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Article ; Online: Aptamer-Modified Homogeneous Catalysts, Heterogenous Nanoparticle Catalysts, and Photocatalysts: Functional "Nucleoapzymes", "Aptananozymes", and "Photoaptazymes".

Ouyang, Yu / O'Hagan, Michael P / Willner, Bilha / Willner, Itamar

Advanced materials (Deerfield Beach, Fla.)

2023 Volume 36, Issue 10, Page(s) e2210885

Abstract: Conjugation of aptamers to homogeneous catalysts ("nucleoapzymes"), heterogeneous nanoparticle catalysts ("aptananozymes"), and photocatalysts ("photoaptazymes") yields superior catalytic/photocatalytic hybrid nanostructures emulating functions of native ...

Abstract	Conjugation of aptamers to homogeneous catalysts ("nucleoapzymes"), heterogeneous nanoparticle catalysts ("aptananozymes"), and photocatalysts ("photoaptazymes") yields superior catalytic/photocatalytic hybrid nanostructures emulating functions of native enzymes and photosystems. The concentration of the substrate in proximity to the catalytic sites ("molarity effect") or spatial concentration of electron-acceptor units in spatial proximity to the photosensitizers, by aptamer-ligand complexes, leads to enhanced catalytic/photocatalytic efficacies of the hybrid nanostructures. This is exemplified by sets of "nucleoapzymes" composed of aptamers conjugated to the hemin/G-quadruplex DNAzymes or metal-ligand complexes as catalysts, catalyzing the oxidation of dopamine to aminochrome, oxygen-insertion into the Ar─H moiety of tyrosinamide and the subsequent oxidation of the catechol product into aminochrome, or the hydrolysis of esters or ATP. Also, aptananozymes consisting of aptamers conjugated to Cu
MeSH term(s)	Photosensitizing Agents ; Dopamine ; Ligands ; Gold ; Metal Nanoparticles ; Oligonucleotides ; Catalysis ; Indolequinones
Chemical Substances	aminochrome 1 (39984-17-3) ; Photosensitizing Agents ; Dopamine (VTD58H1Z2X) ; Ligands ; Gold (7440-57-5) ; Oligonucleotides ; Indolequinones
Language	English
Publishing date	2023-04-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1474949-X
ISSN	1521-4095 ; 0935-9648
ISSN (online)	1521-4095
ISSN	0935-9648
DOI	10.1002/adma.202210885
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Article ; Online: Switchable and dynamic G-quadruplexes and their applications.

Dong, Jiantong / O'Hagan, Michael P / Willner, Itamar

Chemical Society reviews

2022 Volume 51, Issue 17, Page(s) 7631–7661

Abstract: G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, ...

Abstract	G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO
MeSH term(s)	DNA/chemistry ; G-Quadruplexes ; Hydrogels/chemistry ; Nanostructures/chemistry ; Nanotechnology ; Silicon Dioxide
Chemical Substances	Hydrogels ; Silicon Dioxide (7631-86-9) ; DNA (9007-49-2)
Language	English
Publishing date	2022-08-30
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1472875-8
ISSN	1460-4744 ; 0306-0012
ISSN (online)	1460-4744
ISSN	0306-0012
DOI	10.1039/d2cs00317a
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Article ; Online: Functional catalytic nanoparticles (nanozymes) for sensing.

Ouyang, Yu / O'Hagan, Michael P / Willner, Itamar

Biosensors & bioelectronics

2022 Volume 218, Page(s) 114768

Abstract: Nanoparticles exhibiting diverse shapes, high porosity and chemical stability reveal, upon appropriate chemical engineering, enzyme-like catalytic activities, "nanozymes", providing a plethora of nanomaterials for diverse applications. The present review ...

Abstract	Nanoparticles exhibiting diverse shapes, high porosity and chemical stability reveal, upon appropriate chemical engineering, enzyme-like catalytic activities, "nanozymes", providing a plethora of nanomaterials for diverse applications. The present review article addresses the sensing applications of the catalytic functions of nanozymes consisting of metal nanoparticles, metal oxides, metal sulfides and cyanometallate nanoparticles, carbon-based nanomaterials and metal-organic-framework nanoparticles. The nanozymes emulate catalytic functions of oxidases or peroxidases and are employed as amplifying agents for sensing diverse analytes such as glucose, dopamine, NADH, thiols, phosphates and more. Moreover, the immobilization of nanozymes on electrodes provides versatile means to develop electrochemical sensing platforms. Different principles of the electrochemical sensing platforms, synthetic methodologies to deposit nanozymes on electrodes, and methods to establish electrical communication between the bulk conductive support and nanozyme particles are introduced. Electrochemical sensing platforms applying nanozyme-modified electrodes for the detection of analytes such as organophosphates, glucose and more are discussed. In particular, the application of nanozymes as amplifying labels for biosensor devices detecting proteins, DNA and microRNAs are addressed. Finally, the uses of nanozymes as functional constituents to design sense-and-treat systems are discussed. This is exemplified with the assembly of a bioreactor system for the sensing of glucose, the nanozyme-promoted generation of reactive oxygen species as cytotoxic agents towards cancer cells, and the autonomous nanozyme-based glucose-controlled release of insulin from nanocarrier devices. The future challenges in developing nanozyme-based sensors and sense-and-treat systems are presented.
MeSH term(s)	Metal-Organic Frameworks ; Biosensing Techniques/methods ; Dopamine ; Reactive Oxygen Species ; Delayed-Action Preparations ; NAD ; Catalysis ; Nanostructures ; Metal Nanoparticles ; Peroxidases ; Carbon ; Glucose/metabolism ; Oxides ; DNA ; Sulfides ; Phosphates ; Sulfhydryl Compounds ; Organophosphates ; Cytotoxins ; MicroRNAs ; Insulins
Chemical Substances	Metal-Organic Frameworks ; Dopamine (VTD58H1Z2X) ; Reactive Oxygen Species ; Delayed-Action Preparations ; NAD (0U46U6E8UK) ; Peroxidases (EC 1.11.1.-) ; Carbon (7440-44-0) ; Glucose (IY9XDZ35W2) ; Oxides ; DNA (9007-49-2) ; Sulfides ; Phosphates ; Sulfhydryl Compounds ; Organophosphates ; Cytotoxins ; MicroRNAs ; Insulins
Language	English
Publishing date	2022-10-03
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2022.114768
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Article: Switchable and dynamic G-quadruplexes and their applications

Dong, Jiantong / O'Hagan, Michael P. / Willner, Itamar

Chemical Society reviews. 2022 Aug. 30, v. 51, no. 17

2022

Abstract	G-Quadruplexes attract growing interest as functional constituents in biology, chemistry, nanotechnology, and material science. In particular, the reversible dynamic reconfiguration of G-quadruplexes provides versatile means to switch DNA nanostructures, reversibly control catalytic functions of DNA assemblies, and switch material properties and functions. The present review article discusses the switchable dynamic reconfiguration of G-quadruplexes as central functional and structural motifs that enable diverse applications in DNA nanotechnology and material science. The dynamic reconfiguration of G-quadruplexes has a major impact on the development of DNA switches and DNA machines. The integration of G-quadruplexes with enzymes yields supramolecular assemblies exhibiting switchable catalytic functions guided by dynamic G-quadruplex topologies. In addition, G-quadruplexes act as important building blocks to operate constitutional dynamic networks and transient dissipative networks mimicking complex biological dynamic circuitries. Furthermore, the integration of G-quadruplexes with DNA nanostructures, such as origami tiles, introduces dynamic and mechanical features into these static frameworks. Beyond the dynamic operation of G-quadruplex structures in solution, the assembly of G-quadruplexes on bulk surfaces such as electrodes or nanoparticles provides versatile means to engineer diverse electrochemical and photoelectrochemical devices and to switch the dynamic aggregation/deaggregation of nanoparticles, leading to nanoparticle assemblies that reveal switchable optical properties. Finally, the functionalization of hydrogels, hydrogel microcapsules, or nanoparticle carriers, such as SiO₂ nanoparticles or metal–organic framework nanoparticles, yields stimuli-responsive materials exhibiting shape-memory, self-healing, and controlled drug release properties. Indeed, G-quadruplex-modified nanomaterials find growing interest in the area of nanomedicine. Beyond the impressive G-quadruplex-based scientific advances achieved to date, exciting future developments are still anticipated. The review addresses these goals by identifying the potential opportunities and challenges ahead of the field in the coming years.
Keywords	DNA ; coordination polymers ; drug delivery systems ; electrochemistry ; hydrogels ; nanomedicine ; nanoparticles
Language	English
Dates of publication	2022-0830
Size	p. 7631-7661.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472875-8
ISSN	1460-4744 ; 0306-0012
ISSN (online)	1460-4744
ISSN	0306-0012
DOI	10.1039/d2cs00317a
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Aptamer-Protein Structures Guide In Silico and Experimental Discovery of Aptamer-Short Peptide Recognition Complexes or Aptamer-Amino Acid Cluster Complexes.

Fadeev, Michael / O'Hagan, Michael P / Biniuri, Yonatan / Willner, Itamar

The journal of physical chemistry. B

2022 Volume 126, Issue 44, Page(s) 8931–8939

Abstract: A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence ... ...

Abstract	A method to computationally and experimentally identify aptamers against short peptides or amino acid clusters is introduced. The method involves the selection of a well-defined protein aptamer complex and the extraction of the peptide sequence participating in the binding of the protein to the aptamer. The subsequent fragmentation of the peptide sequence into short peptides and the in silico docking-guided identification of affinity complexes between the miniaturized peptides and the antiprotein aptamer, followed by experimental validation of the binding features of the short peptides with the antiprotein aptamers, leads to the identification of new short peptide-aptamer complexes. This is exemplified with the identification of the pentapeptide RYERN as the scaffold that binds thrombin to the DNA thrombin aptamer (DNA TA). In silico docking studies followed by microscale thermophoresis (MST) experiments demonstrate that the miniaturized tripeptides RYE, YER, and ERN reveal selective binding affinities toward the DNA TA. In addition, docking and MST experiments show that the ribonucleotide-translated RNA TA shows related binding affinities of YER to the DNA TA. Most importantly, we demonstrate that the separated amino acids Y/E/R assemble as a three amino acid cluster on the DNA TA and RNA TA aptamers in spatial configurations similar to the tripeptide YER on the respective aptamers. The clustering phenomenon is selective for the YER tripeptide system. The method to identify binding affinities of miniaturized peptides to known antiprotein aptamers and the specific clustering of single amino acids on the aptamers is further demonstrated by in silico and experimental identification of the binding of the tripeptide RET and the selective clustering of the separated amino acids R/E/T onto a derivative of the AS1411 aptamer against the nucleolin receptor protein.
MeSH term(s)	Amino Acids ; Aptamers, Nucleotide/chemistry ; Thrombin/metabolism ; DNA/chemistry ; RNA ; Peptides
Chemical Substances	Amino Acids ; Aptamers, Nucleotide ; Thrombin (EC 3.4.21.5) ; DNA (9007-49-2) ; RNA (63231-63-0) ; Peptides
Language	English
Publishing date	2022-10-31
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c05624
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Article ; Online: Dynamic Fusion of Nucleic Acid Functionalized Nano-/Micro-Cell-Like Containments: From Basic Concepts to Applications.

Li, Zhenzhen / Wang, Jianbang / O'Hagan, Michael P / Huang, Fujian / Xia, Fan / Willner, Itamar

ACS nano

2023 Volume 17, Issue 16, Page(s) 15308–15327

Abstract: Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by ... ...

Abstract	Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.
MeSH term(s)	Nucleic Acids/chemistry ; Liposomes/chemistry ; DNA/chemistry ; Membrane Fusion ; Cell Membrane/metabolism
Chemical Substances	Nucleic Acids ; Liposomes ; DNA (9007-49-2)
Language	English
Publishing date	2023-08-07
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.3c04415
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Article ; Online: Bioinspired Artificial Photosynthetic Systems.

Wang, Chen / O'Hagan, Michael P / Willner, Bilha / Willner, Itamar

Chemistry (Weinheim an der Bergstrasse, Germany)

2021 Volume 28, Issue 9, Page(s) e202103595

Abstract: Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic ... ...

Abstract	Mimicking photosynthesis using artificial systems, as a means for solar energy conversion and green fuel generation, is one of the holy grails of modern science. This perspective presents recent advances towards developing artificial photosynthetic systems. In one approach, native photosystems are interfaced with electrodes to yield photobioelectrochemical cells that transform light energy into electrical power. This is exemplified by interfacing photosystem I (PSI) and photosystem II (PSII) as an electrically contacted assembly mimicking the native Z-scheme, and by the assembly of an electrically wired PSI/glucose oxidase biocatalytic conjugate on an electrode support. Illumination of the functionalized electrodes led to light-induced generation of electrical power, or to the generation of photocurrents using glucose as the fuel. The second approach introduces supramolecular photosensitizer nucleic acid/electron acceptor complexes as functional modules for effective photoinduced electron transfer stimulating the subsequent biocatalyzed generation of NADPH or the Pt-nanoparticle-catalyzed evolution of molecular hydrogen. Application of the DNA machineries for scaling-up the photosystems is demonstrated. A third approach presents the integration of artificial photosynthetic modules into dynamic nucleic acid networks undergoing reversible reconfiguration or dissipative transient operation in the presence of auxiliary triggers. Control over photoinduced electron transfer reactions and photosynthetic transformations by means of the dynamic networks is demonstrated.
MeSH term(s)	Electron Transport ; Photosynthesis ; Photosystem I Protein Complex ; Photosystem II Protein Complex/chemistry ; Photosystem II Protein Complex/metabolism ; Solar Energy
Chemical Substances	Photosystem I Protein Complex ; Photosystem II Protein Complex
Language	English
Publishing date	2021-12-22
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202103595
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Article ; Online: Assembly of Dynamic Gated and Cascaded Transient DNAzyme Networks.

Dong, Jiantong / Ouyang, Yu / Wang, Jianbang / O'Hagan, Michael P / Willner, Itamar

ACS nano

2022 Volume 16, Issue 4, Page(s) 6153–6164

Abstract: The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules ...

Abstract	The dynamic transient formation and depletion of G-quadruplexes regulate gene replication and transcription. This process was found to be related to various diseases such as cancer and premature aging. We report on the engineering of nucleic acid modules revealing dynamic, transient assembly and disassembly of G-quadruplex structures and G-quadruplex-based DNAzymes, gated transient processes, and cascaded dynamic transient reactions that involve G-quadruplex and DNAzyme structures. The dynamic transient processes are driven by functional DNA reaction modules activated by a fuel strand and guided toward dissipative operation by a nicking enzyme (Nt.BbvCI). The dynamic networks were further characterized by computational simulation of the experiments using kinetic models, allowing us to predict the dynamic performance of the networks under different auxiliary conditions applied to the systems. The systems reported herein could provide functional DNA machineries for the spatiotemporal control of G-quadruplex structures perturbing gene expression and thus provide a therapeutic means for related emergent diseases.
MeSH term(s)	DNA, Catalytic/metabolism ; G-Quadruplexes ; DNA/genetics ; DNA/chemistry
Chemical Substances	DNA, Catalytic ; DNA (9007-49-2)
Language	English
Publishing date	2022-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.1c11631
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Article ; Online: Gated Transient Dissipative Dimerization of DNA Tetrahedra Nanostructures for Programmed DNAzymes Catalysis.

Li, Zhenzhen / Wang, Jianbang / Zhou, Zhixin / O'Hagan, Michael P / Willner, Itamar

ACS nano

2022 Volume 16, Issue 3, Page(s) 3625–3636

Abstract: Transient dissipative dimerization and transient gated dimerization of DNA tetrahedra nanostructures are introduced as functional modules to emulate transient and gated protein-protein interactions and emergent protein-protein guided transient catalytic ... ...

Abstract	Transient dissipative dimerization and transient gated dimerization of DNA tetrahedra nanostructures are introduced as functional modules to emulate transient and gated protein-protein interactions and emergent protein-protein guided transient catalytic functions, operating in nature. Four tetrahedra are engineered to yield functional modules that, in the presence of pre-engineered auxiliary nucleic acids and the nicking enzyme Nt.BbvCI, lead to the fueled transient dimerization of two pairs of tetrahedra. The dynamic transient formation and depletion of DNA tetrahedra are followed by transient FRET signals generated by fluorophore-labeled tetrahedra. The integration of two inhibitors within the mixture of the four tetrahedra and two auxiliary modules, fueling the transient dimerization, results in selective inhibitor-guided gated transient dimerization of two different DNA tetrahedra dimers. Kinetic models for the dynamic transient dimerization and gated transient dimerization of the DNA tetrahedra are formulated and computationally simulated. The derived rate-constants allow the prediction and subsequent experimental validation of the performance of the systems under different auxiliary conditions. In addition, by appropriate modification of the four tetrahedra structures, the triggered gated emergence of selective transient catalytic functions driven by the two pairs of DNA tetrahedra dimers is demonstrated.
MeSH term(s)	Catalysis ; DNA/chemistry ; DNA, Catalytic/chemistry ; Dimerization ; Nanostructures/chemistry
Chemical Substances	DNA, Catalytic ; DNA (9007-49-2)
Language	English
Publishing date	2022-02-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.1c06117
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Article ; Online: Photocleavable

O'Hagan, Michael P / Duan, Zhijuan / Huang, Fujian / Laps, Shay / Dong, Jiantong / Xia, Fan / Willner, Itamar

Chemical reviews

2023 Volume 123, Issue 10, Page(s) 6839–6887

Abstract: This review article introduces mechanistic aspects and applications of photochemically ... ...

Abstract	This review article introduces mechanistic aspects and applications of photochemically deprotected
MeSH term(s)	Liposomes ; DNA/chemistry ; Nanostructures/chemistry ; Nanotechnology/methods ; Oligonucleotides
Chemical Substances	Liposomes ; DNA (9007-49-2) ; Oligonucleotides
Language	English
Publishing date	2023-04-20
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.3c00016
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