Speeding up a single-molecule DNA device with a simple catalyst (original) (raw)
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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.
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.
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".
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.