4.8 Article

Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks

Related references

Note: Only part of the references are listed.
Article Chemistry, Multidisciplinary

Dissipative Organization of DNA Oligomers for Transient Catalytic Function

Jie Deng et al.

Summary: The development of synthetic non-equilibrium systems has opened doors for man-made life-like materials. Through ATP-driven dynamic covalent DNA assembly, we have successfully achieved ATP-fueled transient organization and ATP-fueled DNAzymes for substrate cleavage.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Article Chemistry, Multidisciplinary

Rotaxanes as Cages to Control DNA Binding, Cytotoxicity, and Cellular Uptake of a Small Molecule**

Timothy Kench et al.

Summary: The efficacy of many drugs can be limited by undesirable properties, such as poor aqueous solubility, low bioavailability, and off-target interactions. Various drug carriers have been investigated to enhance the pharmacological profile of therapeutic agents. In this work, mechanical protection is used to cage a DNA-targeting metallodrug within a photodegradable rotaxane, which showed enhanced cell permeability and limited cytotoxicity within osteosarcoma cells compared to the free drug. Light activation led to a dramatic increase in cytotoxicity, arising from the translocation of Pt-II-salphen to the nucleus and its binding to DNA.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

Article Chemistry, Multidisciplinary

Transient Dissipative Optical Properties of Aggregated Au Nanoparticles, CdSe/ZnS Quantum Dots, and Supramolecular Nucleic Acid-Stabilized Ag Nanoclusters

Yu Ouyang et al.

Summary: The study introduces a method to control the optical properties of Au NPs or CdSe/ZnS QDs through their dynamic aggregation/deaggregation, achieved by nucleic acid-modified pairs and biocatalytic reactions. It leads to the dynamic recovery of the original NP or QDs modules.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Multidisciplinary

Self-resetting molecular probes for nucleic acids detection enabled by fuel dissipative systems

Na Li et al.

Summary: The COVID-19 pandemic has had a significant impact on human health and the global economy. A self-resetting molecular probe has been developed using DNA nanotechnology to detect SARS-CoV-2 RNA repeatedly, with consistent signal amplitudes and fingerprint signals suitable for high confidential identifications of single-nucleotide variants. The probe also shows the ability to detect multiple human-infectious RNA viruses, enhancing screening capabilities for COVID-19 and other infectious diseases.

NANO TODAY (2021)

Article Chemistry, Multidisciplinary

Dissipative Gated and Cascaded DNA Networks

Zhixin Zhou et al.

Summary: The study presents nucleic acid-based, out-of-equilibrium, dissipative networks driven by nucleic acid fuels and the nicking enzyme Nt.BbvCI. Experiments show activation and regeneration of functional modules, as well as selective gated dissipative operation and intercommunication of two networks. Computational simulations are used to predict transient patterns of the systems under different conditions.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Multidisciplinary

Imaging of Cancer Cells and Dictated Cytotoxicity Using Aptamer-Guided Hybridization Chain Reaction (HCR)-Generated G-Quadruplex Chains

Amily Fang-Ju Jou et al.

Summary: DNA nanotechnology provides a powerful tool for developing cancer theranostics, with autonomous surface-nucleolin-guided HCR leading to the formation of Zn-II PPIX-loaded G-quadruplex polymer chains for selective imaging and cytotoxicity towards TNBC. This method offers a promising platform for targeting TNBC, which has poor prognosis and high risk of recurrence.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2021)

Article Chemistry, Multidisciplinary

Identifying G-Quadruplex-DNA-Disrupting Small Molecules

Jeremie Mitteaux et al.

Summary: This article reports on efforts to develop in vitro assays to reliably identify molecules that can destabilize G4s. The workflow includes a newly designed G4-unfold assay, adapted from the G4-helicase assay with Pif1, as well as biophysical and biochemical techniques traditionally used to study G4/ligand interactions, and a qPCR stop assay adapted from a Taq-based protocol to identify G4s in genomic DNA. This multipronged approach leads to the characterization of a phenylpyrrolocytosine (PhpC)-based G-clamp analog as a prototype of a G4-disrupting small molecule.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2021)

Article Chemistry, Multidisciplinary

Aptamer-modified DNA tetrahedra-gated metal-organic framework nanoparticle carriers for enhanced chemotherapy or photodynamic therapy

Pu Zhang et al.

Summary: UiO-66 metal-organic framework nanoparticles gated by aptamer-functionalized DNA tetrahedra provide superior biomarker-responsive hybrid nano-carriers for biomedical applications, allowing enhanced and selective cytotoxicity towards malignant cells. Association of the released Zn(ii)-PPIX to the G-quadruplex structures generates highly fluorescent supramolecular Zn(ii)-PPIX/G-quadruplex VEGF aptamer-tetrahedra structures, enabling light-induced photosensitized generation of reactive oxygen species (ROS) for high-efficacy PDT treatment of malignant cells.

CHEMICAL SCIENCE (2021)

Article Chemistry, Multidisciplinary

DNAzyme- and light-induced dissipative and gated DNA networks

Jianbang Wang et al.

Summary: Nucleic acid-based dissipative, out-of-equilibrium systems and light-driven non-waste generating systems are introduced in this study, with the ability to predict the transient behavior of networks under different auxiliary conditions.

CHEMICAL SCIENCE (2021)

Review Chemistry, Multidisciplinary

Biosensing with DNAzymes

Erin M. McConnell et al.

Summary: This article provides a comprehensive review of biosensing with DNAzymes, highlighting major progress and contributions to portable biosensor devices and point-of-care diagnostics. It specifically focuses on the incorporation of DNAzymes into bioassays and recent advances in in vivo sensing platforms and portable sensors for molecular recognition, concluding with a critical perspective on the field and potential impacts of DNAzyme-based devices.

CHEMICAL SOCIETY REVIEWS (2021)

Review Biochemistry & Molecular Biology

How to untie G-quadruplex knots and why?

Pauline Lejault et al.

Summary: Researchers have been studying how to use chemicals to interact with and stabilize G-quadruplexes (G4s) in cells for over two decades, achieving success in obtaining mechanistic interpretations. This has led to a fundamental reconsideration of G4-targeting strategies, with ongoing efforts to develop G4-stabilizing ligands and design molecular tools to unfold G4s.

CELL CHEMICAL BIOLOGY (2021)

Review Chemistry, Multidisciplinary

Stimuli-Responsive Biomolecule-Based Hydrogels and Their Applications

Margarita Vazquez-Gonzalez et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Review Genetics & Heredity

Building machines with DNA molecules

Hamid Ramezani et al.

NATURE REVIEWS GENETICS (2020)

Article Chemistry, Multidisciplinary

Dissipative Constitutional Dynamic Networks for Tunable Transient Responses and Catalytic Functions

Shan Wang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Chemistry, Multidisciplinary

Fuel-Responsive Allosteric DNA-Based Aptamers for the Transient Release of ATP and Cocaine

Erica Del Grosso et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Chemistry, Multidisciplinary

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA

Michael P. O'Hagan et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Review Chemistry, Multidisciplinary

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Friedrich C. Simmel et al.

CHEMICAL REVIEWS (2019)

Article Chemistry, Multidisciplinary

Artificial Signal Feedback Network Mimicking Cellular Adaptivity

Hui Liu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Review Chemistry, Organic

Binding and Beyond: What Else Can G-Quadruplex Ligands Do?

Michael P. O'Hagan et al.

EUROPEAN JOURNAL OF ORGANIC CHEMISTRY (2019)

Article Multidisciplinary Sciences

Programmable dynamic steady states in ATP-driven nonequilibrium DNA systems

Laura Heinen et al.

SCIENCE ADVANCES (2019)

Article Chemistry, Multidisciplinary

Nicking-Assisted Reactant Recycle To Implement Entropy-Driven DNA Circuit

Cheng Zhang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Review Chemistry, Multidisciplinary

DNA Quadruple Helices in Nanotechnology

Jean-Louis Mergny et al.

CHEMICAL REVIEWS (2019)

Article Chemistry, Multidisciplinary

Dissipative Synthetic DNA-Based Receptors for the Transient Loading and Release of Molecular Cargo

Erica Del Grosso et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Nanoscience & Nanotechnology

Dissipative adaptation in driven self-assembly leading to self-dividing fibrils

Esra te Brinke et al.

NATURE NANOTECHNOLOGY (2018)

Review Chemistry, Multidisciplinary

G-Quadruplex: A Regulator of Gene Expression and Its Chemical Targeting

Tian Tian et al.

Article Chemistry, Multidisciplinary

Stimuli-Responsive DNA-Functionalized Metal-Organic Frameworks (MOFs)

Jason S. Kahn et al.

ADVANCED MATERIALS (2017)

Article Chemistry, Multidisciplinary

Dissipative Assembly of Aqueous Carboxylic Acid Anhydrides Fueled by Carbodiimides

Lasith S. Kariyawasam et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Materials Science, Multidisciplinary

Biodegradable, multifunctional DNAzyme nanoflowers for enhanced cancer therapy

Yi Jin et al.

NPG ASIA MATERIALS (2017)

Review Chemistry, Multidisciplinary

Triplex DNA Nanostructures: From Basic Properties to Applications

Yuwei Hu et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Article Chemistry, Multidisciplinary

Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore

Fu-Na Meng et al.

CHEMICAL COMMUNICATIONS (2017)

Article Biochemistry & Molecular Biology

DNA Walker-Regulated Cancer Cell Growth Inhibition

Feiran Li et al.

CHEMBIOCHEM (2016)

Article Chemistry, Multidisciplinary

A fuel-limited isothermal DNA machine for the sensitive detection of cellular deoxyribonucleoside triphosphates

Jiantong Dong et al.

CHEMICAL COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

Interaction of metallacrown complexes with G-quadruplex DNA

Ewa Rajczak et al.

JOURNAL OF INORGANIC BIOCHEMISTRY (2016)

Article Chemistry, Multidisciplinary

Biocatalytic Pathway Selection in Transient Tripeptide Nanostructures

Charalampos G. Pappas et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Chemistry, Multidisciplinary

Integration of Switchable DNA-Based Hydrogels with Surfaces by the Hybridization Chain Reaction

Jason S. Kahn et al.

NANO LETTERS (2015)

Article Biochemistry & Molecular Biology

G-quadruplexes and their regulatory roles in biology

Daniela Rhodes et al.

NUCLEIC ACIDS RESEARCH (2015)

Review Chemistry, Multidisciplinary

DNA Switches: From Principles to Applications

Fuan Wang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Chemistry, Multidisciplinary

Gated Mesoporous SiO2 Nanoparticles Using K+-Stabilized G-Quadruplexes

Zhanxia Zhang et al.

ADVANCED FUNCTIONAL MATERIALS (2014)

Article Chemistry, Multidisciplinary

A Twisting Electronic Nanoswitch Made of DNA

Yu Chuan Huang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

Article Chemistry, Multidisciplinary

Switchable Enzyme/DNAzyme Cascades by the Reconfiguration of DNA Nanostructures

Yuwei Hu et al.

CHEMISTRY-A EUROPEAN JOURNAL (2014)

Review Biochemistry & Molecular Biology

Synaptic vesicle recycling: steps and principles

Silvio O. Rizzoli

EMBO JOURNAL (2014)

Article Biochemistry & Molecular Biology

G quadruplexes are genomewide targets of transcriptional helicases XPB and XPD

Lucas T. Gray et al.

NATURE CHEMICAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Type II restriction endonucleases-a historical perspective and more

Alfred Pingoud et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Chemistry, Analytical

A label-free G-quadruplex DNA-based fluorescence method for highly sensitive, direct detection of cisplatin

Hualin Yang et al.

SENSORS AND ACTUATORS B-CHEMICAL (2014)

Article Chemistry, Multidisciplinary

Predator-Prey Molecular Ecosystems

Teruo Fujii et al.

ACS NANO (2013)

Article Chemistry, Multidisciplinary

Switching Photonic and Electrochemical Functions of a DNAzyme by DNA Machines

Xiaoqing Liu et al.

NANO LETTERS (2013)

Review Genetics & Heredity

DNA secondary structures: stability and function of G-quadruplex structures

Matthew L. Bochman et al.

NATURE REVIEWS GENETICS (2012)

Review Cell Biology

Towards a bottom-up reconstitution of bacterial cell division

Ariadna Martos et al.

TRENDS IN CELL BIOLOGY (2012)

Article Chemistry, Multidisciplinary

A Ligation-Triggered DNAzyme Cascade for Amplified Fluorescence Detection of Biological Small Molecules with Zero-Background Signal

Li-Min Lu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)

Article Biochemistry & Molecular Biology

Synthetic in vitro transcriptional oscillators

Jongmin Kim et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Programming an in vitro DNA oscillator using a molecular networking strategy

Kevin Montagne et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Review Chemistry, Multidisciplinary

Dynamic DNA nanotechnology using strand-displacement reactions

David Yu Zhang et al.

NATURE CHEMISTRY (2011)

Article Multidisciplinary Sciences

Timing molecular motion and production with a synthetic transcriptional clock

Elisa Franco et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Chemistry, Multidisciplinary

Amplified Aptamer-Based Assay through Catalytic Recycling of the Analyte

Chun-Hua Lu et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)

Review Biophysics

Control of Actin Filament Treadmilling in Cell Motility

Beata Bugyi et al.

ANNUAL REVIEW OF BIOPHYSICS, VOL 39 (2010)

Review Biochemical Research Methods

Functional nucleic acid nanostructures and DNA machines

Carsten Teller et al.

CURRENT OPINION IN BIOTECHNOLOGY (2010)

Article Chemistry, Multidisciplinary

Sensitive and Selective Amplified Fluorescence DNA Detection Based on Exonuclease III-Aided Target Recycling

Xiaolei Zuo et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Review Cell Biology

Cell adhesion: integrating cytoskeletal dynamics and cellular tension

J. Thomas Parsons et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2010)

Article Chemistry, Multidisciplinary

A metal-mediated conformational switch controls G-quadruplex binding affinity

David Monchaud et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2008)

Article Chemistry, Medicinal

NAD+-dependent DNA ligase:: A novel target waiting for the right inhibitor

Namrata Dwivedi et al.

MEDICINAL RESEARCH REVIEWS (2008)

Review Nanoscience & Nanotechnology

DNA nanomachines

Jonathan Bath et al.

NATURE NANOTECHNOLOGY (2007)

Review Chemistry, Multidisciplinary

Forty years of in vitro evolution

Gerald F. Joyce

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2007)

Article Biochemistry & Molecular Biology

Dynamic roles for G4 DNA in the biology of eukaryotic cells

Nancy Maizels

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2006)

Article Chemistry, Multidisciplinary

Sturdier DNA nanotubes via ligation

Patrick O'Neill et al.

NANO LETTERS (2006)

Article Chemistry, Organic

DNA-based machines

Moritz K. Beissenhirtz et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Construction of an in vitro bistable circuit from synthetic transcriptional switches

Jongmin Kim et al.

MOLECULAR SYSTEMS BIOLOGY (2006)

Review Microbiology

Spatial control of bacterial division-site placement

L Rothfield et al.

NATURE REVIEWS MICROBIOLOGY (2005)

Article Multidisciplinary Sciences

DNA duplex-quadruplex exchange as the basis for a nanomolecular machine

P Alberti et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Multidisciplinary Sciences

Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription

A Siddiqui-Jain et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Chemistry, Multidisciplinary

A single DNA molecule nanomotor

JWJ Li et al.

NANO LETTERS (2002)

Review Biochemistry & Molecular Biology

Structure and function of type II restriction endonucleases

A Pingoud et al.

NUCLEIC ACIDS RESEARCH (2001)