DNA fuel for free-running nanomachines (original) (raw)
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Speeding up a single-molecule DNA device with a simple catalyst
Physical Review E, 2005
Recently, several groups have designed and synthesized single-molecule devices based on DNA that can switch between different configurations in response to sequential addition of fuel DNA strands. There is considerable interest in improving the speed of these 'nanomotors'. One approach is the use of rationally designed DNA catalysts to promote hybridization of complementary oligonucleotides. A particularly simple and robust DNA device reported by Li and Tan is comprised of a singlestrand 17-base oligomer that folds into a chair-like quadruplex structure. We have identified the key rate-limiting barrier in this device as the tendency for one of the fuel strands B to fold into the quadruplex configuration of the device strand. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of B, and shown that the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst remains effective even after repeated cycling.
DNA hybridization catalysts and molecular tweezers
DNA Based Computers V, 2000
We d e m onstrate new methods for the control of DNA hybridization: formation of a loop with a protective s trand is used to inhibit hybridization, and a DNA catalyst that opens the loop is used to catalyse hybridization. A combination of inhibition and catalysis will allow c o n trol of the bonds formed between elements of a self-assembled structure. We a lso demonstrate a new class of nanomachine, made of DNA and using the hybridization of DNA as a source of chemical energy to produce repeated movement. 3' TAMRA (NHS ester hand tagged) by t h e m a n ufacturer.
Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions
Journal of The Royal Society Interface, 2012
Can a wide range of complex biochemical behaviour arise from repeated applications of a highly reduced class of interactions? In particular, can the range of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands of DNA as the only component molecules. Various enzymatic manipulations of these mDNA molecules are simulated via toehold-mediated DNA strand displacement reactions. We provide a formal model to describe the required properties and operations of our mDNA, and show that our proposed DNA nanostructures and hybridization reactions provide these properties and functionality. Our meta-nucleotides are designed to form flexible linear assemblies (single-stranded mDNA ( ss mDNA)) analogous to single-stranded DNA. We describe various isothermal hybridization reactions that manipulate our mDNA in powerful ways analogous to DNA–DNA re...
Chemical Reviews, 2014
CONTENTS 1. Introduction 2881 2. Enzyme-Free Nucleic Acid-Activated Chain Reactions 2883 2.1. Hybridization Chain Reactions (HCR) for Sensing and Tailoring Nanostructures 2884 2.2. Catalytic Hairpin Assembly (CHA) Reactions for Amplified Sensing and Programmed Nanostructuring 2888 2.3. Cascaded Strand-Displacement Processes for Logic Gates and DNA Machines 2893 3. DNAzyme-Activated Chain Reactions 2896 3.1. Isothermal DNAzyme-Activated Catalytic Cascades 2896 3.2. Isothermal Autonomous DNAzyme-Activated Catalytic Cascades 2899 3.3. DNAzyme-Activated Autonomous Cascaded Logic Gates and DNA Machines 2903 4. Enzyme/DNAzyme Coupled Catalytic Cascades 2906 4.1. Biocatalytic Cascades Driven by Coupled DNAzymes and Rolling Circle Amplification (RCA) Processes 2906 4.2. Biocatalytic Cascades Driven by Coupled DNAzymes and Endonucleases/Nicking Enzymes 2910 4.3. Biocatalytic Transformations Driven by Coupled Polymerase/Nicking Enzyme DNAzyme Cascades 2913 4.4. Coupled Ligation-Triggered DNAzyme Cascades 2915 4.5. DNAzyme-Amplified Detection of Telomerase Activity 2917 4.6. Logic Gates with Cascaded Enzyme/DNAzyme Systems 2919 5. Enzyme−Nucleic Acid Systems for Controlled Chemical Processes 2919 5.1.
Rational Design of DNA Nanoarchitectures
Angewandte Chemie International Edition, 2006
DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequencedirected hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view. From the Contents 1. Introduction 1857 2. General Considerations of DNA-Sequence Design 1858 3. One-Dimensional DNA Strands for Assembly and Immobilization of Non-Nucleic Acid Compounds 1859 4. Design and Assembly of DNA Motifs 1860 5. Three-Dimensional Structures from DNA 1866 6. Applications of DNA Nanoarchitectures 1868 7. Conclusions and Perspectives 1872 DNA Nanoarchitectures Angewandte Chemie Udo Feldkamp is a research assistant at the University of Dortmund (Germany). He was born in Duisburg and studied Computer Science in Kaiserslautern and Dortmund, where he also completed his PhD thesis on computer-aided DNA sequence design under the supervision of Prof. Wolfgang Banzhaf. His research still focuses on DNA-based nanotechnology and DNA computing, but he is also interested in other fields of bioinformatics and in computational intelligence. Christof M. Niemeyer has been Professor of Chemistry (chair of Biological and Chemical Microstructuring) at the University of Dortmund (Germany) since 2002. He studied chemistry at the University of Marburg and completed his PhD on organometallic chemistry at the Max-Planck-Institut für Kohlenforschung in Mülheim/Ruhr with Prof. Manfred T. Reetz. He then did postdoctoral research at the Center for Advanced Biotechnology in Boston (USA) with Prof. Charles R. Cantor, and received his habilitation at the University of Bremen. He is interested in semisynthetic DNA-protein and nanoparticle-conjugates as well as their applications in life sciences, catalysis, and molecular nanotechnology.
Directed hybridization of DNA derivatized nanoparticles into higher order structures
Nano letters, 2008
Electric field directed hybridization was used to produce twenty layer nanostructures composed of DNA derivatized nanoparticles. Using an electronic microarray device, DNA nanoparticles could be directed and concentrated such that rapid and specific hybridization occurs only on the activated sites. Nanoparticle layers were formed within 30 s of activation and twenty layer structures completed in under an hour. Results demonstrate a unique combination of bottom-up and top-down techniques for nanofabrication.
DNA Hairpins: Fuel for Autonomous DNA Devices
Biophysical Journal, 2006
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.
Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins
New Journal of Physics
DNA self-assembly has been employed non-conventionally to construct nanoscale structures and dynamic nanoscale machines. The technique of hybridization chain reactions by triggered selfassembly has been shown to form various interesting nanoscale structures ranging from simple linear DNA oligomers to dendritic DNA structures. Inspired by earlier triggered self-assembly works, we present a system for controlled self-assembly of linear cascade DNA hybridization chain reactions using nine distinct DNA hairpins. NUPACK is employed to assist in designing DNA sequences and Matlab has been used to simulate DNA hairpin interactions. Gel electrophoresis and ensemble fluorescence reaction kinetics data indicate strong evidence of linear cascade DNA hybridization chain reactions. The half-time completion of the proposed linear cascade reactions indicates a linear dependency on the number of hairpins.
Light-Driven DNA Nanomachine with a Photoresponsive Molecular Engine
CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A−T and G−C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a D-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans−cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzenederivative molecular photon-fueled engines will be soon science rather than "science fiction".
Localized Cascade DNA Hybridization Chain Reactions of DNA Hairpins on a DNA Track
2015
Theoretical models of localized DNA reactions on platforms indicate potential benefits to conventional DNA hybridization reactions. Recently locality has been proposed as a novel approach to speed up DNA hybridization reactions as well as to minimize incorrect binding among DNA sequences. Here we experimentally report evidence for a 169-fold speedup of localized DNA hybridization chain reactions in the system consisting of six DNA hairpin gates bound to a DNA track. Introduction DNA hybridization reactions have been wellstudied in the past decade and widely used to perform complex state changes and computation in DNA-based molecular computing.1–6 In most systems where DNA hybridization reactions are used for molecular computing, the reactants need to exist in low concentration (in the nano molar range) to avoid unwanted spurious bimolecular interactions. Hence diffusion of certain low concentration reactants generally plays an important factor in determination of the overall time fo...