Publications by Jonathan Bath

Chiral DNA Origami Nanotubes with Well-Defined and Addressable Inside and Outside Surfaces.

Angewandte Chemie (International ed. in English) (2018)

F Benn, NEC Haley, AE Lucas, E Silvester, S Helmi, R Schreiber, J Bath, AJ Turberfield

We report the design and assembly of chiral DNA nanotubes with well-defined and addressable inside and outside surfaces. We demonstrate that the outside surface can be functionalised with a chiral arrangement of gold nanoparticles to create a plasmonic device and that the inside surface can be functionalised with a track for a molecular motor allowing transport of a cargo within the central cavity.

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-Ray Scattering.

ACS nano (2018)

MAB Baker, AJ Tuckwell, JF Berengut, J Bath, F Benn, AP Duff, AE Whitten, KE Dunn, RM Hynson, AJ Turberfield, LK Lee

The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.

DNA T-junctions for studies of DNA origami assembly


KG Young, B Najafi, J Bath, AJ Turberfield

DNA-templated peptide assembly


J Jin, EG Baker, J Bath, DN Woolfson, AJ Turberfield

DNA origami dimensions and structure measured by solution X-ray scattering


MA Baker, AJ Tuckwell, JF Berengut, J Bath, F Benn, AP Duff, AE Whitten, KE Dunn, RM Hynson, AJ Turberfield, LK Lee

Precision control of DNA-based molecular reactions

IET Conference Publications 2016 (2016)

TE Ouldridge, JS Schreck, F Romano, P Sulc, RF Machinek, NEC Haley, AA Louis, JPK Doye, J Bath, AJ Turberfield

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.

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


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.

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.

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.

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

Molecular machinery built from DNA


J Bath, AJ Turberfield

Sequence-specific synthesis of macromolecules using DNA-templated chemistry.

Chem Commun (Camb) 48 (2012) 5614-5616

PJ Milnes, ML McKee, J Bath, L Song, E Stulz, AJ Turberfield, RK O'Reilly

Using a strand exchange mechanism we have prepared, by DNA templated chemistry, two 10-mers with defined and tunable monomer sequences. An optimized reaction protocol achieves 85% coupling yield per step, demonstrating that DNA-templated chemistry is a powerful tool for the synthesis of macromolecules with full sequence control.

Programmable one-pot multistep organic synthesis using DNA junctions.

J Am Chem Soc 134 (2012) 1446-1449

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

A system for multistep DNA-templated synthesis is controlled by the sequential formation of DNA junctions. Reactants are attached to DNA adapters which are brought together by hybridization to DNA template strands. This process can be repeated to allow sequence-controlled oligomer synthesis while maintaining a constant reaction environment, independent of oligomer length, at each reaction step. Synthesis can take place in a single pot containing all required reactive monomers. Different oligomers can be synthesized in parallel in the same vessel, and the products of parallel synthesis can be ligated, reducing the number of reaction steps required to produce an oligomer of a given length.

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.

A DNA network as an information processing system

International Journal of Molecular Sciences 13 (2012) 5125-5137

CC Santini, J Bath, AJ Turberfield, AM Tyrrell

Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications. DNA has been used to design machines, motors, finite automata, logic gates, reaction networks and logic programs, amongst many other structures and dynamic behaviours. Here we design and program a synthetic DNA network to implement computational paradigms abstracted from cellular regulatory networks. These show information processing properties that are desirable in artificial, engineered molecular systems, including robustness of the output in relation to different sources of variation. We show the results of numerical simulations of the dynamic behaviour of the network and preliminary experimental analysis of its main components. © 2012 by the authors.