Spontaneous emergence of autocatalytic information-coding polymers
Abstract
Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical analysis of the problem of spontaneous emergence of autocatalysis for heteropolymers capable of template-assisted ligation driven by cyclic changes in the environment. Our central result is the existence of the first order transition between the regime dominated by free monomers and that with a self-sustaining population of sufficiently long chains. We provide a simple, mathematically tractable model supported by numerical simulations, which predicts the distribution of chain lengths and the onset of autocatalysis in terms of the overall monomer concentration and two fundamental rate constants. Another key result of our study is the emergence of the kinetically limited optimal overlap length between a template and each of its two substrates. The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems.
- Authors:
-
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Brookhaven National Lab. (BNL), Upton, NY (United States); Univ. of Illinois, Champaign, IL (United States)
- Publication Date:
- Research Org.:
- Brookhaven National Laboratory (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1213392
- Alternate Identifier(s):
- OSTI ID: 1228708
- Report Number(s):
- BNL-108290-2015-JA
Journal ID: ISSN 0021-9606; JCPSA6; KC0403020; TRN: US1500647
- Grant/Contract Number:
- SC0012704; PM-031
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Journal of Chemical Physics
- Additional Journal Information:
- Journal Volume: 143; Journal Issue: 4; Journal ID: ISSN 0021-9606
- Publisher:
- American Institute of Physics (AIP)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 77 NANOSCIENCE AND NANOTECHNOLOGY; copolymers; polymerization; free energy; sequence analysis; number theory
Citation Formats
Tkachenko, Alexei V., and Maslov, Sergei. Spontaneous emergence of autocatalytic information-coding polymers. United States: N. p., 2015.
Web. doi:10.1063/1.4922545.
Tkachenko, Alexei V., & Maslov, Sergei. Spontaneous emergence of autocatalytic information-coding polymers. United States. https://doi.org/10.1063/1.4922545
Tkachenko, Alexei V., and Maslov, Sergei. 2015.
"Spontaneous emergence of autocatalytic information-coding polymers". United States. https://doi.org/10.1063/1.4922545. https://www.osti.gov/servlets/purl/1213392.
@article{osti_1213392,
title = {Spontaneous emergence of autocatalytic information-coding polymers},
author = {Tkachenko, Alexei V. and Maslov, Sergei},
abstractNote = {Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical analysis of the problem of spontaneous emergence of autocatalysis for heteropolymers capable of template-assisted ligation driven by cyclic changes in the environment. Our central result is the existence of the first order transition between the regime dominated by free monomers and that with a self-sustaining population of sufficiently long chains. We provide a simple, mathematically tractable model supported by numerical simulations, which predicts the distribution of chain lengths and the onset of autocatalysis in terms of the overall monomer concentration and two fundamental rate constants. Another key result of our study is the emergence of the kinetically limited optimal overlap length between a template and each of its two substrates. The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems.},
doi = {10.1063/1.4922545},
url = {https://www.osti.gov/biblio/1213392},
journal = {Journal of Chemical Physics},
issn = {0021-9606},
number = 4,
volume = 143,
place = {United States},
year = {Tue Jul 28 00:00:00 EDT 2015},
month = {Tue Jul 28 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
A model for the origin of life
journal, September 1982
- Dyson, Freeman J.
- Journal of Molecular Evolution, Vol. 18, Issue 5
Self-replicating colloidal clusters
journal, January 2014
- Zeravcic, Zorana; Brenner, Michael P.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 5
The Origins of the RNA World
journal, April 2010
- Robertson, M. P.; Joyce, G. F.
- Cold Spring Harbor Perspectives in Biology, Vol. 4, Issue 5
Self-Sustained Replication of an RNA Enzyme
journal, February 2009
- Lincoln, T. A.; Joyce, G. F.
- Science, Vol. 323, Issue 5918
A principle of natural self-organization: Part A: Emergence of the hypercycle
journal, November 1977
- Eigen, Manfred; Schuster, Peter
- Naturwissenschaften, Vol. 64, Issue 11
Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences
journal, February 2012
- Derr, Julien; Manapat, Michael L.; Rajamani, Sudha
- Nucleic Acids Research, Vol. 40, Issue 10
Autocatalytic sets of proteins
journal, March 1986
- Kauffman, Stuart A.
- Journal of Theoretical Biology, Vol. 119, Issue 1
RNA-catalysed synthesis of complementary-strand RNA
journal, June 1989
- Doudna, Jennifer A.; Szostak, Jack W.
- Nature, Vol. 339, Issue 6225
Prebiotic Chemistry and the Origin of the RNA World
journal, January 2004
- Leslie E., Orgel
- Critical Reviews in Biochemistry and Molecular Biology, Vol. 39, Issue 2
Genome rhetoric and the emergence of compositional bias
journal, December 2008
- Vetsigian, K.; Goldenfeld, N.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 1
Self-replication of information-bearing nanoscale patterns
journal, October 2011
- Wang, Tong; Sha, Ruojie; Dreyfus, Rémi
- Nature, Vol. 478, Issue 7368
Autocatalytic Sets and the Growth of Complexity in an Evolutionary Model
journal, December 1998
- Jain, Sanjay; Krishna, Sandeep
- Physical Review Letters, Vol. 81, Issue 25
Suggested model for prebiotic evolution: the use of chaos.
journal, June 1983
- Anderson, P. W.
- Proceedings of the National Academy of Sciences, Vol. 80, Issue 11
Liquid crystal self-assembly of random-sequence DNA oligomers
journal, January 2012
- Bellini, T.; Zanchetta, G.; Fraccia, T. P.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 4
Escalation of polymerization in a thermal gradient
journal, April 2013
- Mast, C. B.; Schink, S.; Gerland, U.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 20
Kinetic and Mechanistic Analysis of Nonenzymatic, Template-Directed Oligoribonucleotide Ligation
journal, January 1996
- Rohatgi, Rajat; Bartel, David P.; Szostak, Jack W.
- Journal of the American Chemical Society, Vol. 118, Issue 14
Works referencing / citing this record:
Cooperative ligation breaks sequence symmetry and stabilizes early molecular replication
text, January 2018
- Toyabe, Shoichi; Braun, Dieter
- arXiv
Selection of self-priming molecular replicators
journal, January 2019
- Park, Daechan; Ellington, Andrew D.; Jung, Cheulhee
- Nucleic Acids Research, Vol. 47, Issue 5
Cooperative Ligation Breaks Sequence Symmetry and Stabilizes Early Molecular Replication
journal, March 2019
- Toyabe, Shoichi; Braun, Dieter
- Physical Review X, Vol. 9, Issue 1
The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture
journal, October 2017
- Tupper, Andrew; Shi, Kevin; Higgs, Paul
- Life, Vol. 7, Issue 4
Limited Sequence Diversity Within a Population Supports Prebiotic RNA Reproduction
journal, February 2019
- Mizuuchi, Ryo; Lehman, Niles
- Life, Vol. 9, Issue 1
Survival of self-replicating molecules under transient compartmentalization with natural selection
posted_content, September 2019
- Laurent, Gabin; Peliti, Luca; Lacoste, David
- Life
Survival of self-replicating molecules under transient compartmentalization with natural selection
posted_content, September 2019
- Laurent, Gabin; Peliti, Luca; Lacoste, David
- Life
Open flow non-enzymatic template catalysis and replication
journal, January 2018
- Gonçalves da Silva, Larwsk H.; Hochberg, David
- Physical Chemistry Chemical Physics, Vol. 20, Issue 21
Reaction kinetics in open reactors and serial transfers between closed reactors
journal, April 2018
- Blokhuis, Alex; Lacoste, David; Gaspard, Pierre
- The Journal of Chemical Physics, Vol. 148, Issue 14
Onset of natural selection in populations of autocatalytic heteropolymers
journal, October 2018
- Tkachenko, Alexei V.; Maslov, Sergei
- The Journal of Chemical Physics, Vol. 149, Issue 13
Reaction kinetics in open reactors and serial transfers between closed reactors
text, January 2018
- Blokhuis, Alex; Lacoste, David; Gaspard, Pierre
- arXiv
Length and sequence relaxation of copolymers under recombination reactions
text, January 2017
- Blokhuis, Alex; Lacoste, David
- arXiv
Spontaneous emergence of catalytic cycles with colloidal spheres
journal, April 2017
- Zeravcic, Zorana; Brenner, Michael P.
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 17
Selection of self-priming molecular replicators
journal, January 2019
- Park, Daechan; Ellington, Andrew D.; Jung, Cheulhee
- Nucleic Acids Research, Vol. 47, Issue 5
Limited Sequence Diversity Within a Population Supports Prebiotic RNA Reproduction
journal, February 2019
- Mizuuchi, Ryo; Lehman, Niles
- Life, Vol. 9, Issue 1
Length and sequence relaxation of copolymers under recombination reactions
journal, September 2017
- Blokhuis, Alex; Lacoste, David
- The Journal of Chemical Physics, Vol. 147, Issue 9