Self-Assembly of Informational Polymers by Templated Ligation

The emergence of evermore complex entities from prebiotic building blocks is a key aspect of origins of life research. The RNA-world hypothesis posits that RNA oligomers known as ribozymes acted as the first self-replicating entities. However, the mechanisms governing the self-assembly of complex in...

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Autores principales:	Joachim H. Rosenberger, Tobias Göppel, Patrick W. Kudella, Dieter Braun, Ulrich Gerland, Bernhard Altaner
Formato:	article
Lenguaje:	EN
Publicado:	American Physical Society 2021
Materias:	Physics QC1-999
Acceso en línea:	https://doaj.org/article/0d1a103a49cf4961af5ef350218d0091
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id	oai:doaj.org-article:0d1a103a49cf4961af5ef350218d0091
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spelling	oai:doaj.org-article:0d1a103a49cf4961af5ef350218d00912021-12-02T14:55:00ZSelf-Assembly of Informational Polymers by Templated Ligation10.1103/PhysRevX.11.0310552160-3308https://doaj.org/article/0d1a103a49cf4961af5ef350218d00912021-09-01T00:00:00Zhttp://doi.org/10.1103/PhysRevX.11.031055http://doi.org/10.1103/PhysRevX.11.031055https://doaj.org/toc/2160-3308The emergence of evermore complex entities from prebiotic building blocks is a key aspect of origins of life research. The RNA-world hypothesis posits that RNA oligomers known as ribozymes acted as the first self-replicating entities. However, the mechanisms governing the self-assembly of complex informational polymers from the shortest prebiotic building blocks were unclear. One open issue concerns the relation between concentration and oligonucleotide length, usually assumed to be exponentially decreasing. Here, we show that a competition of timescales in the self-assembly of informational polymers by templated ligation generically leads to nonmonotonic strand-length distributions with two distinct length scales. The first length scale characterizes the onset of a strongly nonequilibrium regime and is visible as a local minimum. Dynamically, this regime is governed by extension cascades, where the elongation of a “primer” with a short building block is more likely than its dehybridization. The second length scale appears as a local concentration maximum and reflects a balance between degradation and dehybridization of completely hybridized double strands in a heterocatalytic extension-reassembly process. Analytical arguments and extensive numerical simulations within a sequence-independent model allowed us to predict and control these emergent length scales. Nonmonotonic strand-length distributions confirming our theory were obtained in thermocycler experiments using random DNA sequences from a binary alphabet. Our work emphasizes the role of structure-forming processes already for the earliest stages of prebiotic evolution. The accumulation of strands with a typical length reveals a possible starting point for higher-order self-organization events that ultimately lead to a self-replicating, evolving system.Joachim H. RosenbergerTobias GöppelPatrick W. KudellaDieter BraunUlrich GerlandBernhard AltanerAmerican Physical SocietyarticlePhysicsQC1-999ENPhysical Review X, Vol 11, Iss 3, p 031055 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Physics QC1-999
spellingShingle	Physics QC1-999 Joachim H. Rosenberger Tobias Göppel Patrick W. Kudella Dieter Braun Ulrich Gerland Bernhard Altaner Self-Assembly of Informational Polymers by Templated Ligation
description	The emergence of evermore complex entities from prebiotic building blocks is a key aspect of origins of life research. The RNA-world hypothesis posits that RNA oligomers known as ribozymes acted as the first self-replicating entities. However, the mechanisms governing the self-assembly of complex informational polymers from the shortest prebiotic building blocks were unclear. One open issue concerns the relation between concentration and oligonucleotide length, usually assumed to be exponentially decreasing. Here, we show that a competition of timescales in the self-assembly of informational polymers by templated ligation generically leads to nonmonotonic strand-length distributions with two distinct length scales. The first length scale characterizes the onset of a strongly nonequilibrium regime and is visible as a local minimum. Dynamically, this regime is governed by extension cascades, where the elongation of a “primer” with a short building block is more likely than its dehybridization. The second length scale appears as a local concentration maximum and reflects a balance between degradation and dehybridization of completely hybridized double strands in a heterocatalytic extension-reassembly process. Analytical arguments and extensive numerical simulations within a sequence-independent model allowed us to predict and control these emergent length scales. Nonmonotonic strand-length distributions confirming our theory were obtained in thermocycler experiments using random DNA sequences from a binary alphabet. Our work emphasizes the role of structure-forming processes already for the earliest stages of prebiotic evolution. The accumulation of strands with a typical length reveals a possible starting point for higher-order self-organization events that ultimately lead to a self-replicating, evolving system.
format	article
author	Joachim H. Rosenberger Tobias Göppel Patrick W. Kudella Dieter Braun Ulrich Gerland Bernhard Altaner
author_facet	Joachim H. Rosenberger Tobias Göppel Patrick W. Kudella Dieter Braun Ulrich Gerland Bernhard Altaner
author_sort	Joachim H. Rosenberger
title	Self-Assembly of Informational Polymers by Templated Ligation
title_short	Self-Assembly of Informational Polymers by Templated Ligation
title_full	Self-Assembly of Informational Polymers by Templated Ligation
title_fullStr	Self-Assembly of Informational Polymers by Templated Ligation
title_full_unstemmed	Self-Assembly of Informational Polymers by Templated Ligation
title_sort	self-assembly of informational polymers by templated ligation
publisher	American Physical Society
publishDate	2021
url	https://doaj.org/article/0d1a103a49cf4961af5ef350218d0091
work_keys_str_mv	AT joachimhrosenberger selfassemblyofinformationalpolymersbytemplatedligation AT tobiasgoppel selfassemblyofinformationalpolymersbytemplatedligation AT patrickwkudella selfassemblyofinformationalpolymersbytemplatedligation AT dieterbraun selfassemblyofinformationalpolymersbytemplatedligation AT ulrichgerland selfassemblyofinformationalpolymersbytemplatedligation AT bernhardaltaner selfassemblyofinformationalpolymersbytemplatedligation
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Self-Assembly of Informational Polymers by Templated Ligation

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