Publications


PHYS 393-Engineering entropy-driven reactions and networks catalyzed by DNA

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 (2007)

DY Zhang, AJ Turberfield, B Yurke, E Winfree


DNA hairpins: fuel for autonomous DNA devices.

Biophys J 91 (2006) 2966-2975

SJ Green, D Lubrich, AJ Turberfield

We present a study of the hybridization of complementary DNA hairpin loops, with particular reference to their use as fuel for autonomous DNA devices. The rate of spontaneous hybridization between complementary hairpins can be reduced by increasing the neck length or decreasing the loop length. Hairpins with larger loops rapidly form long-lived kissed complexes. Hairpin loops may be opened by strand displacement using an opening strand that contains the same sequence as half of the neck and a "toehold" complementary to a single-stranded domain adjacent to the neck. We find loop opening via an external toehold to be 10-100 times faster than via an internal toehold. We measure rates of loop opening by opening strands that are at least 1000 times faster than the spontaneous interaction between hairpins. We discuss suitable choices for loop, neck, and toehold length for hairpin loops to be used as fuel for autonomous DNA devices.


Registration of single quantum dots using cryogenic laser photolithography

APPLIED PHYSICS LETTERS 88 (2006) ARTN 193106

KH Lee, AM Green, RA Taylor, DN Sharp, J Scrimgeour, OM Roche, JH Na, AF Jarjour, AJ Turberfield, FSF Brossard, DA Williams, GAD Briggs


Cryogenic Two-Photon Laser Photolithography with SU-8

Applied Physics Letters 88 (2006) 143123 3pp-

RA Taylor, K.H. Lee, A.M. Green, F.S.F. Brossard


Single-molecule protein encapsulation in a rigid DNA cage.

Angew Chem Int Ed Engl 45 (2006) 7414-7417

CM Erben, RP Goodman, AJ Turberfield


Accuracy of single quantum dot registration using cryogenic laser photolithography

2006 6th IEEE Conference on Nanotechnology, IEEE-NANO 2006 2 (2006) 723-726

KH Lee, AM Green, RA Taylor, FC Waldermann, A Sena, DN Sharp, AJ Turberfield, FSF Brossard, DA Williams

We have registered the position of single InGaAs quantum dots using a novel cryogenic laser photolithography technique. This would be useful in realizing solid state cavity quantum electrodynamics. By fabricating metal alignment markers around the quantum dot, it was registered with an accuracy of 50 nm. Following the marker fabrication process we demonstrated that the same quantum dot was reacquired, with an accuracy of 150 nm. The photoluminescence spectra from the quantum dots before and after processing were identical except for a small red shift (∼1 nm), probably introduced during the reactive ion etching. © 2006 IEEE.


Study of two-photon laser photolithography with SU-8 at cryogenic temperatures

Conference on Lasers and Electro-Optics and 2006 Quantum Electronics and Laser Science Conference, CLEO/QELS 2006 (2006)

KH Lee, AM Green, FSF Brassard, RA Taylor, DN Sharp, AJ Turberfield, DA Williams, GAD Briggs

We show that the SU-8 epoxy resist can be exposed by two-photon absorption at 4 K, allowing spectroscopy and lithography to be performed by the same apparatus. We present a systematic study of the exposure parameters. © 2006 Optical Society of America.


Design of autonomous DNA cellular automata

LECT NOTES COMPUT SC 3892 (2006) 399-416

P Yin, S Sahu, AJ Turberfield, JH Reif

Recent experimental progress in DNA lattice construction, DNA robotics, and DNA computing provides the basis for designing DNA cellular computing devices, i.e. autonomous nano-mechanical DNA computing devices embedded in DNA lattices. Once assembled, DNA cellular computing devices can serve as reusable, compact computing devices that perform (universal) computation, and programmable robotics devices that demonstrate complex motion. As a prototype of such devices, we recently reported the design of an Autonomous DNA Turing Machine, which is capable of universal sequential computation, and universal translational motion, i.e. the motion of the head of a single tape universal mechanical Turing machine. In this paper, we describe the design of an Autonomous DNA Cellular Automaton (ADCA), which can perform parallel universal computation by mimicking a one-dimensional (1D) universal cellular automaton. In the computation process, this device, embedded in a 1D DNA lattice, also demonstrates well coordinated parallel motion. The key technical innovation here is a molecular mechanism that synchronizes pipelined "molecular reaction waves" along a 1D track, and in doing so, realizes parallel computation. We first describe the design of ADCA on an abstract level, and then present detailed DNA sequence level implementation using commercially available protein enzymes. We also discuss how to extend the ID design to 2D.


Designs of autonomous unidirectional walking DNA devices

LECT NOTES COMPUT SC 3384 (2005) 410-425

P Yin, AJ Turberfield, JH Reif

Imagine a host of nanoscale DNA robots move,autonomously over a microscale DNA nanostructure, each following a programmable route and serving as a nanoparticle and/or an information carrier. The-accomplishment of this goal has many applications in nanorobotics, nano-fabrication, nano-electronics, nano-diagnostics/therapeutics, and nano-computing. Recent success in constructing large scale DNA nanostructures in a programmable way provides the structural basis to meet the above challenge. The missing link is a DNA walker that can autonomously move along a route programmably embedded in the underlying nanostructure - existing synthetic DNA mechanical devices only exhibit localized non-extensible motions such as bi-directional rotation, open/close, and contraction/extension, mediated by external environmental changes. We describe in this paper two designs of autonomous DNA walking devices in which a walker moves along a linear track unidirectionally. The track of each device consists of a periodic linear array of anchorage sites. A walker sequentially steps over the anchorages in an autonomous unidirectional way. Each walking device makes use of alternating actions of restriction enzymes and ligase to achieve unidirectional translational motion.


Chemistry: Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication

Science 310 (2005) 1661-1665

RP Goodman, IAT Schaap, CF Tardin, CM Erben, RM Berry, CF Schmidt, AJ Turberfield

Practical components for three-dimensional molecular nanofabrication must be simple to produce, stereopure, rigid, and adaptable. We report a family of DNA tetrahedra, less than 10 nanometers on a side, that can self-assemble in seconds with near-quantitative yield of one diastereomer. They can be connected by programmable DNA linkers. Their triangulated architecture confers structural stability; by compressing a DNA tetrahedron with an atomic force microscope, we have measured the axial compressibility of DNA and observed the buckling of the double helix under high loads.


Design and assembly of double-crossover linear arrays of micrometre length using rolling circle replication

Nanotechnology 16 (2005) 1574-1577

D Lubrich, J Bath, AJ Turberfield

We demonstrate the use of rolling circle replication to template linear DNA arrays whose sizes bridge the gap between nanometre-scale self-assembly and top-down lithographic fabrication. Using rolling circle replication we have produced an oligonucleotide containing several hundred repeats of a short sequence motif. On this template we have constructed, by self-assembly, an array consisting of two parallel duplexes periodically linked by antiparallel Holliday junctions. We have observed arrays up to 10 νm in length by atomic force microscopy. © 2005 IOP Publishing Ltd.


2-D DNA scaffolds for protein structure determination

2nd Conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices, FNANO 2005 (2005) 165-175

J Malo, JC Mitchell, C Vénien-Bryan, JR Harris, H Wille, DJ Sherratt, AJ Turberfield

We report the design and fabrication of two self-assembled DNA crystals and the use of a DNA-binding protein to control the crystal structure. Both arrays are built from the same four oligonucleotides: addition of the bacterial recombination protein RuvA during self-assembly completely changes the lattice symmetry and connectivity. By analyzing transmission electron micrographs we have produced 2-D density maps of both RuvA-DNA and DNA-only crystals to below 30Å. Such specially designed 2-D DNA templates, used to create ordered protein arrays, may provide a tool for determining the structure of proteins that do not readily crystallize.© 2005 by ScienceTechnica, Inc.


Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication.

Science 310 (2005) 1661-1665

RP Goodman, IAT Schaap, CF Tardin, CM Erben, RM Berry, CF Schmidt, AJ Turberfield

Practical components for three-dimensional molecular nanofabrication must be simple to produce, stereopure, rigid, and adaptable. We report a family of DNA tetrahedra, less than 10 nanometers on a side, that can self-assemble in seconds with near-quantitative yield of one diastereomer. They can be connected by programmable DNA linkers. Their triangulated architecture confers structural stability; by compressing a DNA tetrahedron with an atomic force microscope, we have measured the axial compressibility of DNA and observed the buckling of the double helix under high loads.


Registration of single quantum dots for solid state cavity quantum electrodynamics

Conference Proceedings - Lasers and Electro-Optics Society Annual Meeting-LEOS 2005 (2005) 113-114

KH Lee, AM Green, FSF Brossard, RA Taylor, AJ Turberfield, DA Williams, GAD Briggs

We discuss a novel technique to register the spatial and spectral characteristics of a single quantum dot using two photon absorption laser lithography. This would be useful in realizing solid state cavity quantum electrodynamics. © 2005 British Crown Copyright.


Engineering a 2D protein-DNA crystal

Angewandte Chemie - International Edition 44 (2005) 3057-3061

AJ Turberfield, C. Venien-Bryan, D. J. Sherratt, J. Malo


Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion

LECT NOTES COMPUT SC 3384 (2005) 426-444

P Yin, AJ Turberfield, S Sahu, JH Reif

Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nano-structures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5-color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion.


A free-running DNA motor powered by a nicking enzyme.

Angew Chem Int Ed Engl 44 (2005) 4358-4361

J Bath, SJ Green, AJ Turberfield


The single-step synthesis of a DNA tetrahedron.

Chem Commun (Camb) (2004) 1372-1373

RP Goodman, RM Berry, AJ Turberfield

A tetrahedral nanostructure whose edges are DNA double helices self-assembles spontaneously when four appropriately designed oligonucleotides are annealed together in solution; the ease of synthesis, rigidity, and adaptability of this construct make it a promising candidate as a cage for other large molecules and as a building block for more complicated nanostructures.


Self-assembly of chiral DNA nanotubes.

J Am Chem Soc 126 (2004) 16342-16343

JC Mitchell, JR Harris, J Malo, J Bath, AJ Turberfield

A system of DNA "tiles" that is designed to assemble to form two-dimensional arrays is observed to form narrow ribbons several micrometers in length. The uniform width of the ribbons and lack of frayed edges lead us to propose that they are arrays that have curled and closed on themselves to form tubes. This proposal is confirmed by the observation of tubes with helical order.


A unidirectional DNA walker that moves autonomously along a track.

Angew Chem Int Ed Engl 43 (2004) 4906-4911

P Yin, H Yan, XG Daniell, AJ Turberfield, JH Reif

Pages