability of higher-order multistranded complexes.

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Self-Assembly of Informational Polymers by Templated Ligation

Cited by 22 publications

References 78 publications

Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions

Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions

Abiogenesis through gradual evolution of autocatalysis into template‐based replication

RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends

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