Publications


Automated design and verification of localized DNA computation circuits

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 9211 (2015) 168-180

MA Boemo, AJ Turberfield, L Cardelli

© Springer International Publishing Switzerland 2015. Simple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a DNA circuit, linking an abstract propositional formula to a physical DNA computation system that is capable of evaluating it.


Guiding the folding pathway of DNA origami.

Nature 525 (2015) 82-86

KE Dunn, F Dannenberg, TE Ouldridge, M Kwiatkowska, AJ Turberfield, J Bath

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its rapid development and become a reliable manufacturing technology.


Modelling DNA origami self-assembly at the domain level.

The Journal of chemical physics 143 (2015) 165102-

F Dannenberg, KE Dunn, J Bath, M Kwiatkowska, AJ Turberfield, TE Ouldridge

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.


DNA walker circuits: computational potential, design, and verification

Natural Computing 14 (2015) 195-211

F Dannenberg, M Kwiatkowska, C Thachuk, AJ Turberfield

© 2014, Springer Science+Business Media Dordrecht. Unlike their traditional, silicon counterparts, DNA computers have natural interfaces with both chemical and biological systems. These can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, DNA strand displacement systems (DSD) can evaluate non-trivial functions. However, these systems can be slow and are susceptible to errors. It has been suggested that localised hybridization reactions could overcome some of these challenges. Localised reactions occur in DNA ‘walker’ systems which were recently shown to be capable of navigating a programmable track tethered to an origami tile. We investigate the computational potential of these systems for evaluating Boolean functions and forming composable circuits. We find that systems of multiple walkers have severely limited potential for parallel circuit evaluation. DNA walkers, like DSDs, are also susceptible to errors. We develop a discrete stochastic model of DNA walker ‘circuits’ based on experimental data, and demonstrate the merit of using probabilistic model checking techniques to analyse their reliability, performance and correctness. This analysis aids in the design of reliable and efficient DNA walker circuits.


Molecular Machinery from DNA: Synthetic Biology from the Bottom up

BIOPHYSICAL JOURNAL 106 (2014) 23A-23A

AJ Turberfield


Transport and self-organization across different length scales powered by motor proteins and programmed by DNA

Nature Nanotechnology 9 (2014) 44-47

AJM Wollman, C Sanchez-Cano, HMJ Carstairs, RA Cross, AJ Turberfield

In eukaryotic cells, cargo is transported on self-organized networks of microtubule trackways by kinesin and dynein motor proteins. Synthetic microtubule networks have previously been assembled in vitro, and microtubules have been used as shuttles to carry cargoes on lithographically defined tracks consisting of surface-bound kinesin motors. Here, we show that molecular signals can be used to program both the architecture and the operation of a self-organized transport system that is based on kinesin and microtubules and spans three orders of magnitude in length scale. A single motor protein, dimeric kinesin-1, is conjugated to various DNA nanostructures to accomplish different tasks. Instructions encoded into the DNA sequences are used to direct the assembly of a polar array of microtubules and can be used to control the loading, active concentration and unloading of cargo on this track network, or to trigger the disassembly of the network. © 2014 Macmillan Publishers Limited.


Transport and self-organization across different length scales powered by motor proteins and programmed by DNA.

Nat Nanotechnol 9 (2014) 44-47

AJM Wollman, C Sanchez-Cano, HMJ Carstairs, RA Cross, AJ Turberfield

In eukaryotic cells, cargo is transported on self-organized networks of microtubule trackways by kinesin and dynein motor proteins. Synthetic microtubule networks have previously been assembled in vitro, and microtubules have been used as shuttles to carry cargoes on lithographically defined tracks consisting of surface-bound kinesin motors. Here, we show that molecular signals can be used to program both the architecture and the operation of a self-organized transport system that is based on kinesin and microtubules and spans three orders of magnitude in length scale. A single motor protein, dimeric kinesin-1, is conjugated to various DNA nanostructures to accomplish different tasks. Instructions encoded into the DNA sequences are used to direct the assembly of a polar array of microtubules and can be used to control the loading, active concentration and unloading of cargo on this track network, or to trigger the disassembly of the network.


Programmable energy landscapes for kinetic control of DNA strand displacement.

Nature communications 5 (2014) 5324-

RRF Machinek, TE Ouldridge, NEC Haley, J Bath, AJ Turberfield

DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.


Part 1: Special Issue: Quantum Cryptography - celebrating 30 years of BB84, Part 2: Special Issue: DNA Computing and Molecular Programming 2012 Preface

NATURAL COMPUTING 13 (2014) 497-498

D Stefanovic, A Turberfield


A clocked finite state machine built from DNA.

Chem Commun (Camb) 49 (2013) 237-239

C Costa Santini, J Bath, AM Tyrrell, AJ Turberfield

We implement a finite state machine by representing state, transition rules and input symbols with DNA components. Transitions between states are triggered by a clock signal which allows synchronized, parallel operation of two (or more) state machines. The state machine can be re-programmed by changing the input symbols.


Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.

ACS Nano 7 (2013) 2479-2490

TE Ouldridge, RL Hoare, AA Louis, JPK Doye, J Bath, AJ Turberfield

DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands. In this article, we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems. We find that applying moderate tension to the track can have a large influence on the operation of the walker, providing a bias for stepping forward and helping the walker to recover from undesirable overstepped states. Further, we show that the process by which spent fuel detaches from the walker can have a significant impact on the rebinding of the walker to the track, strongly influencing walker efficiency and speed. Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation.


"Giant surfactants" created by the fast and efficient functionalization of a DNA tetrahedron with a temperature-responsive polymer.

ACS Nano 7 (2013) 8561-8572

TR Wilks, J Bath, JW de Vries, JE Raymond, A Herrmann, AJ Turberfield, RK O'Reilly

Copper catalyzed azide-alkyne cycloaddition (CuAAC) was employed to synthesize DNA block copolymers (DBCs) with a range of polymer blocks including temperature-responsive poly(N-isoproylacrylamide) (poly(NIPAM)) and highly hydrophobic poly(styrene). Exceptionally high yields were achieved at low DNA concentrations, in organic solvents, and in the absence of any solid support. The DNA segment of the DBC remained capable of sequence-specific hybridization: it was used to assemble a precisely defined nanostructure, a DNA tetrahedron, with pendant poly(NIPAM) segments. In the presence of an excess of poly(NIPAM) homopolymer, the tetrahedron-poly(NIPAM) conjugate nucleated the formation of large, well-defined nanoparticles at 40 °C, a temperature at which the homopolymer precipitated from solution. These composite nanoparticles were observed by dynamic light scattering and cryoTEM, and their hybrid nature was confirmed by AFM imaging. As a result of the large effective surface area of the tetrahedron, only very low concentrations of the conjugate were required in order for this surfactant-like behavior to be observed.


Probing GPCR-G alpha interactions: A functional study by EM and SPR

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 42 (2013) S172-S172

RJ Adamson, TH Sharp, DN Selmi, AD Goddard, RJ Gilbert, AJ Turberfield, A Watts


Combinatorial displacement of DNA strands: application to matrix multiplication and weighted sums.

Angew Chem Int Ed Engl 52 (2013) 1189-1192

AJ Genot, J Bath, AJ Turberfield


DNA Walker Circuits: Computational Potential, Design, and Verification

DNA COMPUTING AND MOLECULAR PROGRAMMING, DNA 2013 8141 (2013) 31-45

F Dannenberg, M Kwiatkowska, C Thachuk, AJ Turberfield


Non-covalent single transcription factor encapsulation inside a DNA cage.

Angew Chem Int Ed Engl 52 (2013) 2284-2288

R Crawford, CM Erben, J Periz, LM Hall, T Brown, AJ Turberfield, AN Kapanidis


Molecular machinery built from DNA

NOBEL SYMPOSIUM 153: NANOSCALE ENERGY CONVERTERS 1519 (2013) 81-82

J Bath, AJ Turberfield


A DNA-based molecular motor that can navigate a network of tracks.

Nat Nanotechnol 7 (2012) 169-173

SFJ Wickham, J Bath, Y Katsuda, M Endo, K Hidaka, H Sugiyama, AJ Turberfield

Synthetic molecular motors can be fuelled by the hydrolysis or hybridization of DNA. Such motors can move autonomously and programmably, and long-range transport has been observed on linear tracks. It has also been shown that DNA systems can compute. Here, we report a synthetic DNA-based system that integrates long-range transport and information processing. We show that the path of a motor through a network of tracks containing four possible routes can be programmed using instructions that are added externally or carried by the motor itself. When external control is used we find that 87% of the motors follow the correct path, and when internal control is used 71% of the motors follow the correct path. Programmable motion will allow the development of computing networks, molecular systems that can sort and process cargoes according to instructions that they carry, and assembly lines that can be reconfigured dynamically in response to changing demands.


Macromolecule synthesis by DNA templated chemistry

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 243 (2012)

PJ Milnes, ML Mckee, J Bath, E Stulz, AJ Turberfield, RK O'Reilly


A DNA-based molecular motor that can navigate a network of tracks

Nature Nanotechnology 7 (2012) 169-173

SFJ Wickham, J Bath, Y Katsuda, M Endo, K Hidaka, H Sugiyama, AJ Turberfield

Synthetic molecular motors can be fuelled by the hydrolysis or hybridization of DNA. Such motors can move autonomously and programmably, and long-range transport has been observed on linear tracks. It has also been shown that DNA systems can compute. Here, we report a synthetic DNA-based system that integrates long-range transport and information processing. We show that the path of a motor through a network of tracks containing four possible routes can be programmed using instructions that are added externally or carried by the motor itself. When external control is used we find that 87% of the motors follow the correct path, and when internal control is used 71% of the motors follow the correct path. Programmable motion will allow the development of computing networks, molecular systems that can sort and process cargoes according to instructions that they carry, and assembly lines that can be reconfigured dynamically in response to changing demands. © 2012 Macmillan Publishers Limited. All rights reserved.

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