Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation

Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes

(2017) Florian Praetorius et al.   SCIENCE

An Epigenetics-Inspired DNA-Based Data Storage System

(2016) Clemens Mayer et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering

(2016) Addison V. Wright et al.   CELL

Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches

(2016) Eckart Bindewald et al.   NANO LETTERS

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

High-resolution mapping of bifurcations in nonlinear biochemical circuits

(2016) A. J. Genot et al.   Nature Chemistry

DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction

(2016) S. Ohta et al.   SCIENCE

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Genetic encoding of DNA nanostructures and their self-assembly in living bacteria

(2016) Johann Elbaz et al.   Nature Communications

Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

(2016) Zhao Zhao et al.   Nature Communications

A DNA dual lock-and-key strategy for cell-subtype-specific siRNA delivery

(2016) Kewei Ren et al.   Nature Communications

Analog Computation by DNA Strand Displacement Circuits

(2016) Tianqi Song et al.   ACS Synthetic Biology

Increasing Redundancy Exponentially Reduces Error Rates during Algorithmic Self-Assembly

(2015) Rebecca Schulman et al.   ACS Nano

One-Step Formation of “Chain-Armor”-Stabilized DNA Nanostructures

(2015) Valentina Cassinelli et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Growth and Origami Folding of DNA on Nanoparticles for High-Efficiency Molecular Transport in Cellular Imaging and Drug Delivery

(2015) Juan Yan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing

(2015) Wujin Sun et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Stimuli-Responsive DNA-Functionalized Nano-/Microcontainers for Switchable and Controlled Release

(2015) Chun-Hua Lu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Designed Intercalators for Modification of DNA Origami Surface Properties

(2015) Josipa Brglez et al.   CHEMISTRY-A EUROPEAN JOURNAL

Multifunctional DNA Nanomaterials for Biomedical Applications

(2015) Dick Yan Tam et al.   Journal of Nanomaterials

Switchable Catalytic DNA Catenanes

(2015) Lianzhe Hu et al.   NANO LETTERS

DNA rendering of polyhedral meshes at the nanoscale

(2015) Erik Benson et al.   NATURE

Creating small transcription activating RNAs

(2015) James Chappell et al.   Nature Chemical Biology

A small-molecule dye for NIR-II imaging

(2015) Alexander L. Antaris et al.   NATURE MATERIALS

Computing in mammalian cells with nucleic acid strand exchange

(2015) Benjamin Groves et al.   Nature Nanotechnology

Complex wireframe DNA origami nanostructures with multi-arm junction vertices

(2015) Fei Zhang et al.   Nature Nanotechnology

Self-replication of DNA rings

(2015) Junghoon Kim et al.   Nature Nanotechnology

Using synthetic RNAs as scaffolds and regulators

(2015) Cameron Myhrvold et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The mutagenic chain reaction: A method for converting heterozygous to homozygous mutations

(2015) V. M. Gantz et al.   SCIENCE

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

(2015) T. Gerling et al.   SCIENCE

Programmable materials and the nature of the DNA bond

(2015) M. R. Jones et al.   SCIENCE

Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries

(2015) Thorsten L. Schmidt et al.   Nature Communications

Using synthetic RNAs as scaffolds and regulators

(2015) Cameron Myhrvold et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNA Self-Assembly and RNA Nanotechnology

(2014) Wade W. Grabow et al.   ACCOUNTS OF CHEMICAL RESEARCH

Virus-Inspired Membrane Encapsulation of DNA Nanostructures To Achieve In Vivo Stability

(2014) Steven D. Perrault et al.   ACS Nano

Addressing the Instability of DNA Nanostructures in Tissue Culture

(2014) Jaeseung Hahn et al.   ACS Nano

Hybridization Chain Reaction Amplification of MicroRNA Detection with a Tetrahedral DNA Nanostructure-Based Electrochemical Biosensor

(2014) Zhilei Ge et al.   ANALYTICAL CHEMISTRY

DNA Nanoflowers for Multiplexed Cellular Imaging and Traceable Targeted Drug Delivery

(2014) Rong Hu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Logic Gating by Macrocycle Displacement Using a Double-Stranded DNA [3]Rotaxane Shuttle

(2014) Finn Lohmann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-Particle Tracking and Modulation of Cell Entry Pathways of a Tetrahedral DNA Nanostructure in Live Cells

(2014) Le Liang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

Paper-Based Synthetic Gene Networks

(2014) Keith Pardee et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

Cocoon-Like Self-Degradable DNA Nanoclew for Anticancer Drug Delivery

(2014) Wujin Sun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

(2014) Ralf Jungmann et al.   NATURE METHODS

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

CRISPR transcriptional repression devices and layered circuits in mammalian cells

(2014) Samira Kiani et al.   NATURE METHODS

Universal computing by DNA origami robots in a living animal

(2014) Yaniv Amir et al.   Nature Nanotechnology

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm

(2014) Jinglin Fu et al.   Nature Nanotechnology

Realizing the potential of synthetic biology

(2014) George M. Church et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A single-stranded architecture for cotranscriptional folding of RNA nanostructures

(2014) C. Geary et al.   SCIENCE

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Interlocked DNA nanostructures controlled by a reversible logic circuit

(2014) Tao Li et al.   Nature Communications

Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells

(2014) Yuchen Liu et al.   Nature Communications

Smart Drug Delivery Nanocarriers with Self-Assembled DNA Nanostructures

(2013) Jiang Li et al.   ADVANCED MATERIALS

Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage

(2013) Robert Crawford et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Controlled Release of Encapsulated Cargo from a DNA Icosahedron using a Chemical Trigger

(2013) Anusuya Banerjee et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Sentinel lymph node imaging by a fluorescently labeled DNA tetrahedron

(2013) Kyoung-Ran Kim et al.   BIOMATERIALS

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Noncanonical Self-Assembly of Multifunctional DNA Nanoflowers for Biomedical Applications

(2013) Guizhi Zhu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Isothermal Self-Assembly of Complex DNA Structures under Diverse and Biocompatible Conditions

(2013) Cameron Myhrvold et al.   NANO LETTERS

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

(2013) Nick Goldman et al.   NATURE

Synthetic analog computation in living cells

(2013) Ramiz Daniel et al.   NATURE

Synthetic circuits integrating logic and memory in living cells

(2013) Piro Siuti et al.   NATURE BIOTECHNOLOGY

Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell

(2013) Souvik Modi et al.   Nature Nanotechnology

A modular strategy for engineering orthogonal chimeric RNA transcription regulators

(2013) Melissa K. Takahashi et al.   NUCLEIC ACIDS RESEARCH

Amplifying Genetic Logic Gates

(2013) J. Bonnet et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Nanoneedle-Assisted Delivery of Site-Selective Peptide-Functionalized DNA Nanocages for Targeting Mitochondria and Nuclei

(2013) Miu Shan Chan et al.   Small

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures

(2012) Eiji Nakata et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Reconfigurable Three-Dimensional DNA Nanostructures for the Construction of Intracellular Logic Sensors

(2012) Hao Pei et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Interenzyme Substrate Diffusion for an Enzyme Cascade Organized on Spatially Addressable DNA Nanostructures

(2012) Jinglin Fu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA Origami as a Carrier for Circumvention of Drug Resistance

(2012) Qiao Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rolling Circle Amplification-Templated DNA Nanotubes Show Increased Stability and Cell Penetration Ability

(2012) Graham D. Hamblin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-Step Rapid Assembly of DNA Origami Nanostructures for Addressable Nanoscale Bioreactors

(2012) Yanming Fu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Spherical Nucleic Acids

(2012) Joshua I. Cutler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A DNA Nanostructure Platform for Directed Assembly of Synthetic Vaccines

(2012) Xiaowei Liu et al.   NANO LETTERS

Rationally designed families of orthogonal RNA regulators of translation

(2012) Vivek K Mutalik et al.   Nature Chemical Biology

Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

(2012) Chenxiang Lin et al.   Nature Chemistry

Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery

(2012) Hyukjin Lee et al.   Nature Nanotechnology

Biomolecular computing systems: principles, progress and potential

(2012) Yaakov Benenson   NATURE REVIEWS GENETICS

Optogenetic investigation of neural circuits underlying brain disease in animal models

(2012) Kay M. Tye et al.   NATURE REVIEWS NEUROSCIENCE

Fast production of homogeneous recombinant RNA—towards large-scale production of RNA

(2012) Frank H.T. Nelissen et al.   NUCLEIC ACIDS RESEARCH

Synthetic in vivo validation of gene network circuitry

(2012) S. S. Damle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic switchboard for synthetic biology applications

(2012) J. M. Callura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescence Imaging of Cellular Metabolites with RNA

(2012) Jeremy S. Paige et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Next-Generation Digital Information Storage in DNA

(2012) G. M. Church et al.   SCIENCE

Three-Dimensional Structures Self-Assembled from DNA Bricks

(2012) Y. Ke et al.   SCIENCE

A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads

(2012) S. M. Douglas et al.   SCIENCE

DNA Cage Delivery to Mammalian Cells

(2011) Anthony S. Walsh et al.   ACS Nano

Self-Assembled Multivalent DNA Nanostructures for Noninvasive Intracellular Delivery of Immunostimulatory CpG Oligonucleotides

(2011) Jiang Li et al.   ACS Nano

Reversible Logic Circuits Made of DNA

(2011) Anthony J. Genot et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA Directed Self-Assembly of Anisotropic Plasmonic Nanostructures

(2011) Suchetan Pal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A simple DNA gate motif for synthesizing large-scale circuits

(2011) L. Qian et al.   Journal of the Royal Society Interface

Organizing DNA Origami Tiles into Larger Structures Using Preformed Scaffold Frames

(2011) Zhao Zhao et al.   NANO LETTERS

The Label-Free Unambiguous Detection and Symbolic Display of Single Nucleotide Polymorphisms on DNA Origami

(2011) Hari K. K. Subramanian et al.   NANO LETTERS

Stability of DNA Origami Nanoarrays in Cell Lysate

(2011) Qian Mei et al.   NANO LETTERS

CCL2 recruits inflammatory monocytes to facilitate breast-tumour metastasis

(2011) Bin-Zhi Qian et al.   NATURE

Aptamers for allosteric regulation

(2011) Jan L Vinkenborg et al.   Nature Chemical Biology

Dynamic DNA nanotechnology using strand-displacement reactions

(2011) David Yu Zhang et al.   Nature Chemistry

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

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

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

(2011) L. Qian et al.   SCIENCE

DNA Origami with Complex Curvatures in Three-Dimensional Space

(2011) D. Han et al.   SCIENCE

A synthetic icosahedral DNA-based host–cargo complex for functional in vivo imaging

(2011) Dhiraj Bhatia et al.   Nature Communications

A Light-Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion

(2010) Mengguang Zhou et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Single-Molecule Kinetics and Super-Resolution Microscopy by Fluorescence Imaging of Transient Binding on DNA Origami

(2010) Ralf Jungmann et al.   NANO LETTERS

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Self-sufficient control of urate homeostasis in mice by a synthetic circuit

(2010) Christian Kemmer et al.   NATURE BIOTECHNOLOGY

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

DNA computing circuits using libraries of DNAzyme subunits

(2010) Johann Elbaz et al.   Nature Nanotechnology

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

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

A DNA-Origami Chip Platform for Label-Free SNP Genotyping Using Toehold-Mediated Strand Displacement

(2010) Zhao Zhang et al.   Small

Extracellular Production of an RNA Aptamer by Ribonuclease-Free Marine Bacteria Harboring Engineered Plasmids: a Proposal for Industrial RNA Drug Production

(2009) H. Suzuki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced resistance of DNA nanostructures to enzymatic digestion

(2009) Jung-Won Keum et al.   CHEMICAL COMMUNICATIONS

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

(2009) David Yu Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal

(2009) Jianping Zheng et al.   NATURE

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

(2009) Ebbe S. Andersen et al.   NATURE

A DNA nanomachine that maps spatial and temporal pH changes inside living cells

(2009) Souvik Modi et al.   Nature Nanotechnology

Enzyme cascades activated on topologically programmed DNA scaffolds

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

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

(2009) Hareem T. Maune et al.   Nature Nanotechnology

DNAzymes for sensing, nanobiotechnology and logic gate applications

(2008) Itamar Willner et al.   CHEMICAL SOCIETY REVIEWS

Error suppression mechanisms for DNA tile self-assembly and their simulation

(2008) Kenichi Fujibayashi et al.   Natural Computing

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra

(2008) Yu He et al.   NATURE

Peptide antisense nanoparticles

(2008) P. C. Patel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vivo cloning of artificial DNA nanostructures

(2008) C. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE