Publications


The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery.

Accounts of chemical research 50 (2017) 2496-2509

RK O'Reilly, AJ Turberfield, TR Wilks

Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures. The largest libraries made by conventional synthesis are currently of the order of 108 distinct molecules. To put this in context, there are 1013 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure-a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery-imagine being able to evolve molecules for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous "DNA robots" have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution.


An autonomous molecular assembler for programmable chemical synthesis.

Nature chemistry 8 (2016) 542-548

W Meng, RA Muscat, ML McKee, PJ Milnes, AH El-Sagheer, J Bath, BG Davis, T Brown, RK O'Reilly, AJ Turberfield

Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing.


The Formal Language and Design Principles of Autonomous DNA Walker Circuits.

ACS synthetic biology 5 (2016) 878-884

MA Boemo, AE Lucas, AJ Turberfield, L Cardelli

Simple computation 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. We conclude by introducing example mechanisms that can implement such circuits experimentally and discuss their individual strengths and weaknesses.


Domain-swap polymerization drives the self-assembly of the bacterial flagellar motor.

Nature structural & molecular biology 23 (2016) 197-203

MA Baker, RM Hynson, LA Ganuelas, NS Mohammadi, CW Liew, AA Rey, AP Duff, AE Whitten, CM Jeffries, NJ Delalez, YV Morimoto, D Stock, JP Armitage, AJ Turberfield, K Namba, RM Berry, LK Lee

Large protein complexes assemble spontaneously, yet their subunits do not prematurely form unwanted aggregates. This paradox is epitomized in the bacterial flagellar motor, a sophisticated rotary motor and sensory switch consisting of hundreds of subunits. Here we demonstrate that Escherichia coli FliG, one of the earliest-assembling flagellar motor proteins, forms ordered ring structures via domain-swap polymerization, which in other proteins has been associated with uncontrolled and deleterious protein aggregation. Solution structural data, in combination with in vivo biochemical cross-linking experiments and evolutionary covariance analysis, revealed that FliG exists predominantly as a monomer in solution but only as domain-swapped polymers in assembled flagellar motors. We propose a general structural and thermodynamic model for self-assembly, in which a structural template controls assembly and shapes polymer formation into rings.


Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas.

ACS nano 10 (2016) 9809-9815

S Simoncelli, EM Roller, P Urban, R Schreiber, AJ Turberfield, T Liedl, T Lohmüller

DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.


Ordering Gold Nanoparticles with DNA Origami Nanoflowers.

ACS nano 10 (2016) 7303-7306

R Schreiber, I Santiago, A Ardavan, AJ Turberfield

Nanostructured materials, including plasmonic metamaterials made from gold and silver nanoparticles, provide access to new materials properties. The assembly of nanoparticles into extended arrays can be controlled through surface functionalization and the use of increasingly sophisticated linkers. We present a versatile way to control the bonding symmetry of gold nanoparticles by wrapping them in flower-shaped DNA origami structures. These "nanoflowers" assemble into two-dimensonal gold nanoparticle lattices with symmetries that can be controlled through auxiliary DNA linker strands. Nanoflower lattices are true composites: interactions between the gold nanoparticles are mediated entirely by DNA, and the DNA origami will fold into its designed form only in the presence of the gold nanoparticles.


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.


Folding pathways: DNA origami as a model system

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 44 (2015) S67-S67

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


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


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.

Nat Nanotechnol 9 (2014) 44-47

AJ Wollman, C Sanchez-Cano, HM 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-

RR Machinek, TE Ouldridge, NE 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.


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, JP 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.


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

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