Publications by Jonathan Bath


Reconfigurable T‐junction DNA origami

Angewandte Chemie International Edition Wiley (2020) anie.202006281

K Young, B Najafi, W Sant, S Contera, A Louis, J Doye, A Turberfield, J Bath


Reconfigurable T‐junction DNA origami

Angewandte Chemie Wiley (2020) ange.202006281

K Young, B Najafi, W Sant, S Contera, A Louis, J Doye, A Turberfield, J Bath


Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

Nature Communications Springer Nature 11 (2020) 2562

NEC Haley, TE Ouldridge, I Mullor Ruiz, A Geraldini, A Louis, J Bath, AJ Turberfield

Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.


Controlling the bioreceptor spatial distribution at the nanoscale for single molecule counting in microwell arrays

ACS Sensors American Chemical Society 4 (2019) 2327-2335

D Daems, I Rutten, J Bath, D Decrop, H Van Gorp, E Pérez Ruiz, S De Feyter, A Turberfield, J Lammertyn

The ability to detect low concentrations of protein biomarkers is crucial for the early-stage detection of many diseases and therefore indispensable for improving diagnostic devices for healthcare. Here, we demonstrate that by integrating DNA nanotechnologies like DNA origami and aptamers, we can design innovative biosensing concepts for reproducible and sensitive detection of specific targets. DNA origami structures decorated with aptamers were studied as a novel tool to structure the biosensor surface with nanoscale precision in a digital detection bioassay, enabling control of the density, orientation, and accessibility of the bioreceptor to optimize the interaction between target and aptamer. DNA origami was used to control the spatial distribution of an in-house-generated aptamer on superparamagnetic microparticles, resulting in an origami-linked digital aptamer bioassay to detect the main peanut antigen Ara h1 with 2-fold improved signal-to-noise ratio and 15-fold improved limit of detection compared to a digital bioassay without DNA origami. Moreover, the sensitivity achieved was 4 orders of magnitude higher than commercially available and literature-reported enzyme-linked immunosorbent assay techniques. In conclusion, this novel and innovative approach to engineer biosensing interfaces will be of major interest to scientists and clinicians looking for new molecular insights and ultrasensitive detection of a broad range of targets, and, for the next generation of diagnostics.


Peptide assembly directed and quantified using megadalton DNA nanostructures

ACS Nano American Chemical Society 13 (2019) 9927-9935

J Jin, EG Baker, CW Wood, J Bath, DN Woolfson, A Turberfield

<p>In nature, co-assembly of polypeptides, nucleic acids, and polysaccharides is used to create functional supramolecular structures. Here, we show that DNA nanostructures can be used to template interactions between peptides and to enable the quantification of multivalent interactions that would otherwise not be observable. Our functional building blocks are peptide–oligonucleotide conjugates comprising <em>de novo</em> designed dimeric coiled-coil peptides covalently linked to oligonucleotide tags. These conjugates are incorporated in megadalton DNA origami nanostructures and direct nanostructure association through peptide–peptide interactions. Free and bound nanostructures can be counted directly from electron micrographs, allowing estimation of the dissociation constants of the peptides linking them. Results for a single peptide–peptide interaction are consistent with the measured solution-phase free energy; DNA nanostructures displaying multiple peptides allow the effects of polyvalency to be probed. This use of DNA nanostructures as identifiers allows the binding strengths of homo- and heterodimeric peptide combinations to be measured in a single experiment and gives access to dissociation constants that are too low to be quantified by conventional techniques. The work also demonstrates that hybrid biomolecules can be programmed to achieve spatial organization of complex synthetic biomolecular assemblies.</p>


Chiral DNA origami nanotubes with well‐defined and addressable inside and outside surfaces

Angewandte Chemie International Edition Wiley‐VCH Verlag 57 (2018) 7687-7690

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 American Chemical Society 12 (2018) 5791-5799

MAB Baker, AJ Tuckwell, JF Berengut, J Bath, F Benn, AP Duff, AE Whitten, K Dunn, RM Hynson, A 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

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46 (2017) S139-S139

KG Young, B Najafi, J Bath, AJ Turberfield


DNA-templated peptide assembly

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46 (2017) S303-S303

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


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

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 46 (2017) S137-S137

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 Nature Publishing Group (2016)

Meng, RA Muscat, ML McKee, PJ Milnes, El-Sagheer, JN Bath, Davis, Brown, RK O'Reilly, 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 which 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

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.

Journal of Chemical Physics AIP Publishing 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.


Modelling DNA origami self-assembly at the domain level

Journal of Chemical Physics American Institute of Physics 143 (2015) 165102

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

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) 5324-5324

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.


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

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