Publications


A geometrical allosteric DNA switch

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6079 LNCS (2010) 189-

AJ Genot, J Bath, AJ Turberfield


Multistep DNA-templated reactions for the synthesis of functional sequence controlled oligomers.

Angew Chem Int Ed Engl 49 (2010) 7948-7951

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


A Geometrical Allosteric DNA Switch

UNCONVENTIONAL COMPUTATION, PROCEEDINGS 6079 (2010) 189-189

AJ Genot, J Bath, AJ Turberfield


Erratum: Coordinated chemomechanical cycles: A mechanism for autonomous molecular motion (Physical Review Letters (2008) 101 (238101))

Physical Review Letters 102 (2009)

SJ Green, J Bath, AJ Turberfield


High-resolution structural analysis of a DNA nanostructure by cryoEM.

Nano Lett 9 (2009) 2747-2750

T Kato, RP Goodman, CM Erben, AJ Turberfield, K Namba

Many DNA nanostructures have been produced and a wide range of potential applications have been proposed. However, confirmation of accurate 3D construction is particularly challenging. Here, we demonstrate that cryoEM may be exploited to obtain structural information at sufficient resolution to visualize the DNA helix and reveal the absolute stereochemistry of a 7 nm self-assembled DNA tetrahedron. Structural analysis at such high resolution by cryoEM image analysis is unprecedented for any biological molecule of this size.


Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion (vol 101, 238101, 2008)

PHYSICAL REVIEW LETTERS 102 (2009) ARTN 139901

SJ Green, J Bath, AJ Turberfield


A facile method for reversibly linking a recombinant protein to DNA.

Chembiochem 10 (2009) 1551-1557

RP Goodman, CM Erben, J Malo, WM Ho, ML McKee, AN Kapanidis, AJ Turberfield

We present a facile method for linking recombinant proteins to DNA. It is based on the nickel-mediated interaction between a hexahistidine tag (His(6)-tag) and DNA functionalized with three nitrilotriacetic acid (NTA) groups. The resulting DNA-protein linkage is site-specific. It can be broken quickly and controllably by the addition of a chelating agent that binds nickel. We have used this new linker to bind proteins to a variety of DNA motifs commonly used in the fabrication of nanostructures by DNA self-assembly.


Algorithmic Control: The Assembly and Operation of DNA Nanostructures and Molecular Machinery

ALGORITHMIC BIOPROCESSES (2009) 215-225

AJ Turberfield


DNA monofunctionalization of quantum dots.

Chembiochem 10 (2009) 1781-1783

HMJ Carstairs, K Lymperopoulos, AN Kapanidis, J Bath, AJ Turberfield


DNA nanomachines

in Nanoscience and Technology: A Collection of Reviews from Nature Journals, (2009) 124-136

J Bath, AJ Turberfield

© 2010 Nature Publishing Group, a division of Macmillan Publishers Limited and published by World Scientific Publishing Co. under licence. All Rights Reserved. We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specifi c interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specifi c signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.


Kinetically controlled self-assembly of DNA oligomers.

J Am Chem Soc 131 (2009) 2422-2423

D Lubrich, SJ Green, AJ Turberfield

Metastable two-stranded DNA loops can be assembled into extended DNA oligomers by kinetically controlled self-assembly. Along the designed reaction pathway, the sequence of hybridization reactions is controlled by progressively revealing toeholds required to initiate strand-displacement reactions. The product length depends inversely on seed concentration and ranges from a few hundred to several thousand base-pairs.


A two-dimensional DNA array: the three-layer logpile.

J Am Chem Soc 131 (2009) 13574-13575

J Malo, JC Mitchell, AJ Turberfield

We describe the three-layer logpile (3LL), a two-dimensional DNA array which self-assembles from four synthetic oligonucleotides via a four-armed Holliday junction motif. It consists of three layers of helices, each running at 60 degrees to the others. DNA arrays can be used as periodic templates to create, for example, synthetic protein crystals: this array is designed to maximize structural order by ensuring that helices run continuously, without bending, through the structure. UV absorbance measurements show a rate-dependent hysteresis associated with the assembly of the 3LL. Negative-stain transmission electron microscopy (TEM) of 3LL samples shows that the arrays form extensive sheets (approximately microm(2)) and a process of iterative correlation mapping and averaging of small subsets of digitized TEM micrographs yields an averaged projection image that is consistent with a computer-generated model of the crystal.


Mechanism for a directional, processive, and reversible DNA motor.

Small 5 (2009) 1513-1516

J Bath, SJ Green, KE Allen, AJ Turberfield


Reconfigurable, braced, three-dimensional DNA nanostructures.

Nat Nanotechnol 3 (2008) 93-96

RP Goodman, M Heilemann, S Doose, CM Erben, AN Kapanidis, AJ Turberfield

DNA nanotechnology makes use of the exquisite self-recognition of DNA in order to build on a molecular scale. Although static structures may find applications in structural biology and computer science, many applications in nanomedicine and nanorobotics require the additional capacity for controlled three-dimensional movement. DNA architectures can span three dimensions and DNA devices are capable of movement, but active control of well-defined three-dimensional structures has not been achieved. We demonstrate the operation of reconfigurable DNA tetrahedra whose shapes change precisely and reversibly in response to specific molecular signals. Shape changes are confirmed by gel electrophoresis and by bulk and single-molecule Förster resonance energy transfer measurements. DNA tetrahedra are natural building blocks for three-dimensional construction; they may be synthesized rapidly with high yield of a single stereoisomer, and their triangulated architecture conveys structural stability. The introduction of shape-changing structural modules opens new avenues for the manipulation of matter on the nanometre scale.


Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion.

Phys Rev Lett 101 (2008) 238101-

SJ Green, J Bath, AJ Turberfield

The second law of thermodynamics requires that directed motion be accompanied by dissipation of energy. Here we demonstrate the working principles of a bipedal molecular motor. The motor is constructed from DNA and is driven by the hybridization of a DNA fuel. We show how the catalytic activities of the feet can be coordinated to create a Brownian ratchet that is in principle capable of directional and processive movement along a track. This system can be driven away from equilibrium, demonstrating the potential of the motor to do work.


Templated self-assembly of wedge-shaped DNA arrays

Tetrahedron 64 (2008) 8530-8534

D Lubrich, J Bath, AJ Turberfield

We demonstrate the use of a one-dimensional template to control the shape of a two-dimensional array self-assembled from a minimal set of DNA tiles. A periodic single-stranded template seeds tile assembly. A unique vertex tile at the 5′ end of the template controls the positioning of edge and body tiles to create a wedge-shaped array. The vertex angle of the array is approximately 12°; edge lengths are of the order of 1 μm. © 2008 Elsevier Ltd. All rights reserved.


Towards registered single quantum dot photonic devices.

Nanotechnology 19 (2008) 455307-

KH Lee, FSF Brossard, M Hadjipanayi, X Xu, F Waldermann, AM Green, DN Sharp, AJ Turberfield, DA Williams, RA Taylor

We have registered the position and wavelength of a single InGaAs quantum dot using an innovative cryogenic laser lithography technique. This approach provides accurate marking of the location of self-organized dots and is particularly important for realizing any solid-state cavity quantum electrodynamics scheme where the overlap of the spectral and spatial characteristics of an emitter and a cavity is essential. We demonstrate progress in two key areas towards efficient single quantum dot photonic device implementation. Firstly, we show the registration and reacquisition of a single quantum dot with 50 and 150 nm accuracy, respectively. Secondly, we present data on the successful fabrication of a photonic crystal L3 cavity following the registration process.


DNA nanomachines.

Nat Nanotechnol 2 (2007) 275-284

J Bath, AJ Turberfield

We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.


Engineering entropy-driven reactions and networks catalyzed by DNA.

Science 318 (2007) 1121-1125

DY Zhang, AJ Turberfield, B Yurke, E Winfree

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.


A self-assembled DNA bipyramid.

J Am Chem Soc 129 (2007) 6992-6993

CM Erben, RP Goodman, AJ Turberfield

Pages