Literature DB >> 22493232

Robust self-replication of combinatorial information via crystal growth and scission.

Rebecca Schulman1, Bernard Yurke, Erik Winfree.   

Abstract

Understanding how a simple chemical system can accurately replicate combinatorial information, such as a sequence, is an important question for both the study of life in the universe and for the development of evolutionary molecular design techniques. During biological sequence replication, a nucleic acid polymer serves as a template for the enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next round of replication. Attempts to understand how replication could occur more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes. Crystal growth propagates a sequence of bits while mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of bits are copied correctly and 78% of 4-bit sequences are correct after two generations; roughly 40 sequence copies are made per growth front per generation. In principle, this process is accurate enough for 1,000-fold replication of 4-bit sequences with 50% yield, replication of longer sequences, and darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for robust chemical sequence replication. The form of the replicated information is also compatible with the replication and evolution of a wide class of materials with precise nanoscale geometry such as plasmonic nanostructures or heterogeneous protein assemblies.

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Year:  2012        PMID: 22493232      PMCID: PMC3340064          DOI: 10.1073/pnas.1117813109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  32 in total

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2.  Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions.

Authors:  Harish Chandran; Nikhil Gopalkrishnan; Bernard Yurke; John Reif
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3.  Plasmonic nanostructures: artificial molecules.

Authors:  Hui Wang; Daniel W Brandl; Peter Nordlander; Naomi J Halas
Journal:  Acc Chem Res       Date:  2007-01       Impact factor: 22.384

4.  Test of Cairns-Smith's 'crystals-as-genes' hypothesis.

Authors:  Theresa Bullard; John Freudenthal; Serine Avagyan; Bart Kahr
Journal:  Faraday Discuss       Date:  2007       Impact factor: 4.008

5.  Folding DNA to create nanoscale shapes and patterns.

Authors:  Paul W K Rothemund
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

6.  An information-bearing seed for nucleating algorithmic self-assembly.

Authors:  Robert D Barish; Rebecca Schulman; Paul W K Rothemund; Erik Winfree
Journal:  Proc Natl Acad Sci U S A       Date:  2009-03-24       Impact factor: 11.205

7.  An analytical solution to the kinetics of breakable filament assembly.

Authors:  Tuomas P J Knowles; Christopher A Waudby; Glyn L Devlin; Samuel I A Cohen; Adriano Aguzzi; Michele Vendruscolo; Eugene M Terentjev; Mark E Welland; Christopher M Dobson
Journal:  Science       Date:  2009-12-11       Impact factor: 47.728

8.  Ribozyme-catalyzed transcription of an active ribozyme.

Authors:  Aniela Wochner; James Attwater; Alan Coulson; Philipp Holliger
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

9.  Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.

Authors:  S B Smith; Y Cui; C Bustamante
Journal:  Science       Date:  1996-02-09       Impact factor: 47.728

10.  Elongational-flow-induced scission of DNA nanotubes in laminar flow.

Authors:  Rizal F Hariadi; Bernard Yurke
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-10-19
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  19 in total

1.  Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics.

Authors:  Rizal F Hariadi; Erik Winfree; Bernard Yurke
Journal:  Proc Natl Acad Sci U S A       Date:  2015-10-26       Impact factor: 11.205

2.  Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly.

Authors:  Thomas G W Edwardson; Karina M M Carneiro; Christopher K McLaughlin; Christopher J Serpell; Hanadi F Sleiman
Journal:  Nat Chem       Date:  2013-09-01       Impact factor: 24.427

3.  Self-replication of DNA rings.

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Journal:  Nat Nanotechnol       Date:  2015-05-11       Impact factor: 39.213

4.  Litters of self-replicating origami cross-tiles.

Authors:  Rebecca Zhuo; Feng Zhou; Xiaojin He; Ruojie Sha; Nadrian C Seeman; Paul M Chaikin
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-23       Impact factor: 11.205

Review 5.  Protocells and RNA Self-Replication.

Authors:  Gerald F Joyce; Jack W Szostak
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-09-04       Impact factor: 10.005

6.  Defining and simulating open-ended novelty: requirements, guidelines, and challenges.

Authors:  Wolfgang Banzhaf; Bert Baumgaertner; Guillaume Beslon; René Doursat; James A Foster; Barry McMullin; Vinicius Veloso de Melo; Thomas Miconi; Lee Spector; Susan Stepney; Roger White
Journal:  Theory Biosci       Date:  2016-05-19       Impact factor: 1.919

7.  Exponential growth and selection in self-replicating materials from DNA origami rafts.

Authors:  Xiaojin He; Ruojie Sha; Rebecca Zhuo; Yongli Mi; Paul M Chaikin; Nadrian C Seeman
Journal:  Nat Mater       Date:  2017-09-18       Impact factor: 43.841

8.  Nonequilibrium correlations in minimal dynamical models of polymer copying.

Authors:  Jenny M Poulton; Pieter Rein Ten Wolde; Thomas E Ouldridge
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-18       Impact factor: 11.205

9.  Kinetic properties of an RNA enzyme that undergoes self-sustained exponential amplification.

Authors:  Antonio C Ferretti; Gerald F Joyce
Journal:  Biochemistry       Date:  2013-02-05       Impact factor: 3.162

10.  Escalation of polymerization in a thermal gradient.

Authors:  Christof B Mast; Severin Schink; Ulrich Gerland; Dieter Braun
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-29       Impact factor: 11.205

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