Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications

Molecules with a sense of logic: a progress report

(2015) Joakim Andréasson et al.   CHEMICAL SOCIETY REVIEWS

Switchable Bifunctional Stimuli-Triggered Poly-N-Isopropylacrylamide/DNA Hydrogels

(2014) Weiwei Guo et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Signal Propagation in Multi-Layer DNAzyme Cascades Using Structured Chimeric Substrates

(2014) Carl W. Brown et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Reversible Ag+-crosslinked DNA hydrogels

(2014) Weiwei Guo et al.   CHEMICAL COMMUNICATIONS

Programmable pH-Triggered DNA Nanoswitches

(2014) Andrea Idili et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A full-adder based on reconfigurable DNA-hairpin inputs and DNAzyme computing modules

(2014) Ron Orbach et al.   Chemical Science

Nucleic Acid/Quantum Dots (QDs) Hybrid Systems for Optical and Photoelectrochemical Sensing

(2013) Ronit Freeman et al.   ACS Applied Materials & Interfaces

DNA Nanotechnology: From Sensing and DNA Machines to Drug-Delivery Systems

(2013) Chun-Hua Lu et al.   ACS Nano

Deoxyribozyme Cascade for Visual Detection of Bacterial RNA

(2013) Yulia V. Gerasimova et al.   CHEMBIOCHEM

Colorimetric Logic Gates Based on Ion-Dependent DNAzymes

(2013) Li Zhang et al.   Journal of Physical Chemistry C

Smart Mesoporous SiO2 Nanoparticles for the DNAzyme-Induced Multiplexed Release of Substrates

(2013) Zhanxia Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Switchable Catalytic Acrylamide Hydrogels Cross-Linked by Hemin/G-Quadruplexes

(2013) Chun-Hua Lu et al.   NANO LETTERS

Switchable mechanical DNA “arms” operating on nucleic acid scaffolds associated with electrodes or semiconductor quantum dots

(2013) Gilad Pelossof et al.   Nanoscale

DNAzyme-based 2:1 and 4:1 multiplexers and 1:2 demultiplexer

(2013) Ron Orbach et al.   Chemical Science

A library of programmable DNAzymes that operate in a cellular environment

(2013) Maya Kahan-Hanum et al.   Scientific Reports

“Fitting” Makes “Sensing” Simple: Label-Free Detection Strategies Based on Nucleic Acid Aptamers

(2012) Yan Du et al.   ACCOUNTS OF CHEMICAL RESEARCH

Graphene-Based Aptamer Logic Gates and Their Application to Multiplex Detection

(2012) Li Wang et al.   ACS Nano

Amplified Surface Plasmon Resonance and Electrochemical Detection of Pb2+ Ions Using the Pb2+-Dependent DNAzyme and Hemin/G-Quadruplex as a Label

(2012) Gilad Pelossof et al.   ANALYTICAL CHEMISTRY

Functionalized DNA Nanostructures

(2012) Ofer I. Wilner et al.   CHEMICAL REVIEWS

Detection of Metal Ions (Cu2+, Hg2+) and Cocaine by Using Ligation DNAzyme Machinery

(2012) Fuan Wang et al.   CHEMISTRY-A EUROPEAN JOURNAL

Nucleic Acid Driven DNA Machineries Synthesizing Mg2+-Dependent DNAzymes: An Interplay between DNA Sensing and Logic-Gate Operations

(2012) Ron Orbach et al.   CHEMISTRY-A EUROPEAN JOURNAL

Nucleic acids for the rational design of reaction circuits

(2012) Adrien Padirac et al.   CURRENT OPINION IN BIOTECHNOLOGY

pH-Programmable DNA Logic Arrays Powered by Modular DNAzyme Libraries

(2012) Johann Elbaz et al.   NANO LETTERS

Switching Photonic and Electrochemical Functions of a DNAzyme by DNA Machines

(2012) Xiaoqing Liu et al.   NANO LETTERS

Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates

(2012) R. Orbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional Structures Self-Assembled from DNA Bricks

(2012) Y. Ke et al.   SCIENCE

pH-programmable DNAzyme nanostructures

(2011) Simcha Shimron et al.   CHEMICAL COMMUNICATIONS

DNAzyme crosslinked hydrogel: a new platform for visual detection of metal ions

(2011) Haoxue Lin et al.   CHEMICAL COMMUNICATIONS

DNA-guided display of proteins and protein ligands for the interrogation of biology

(2011) Franziska Diezmann et al.   CHEMICAL SOCIETY REVIEWS

Sequential logic and random access memory (RAM): a molecular approach

(2011) Graham de Ruiter et al.   JOURNAL OF MATERIALS CHEMISTRY

Neural network computation with DNA strand displacement cascades

(2011) Lulu Qian et al.   NATURE

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

(2011) L. Qian et al.   SCIENCE

“Illusionary” Polymerase Activity Triggered by Metal Ions: Use for Molecular Logic-Gate Operations

(2010) Ki Soo Park et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

pH-triggered switchable Mg2+-dependent DNAzymes

(2010) Johann Elbaz et al.   CHEMICAL COMMUNICATIONS

Ion-induced DNAzyme switches

(2010) Simcha Shimron et al.   CHEMICAL COMMUNICATIONS

A graphene-based fluorescent nanoprobe for silver(i) ions detection by using graphene oxide and a silver-specific oligonucleotide

(2010) Yanqin Wen et al.   CHEMICAL COMMUNICATIONS

Binary Probes for Nucleic Acid Analysis

(2010) Dmitry M. Kolpashchikov   CHEMICAL REVIEWS

Nucleic Acid Detection using MNAzymes

(2010) Yulia V. Gerasimova et al.   CHEMISTRY & BIOLOGY

Signal processing with multicomponent systems based on metal complexes

(2010) Matteo Amelia et al.   COORDINATION CHEMISTRY REVIEWS

Functional nucleic acid nanostructures and DNA machines

(2010) Carsten Teller et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA computing circuits using libraries of DNAzyme subunits

(2010) Johann Elbaz et al.   Nature Nanotechnology

DNA as a universal substrate for chemical kinetics

(2010) D. Soloveichik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescent DNA Nanotags Based on a Self-Assembled DNA Tetrahedron

(2009) Hayriye Özhalıcı-Ünal et al.   ACS Nano

Highly Sensitive Electrochemical Sensor for Mercury(II) Ions by Using a Mercury-Specific Oligonucleotide Probe and Gold Nanoparticle-Based Amplification

(2009) Zhiqiang Zhu et al.   ANALYTICAL CHEMISTRY

Aptamer−DNAzyme Hairpins for Amplified Biosensing

(2009) Carsten Teller et al.   ANALYTICAL CHEMISTRY

A pH-Triggered, Fast-Responding DNA Hydrogel

(2009) Enjun Cheng et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Cooperative Multicomponent Self-Assembly of Nucleic Acid Structures for the Activation of DNAzyme Cascades: A Paradigm for DNA Sensors and Aptasensors

(2009) Johann Elbaz et al.   CHEMISTRY-A EUROPEAN JOURNAL

Universal Translators for Nucleic Acid Diagnosis

(2009) John M. Picuri et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Sensing of UO22+and Design of Logic Gates by the Application of Supramolecular Constructs of Ion-Dependent DNAzymes

(2009) Michal Moshe et al.   NANO LETTERS

Scaffolded DNA Origami of a DNA Tetrahedron Molecular Container

(2009) Yonggang Ke et al.   NANO LETTERS

Self-assembly of a nanoscale DNA box with a controllable lid

(2009) Ebbe S. Andersen et al.   NATURE

Enzyme cascades activated on topologically programmed DNA scaffolds

(2009) Ofer I. Wilner et al.   Nature Nanotechnology

A Simple Unimolecular Multiplexer/Demultiplexer

(2008) Matteo Amelia et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Au nanoparticles grafted sandwich platform used amplified small molecule electrochemical aptasensor

(2008) Yan Du et al.   BIOSENSORS & BIOELECTRONICS

Detection of mercury(ii) based on Hg2+–DNA complexes inducing the aggregation of gold nanoparticles

(2008) Chi-Wei Liu et al.   CHEMICAL COMMUNICATIONS

Specific interactions between silver(i) ions and cytosine–cytosine pairs in DNA duplexes

(2008) Akira Ono et al.   CHEMICAL COMMUNICATIONS

DNAzymes for sensing, nanobiotechnology and logic gate applications

(2008) Itamar Willner et al.   CHEMICAL SOCIETY REVIEWS

Reconfigurable, braced, three-dimensional DNA nanostructures

(2008) Russell P. Goodman et al.   Nature Nanotechnology

Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding

(2008) Sherri Rinker et al.   Nature Nanotechnology

A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures

(2008) Y. Weizmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assembling Materials with DNA as the Guide

(2008) F. A. Aldaye et al.   SCIENCE