Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Zhang, David Y.; Turberfield, Andrew J.; Yurke, Bernard; Winfree, Erik

doi:10.1126/science.1148532

Cited by 1,063 publications

(1,115 citation statements)

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“…The field of structural DNA nanotechnology (Seeman, 1998) has produced several powerful self-assembly approaches, including DNA origami (Rothemund, 2006) and bricks (Ke et al, 2012), that are capable of making complex structures from pure DNA. Meanwhile, the complementary field of dynamic DNA nanotechnology has shown how to create DNA reaction networks that incorporate feedback and logic gates (Zhang et al, 2007). These networks use DNA itself as the fuel source, in the form of hybridized structures such as hairpins.…”

Section: A Experimental Advances In Particle Interactionsmentioning

confidence: 99%

Colloquium : Toward living matter with colloidal particles

2017

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A fundamental unsolved problem is to understand the differences between inanimate matter and living matter. Although this question might be framed as philosophical, there are many fundamental and practical reasons to pursue the development of synthetic materials with the properties of living ones. There are three fundamental properties of living materials that we seek to reproduce: The ability to spontaneously assemble complex structures; the ability to self-replicate; and the ability to perform complex and coordinated reactions that enable transformations impossible to realize if a single structure acted alone. The conditions that are required for a synthetic material to have these properties are currently unknown. This colloquium examines whether these phenomena could emerge by programming interactions between colloidal particles, an approach that bootstraps off of recent advances in DNA nanotechnology and in the mathematics of sphere packings. We argue that the essential properties of living matter could emerge from colloidal interactions that are specific -so that each particle can be programmed to bind or not bind to any other particleand also time-dependent -so that the binding strength between two particles could increase or decrease in time at a controlled rate. There is a small regime of interaction parameters that give rise to colloidal particles with life-like properties, including self-assembly, self-replication and metabolism. The parameter range for these phenomena can be identified using a combinatorial search over the set of known sphere packings. * zorana.zeravcic@espci.fr 2 CONTENTS

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Section: A Experimental Advances In Particle Interactionsmentioning

confidence: 99%

Colloquium : Toward living matter with colloidal particles

2017

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“…DNA strand displacement systems (DSDs) (Yurke and Mills 2003;Zhang et al 2007) and chemical reaction networks (CRNs) (Cook et al 2009;Soloveichik 2009Soloveichik , 2008 are important molecular programming models. DSDs provide sophisticated molecular realizations of logic circuits and even artificial neurons Qian et al 2011b), while CRNs elegantly express chemical programs that can then be translated into DSDs (Chen et al 2012;Soloveichik et al 2008Soloveichik et al , 2010.…”

Section: Introductionmentioning

confidence: 99%

Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems

Condon

Kirkpatrick

Maňuch

2012

Lecture Notes in Computer Science

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Chemical reaction networks (CRNs) and DNA strand displacement systems (DSDs) are widely-studied and useful models of molecular programming. However, in order for some DSDs in the literature to behave in an expected manner, the initial number of copies of some reagents is required to be fixed. In this paper we show that, when multiple copies of all initial molecules are present, general types of CRNs and DSDs fail to work correctly if the length of the shortest sequence of reactions needed to produce any given molecule exceeds a threshold that grows polynomially with attributes of the system.

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“…(Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision 2,4,8,9,11,12,19 . A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result.…”

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confidence: 96%

“…Biomolecular implementations of finite automata 8,9 and logic gates 4,[10][11][12][13] have already been developed [14][15][16][17][18] . Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions.…”

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confidence: 99%

“…In contrast, our system has a half time of 3 min per logical deduction, and deductions do not slow down measurably when cascaded. In addition, our molecular implementation maintains efficient digital behaviour, exhibiting very low signal leakage and keeping a high signal yield and strength when cascaded, eliminating the need for signal restoration thresholds and amplifier gates to protect against noise, signal loss and leaky reactions as needed in earlier systems 4,12 . To demonstrate these features of our system, we designed a simple four-step cascaded deduction experiment.…”

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Molecular implementation of simple logic programs

2009

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Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications [1][2][3][4][5][6][7] . Biomolecular implementations of finite automata 8,9 and logic gates 4,10-13 have already been developed [14][15][16][17][18] . Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) Man(X) (Every Man is Mortal), the system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision 2,4,8,9,11,12,19 . A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.Our logic system consists of propositions, implications and queries, represented by short DNA molecules, some single-stranded and some double-stranded, as shown in Fig. 1a. A proposition p, such as 'Socrates is a Man', is represented by a double-stranded (ds) DNA molecule with a sticky end representing p on one end and a fluorophore (a fluorescent molecule) with a matching quencher (a molecule that absorbs excitation energy from a fluorophore) at its other end. A query p?, such as 'Is Socrates a Man?', is represented by a dsDNA molecule with a sticky end complementary to the representation of p and a recognition site (marked light red) for the restriction enzyme FokI. A molecular query p? can be positively answered by the molecular proposition p, because they have complementary sticky ends, as shown in Fig. 1b. The sticky end of the query molecule q? hybridizes with that of the proposition molecule q. FokI is attracted to its recognition site on the query (before hybridization or possibly following it) and cleaves the proposition molecule q. This results in the separation of its remaining sense and antisense strands, which in turn abolishes the quenching of the green fluorophore, allowing the fluorophore to emit green light in response to light excitation. This green emission can be interpreted by an outside observer as a positive response to the query.An implication p q (for example 'Socrates is Mortal if Socrates is a Man') is represented by a hairpin single-stranded (ss) DNA with three components: a sticky end representing the proposition p, a segment complementary to the representation of q and a segment that together with an auxiliary complementary strand forms a recognition site for FokI. The implication p q can be used to reduce the query p? to the query q?, meaning that to positively answer p? it suffices to positively answer q? This query reduction is justified by the d...

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Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Cited by 1,063 publications

References 30 publications

Colloquium : Toward living matter with colloidal particles

Colloquium : Toward living matter with colloidal particles

Reachability Bounds for Chemical Reaction Networks and Strand Displacement Systems

Molecular implementation of simple logic programs

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