1
|
Rivero-Barbarroja G, Carmen Padilla-Pérez M, Maisonneuve S, Isabel García-Moreno M, Tiet B, Vocadlo DJ, Xie J, García Fernández JM, Ortiz Mellet C. sp 2-Iminosugar azobenzene O-glycosides: Light-sensitive glycosidase inhibitors with unprecedented tunability and switching factors. Bioorg Chem 2024; 150:107555. [PMID: 38885548 DOI: 10.1016/j.bioorg.2024.107555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
The conventional approach to developing light-sensitive glycosidase activity regulators, involving the combination of a glycomimetic moiety and a photoactive azobenzene module, results in conjugates with differences in glycosidase inhibitory activity between the interchangeable E and Z-isomers at the azo group that are generally below one-order of magnitude. In this study, we have exploited the chemical mimic character of sp2-iminosugars to access photoswitchable p- and o-azobenzene α-O-glycosides based on the gluco-configured representative ONJ. Notably, we achieved remarkably high switching factors for glycosidase inhibition, favoring either the E- or Z-isomer depending on the aglycone structure. Our data also indicate a correlation between the isomeric state of the azobenzene module and the selectivity towards α- and β-glucosidase isoenzymes. The most effective derivative reached over a 103-fold higher inhibitory potency towards human β-glucocerebrosidase in the Z as compared with the E isomeric form. This sharp contrast is compatible with ex-vivo activation and programmed self-deactivation at physiological temperatures, positioning it as a prime candidate for pharmacological chaperone therapy in Gaucher disease. Additionally, our results illustrate that chemical tailoring enables the engineering of photocommutators with the ability to toggle inhibition between α- and β-glucosidase enzymes in a reversible manner, thus expanding the versatility and potential therapeutic applications of this approach.
Collapse
Affiliation(s)
- Gonzalo Rivero-Barbarroja
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, c/ Profesor García González 1, 41012 Sevilla, Spain
| | - M Carmen Padilla-Pérez
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, c/ Profesor García González 1, 41012 Sevilla, Spain
| | - Stéphane Maisonneuve
- ENS Paris-Saclay, CNRS, Photophysique et Photochimie Supramoléculaires et Macromoléculaires, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - M Isabel García-Moreno
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, c/ Profesor García González 1, 41012 Sevilla, Spain
| | - Ben Tiet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Juan Xie
- ENS Paris-Saclay, CNRS, Photophysique et Photochimie Supramoléculaires et Macromoléculaires, Université Paris-Saclay, Gif-sur-Yvette 91190, France.
| | - José M García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
| | - Carmen Ortiz Mellet
- Department of Organic Chemistry, Faculty of Chemistry, University of Seville, c/ Profesor García González 1, 41012 Sevilla, Spain.
| |
Collapse
|
2
|
Yang F, Li S, Wu J, Liu S. 2-Aminopurine-based quencher-free DNA tweezers with fluorescence properties well tuned by surrounding bases. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:576-582. [PMID: 38189219 DOI: 10.1039/d3ay01973j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Reversible structural changes in DNA nanomachines have great potential in the field of bioanalysis. Here, we demonstrate an assembly strategy for quencher-free and tunable DNA tweezers based on 2-aminopurine (2-AP), avoiding the tedious fluorescence labelling step. The conformational state of the tweezers could be controlled by specific oligonucleotides (fuel or anti-fuel). Taking advantage of the local environmental sensitivity of 2-AP, the structural changes of the tweezers were easily tracked, and multiple cyclic switching of the tweezers between the open and closed states was achieved. In addition, the influence of oligonucleotide structure on the fluorescence properties of 2-AP was deeply explored. We figured out that the fluorescence of 2-AP was highly quenched by the base-stacking of natural bases in DNA oligonucleotides. Moreover, by comprehensively regulating the type of bases surrounding the inserted 2-AP site, a sensitive fluorescence response towards dynamic change can be obtained. This principle of quencher-free nanodevices based on 2-AP provides a convenient method for monitoring the structural changes of DNA nanomachines.
Collapse
Affiliation(s)
- Fangfang Yang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Shuang Li
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Jialiang Wu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| |
Collapse
|
3
|
Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
Collapse
Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
4
|
Takezawa Y, Mori K, Huang WE, Nishiyama K, Xing T, Nakama T, Shionoya M. Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases. Nat Commun 2023; 14:4759. [PMID: 37620299 PMCID: PMC10449808 DOI: 10.1038/s41467-023-40353-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH-A base pair and a metal-mediated UOH-GdIII-UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH-A and UOH-GdIII-UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.
Collapse
Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Wei-En Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kotaro Nishiyama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tong Xing
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
5
|
O’Hagan M, Duan Z, Huang F, Laps S, Dong J, Xia F, Willner I. Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications. Chem Rev 2023; 123:6839-6887. [PMID: 37078690 PMCID: PMC10214457 DOI: 10.1021/acs.chemrev.3c00016] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/21/2023]
Abstract
This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.
Collapse
Affiliation(s)
- Michael
P. O’Hagan
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Shay Laps
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
6
|
Paolino M, Saletti M, Reale A, Licciardi M, Varvarà P, Marquette A, Léonard J, Bonechi C, Donati A, Giorgi G, Giuliani G, Carlotti B, Ortica F, Latterini L, Gentile M, Paccagnini E, Olivucci M, Cappelli A. Design, Synthesis and Characterization of a Visible-Light-Sensitive Molecular Switch and Its PEGylation Towards a Self-Assembling Molecule. Chemistry 2022; 28:e202201477. [PMID: 35695822 PMCID: PMC9541190 DOI: 10.1002/chem.202201477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/07/2022]
Abstract
HBDI-like chromophores represent a novel set of biomimetic switches mimicking the fluorophore of the green fluorescent protein that are currently studied with the hope to expand the molecular switch/motor toolbox. However, until now members capable of absorbing visible light in their neutral (i. e. non-anionic) form have not been reported. In this contribution we report the preparation of an HBDI-like chromophore based on a 3-phenylbenzofulvene scaffold capable of absorbing blue light and photoisomerizing on the picosecond timescale. More specifically, we show that double-bond photoisomerization occurs in both the E-to-Z and Z-to-E directions and that these can be controlled by irradiating with blue and UV light, respectively. Finally, as a preliminary applicative result, we report the incorporation of the chromophore in an amphiphilic molecule and demonstrate the formation of a visible-light-sensitive nanoaggregated state in water.
Collapse
Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Mario Saletti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Mariano Licciardi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF)Università degli Studi di PalermoVia Archirafi 3290123PalermoItaly
| | - Paola Varvarà
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF)Università degli Studi di PalermoVia Archirafi 3290123PalermoItaly
| | - Arnaud Marquette
- Institut de Physique et Chimie des Matériaux de StrasbourgUniversité de StrasbourgCNRS UMR7504StrasbourgFrance
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de StrasbourgUniversité de StrasbourgCNRS UMR7504StrasbourgFrance
| | - Claudia Bonechi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Alessandro Donati
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e BiotecnologieUniversità di PerugiaVia Elce di Sotto, 806123PerugiaItaly
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e BiotecnologieUniversità di PerugiaVia Elce di Sotto, 806123PerugiaItaly
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e BiotecnologieUniversità di PerugiaVia Elce di Sotto, 806123PerugiaItaly
| | - Mariangela Gentile
- Dipartimento di Scienze della VitaUniversità degli Studi di SienaVia A. Moro53100SienaItaly
| | - Eugenio Paccagnini
- Dipartimento di Scienze della VitaUniversità degli Studi di SienaVia A. Moro53100SienaItaly
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
- Chemistry DepartmentBowling Green State University43403Bowling GreenOHUSA) ok
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| |
Collapse
|
7
|
Lee JY, Yang Q, Chang X, Wisniewski H, Olivera TR, Saji M, Kim S, Perumal D, Zhang F. Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications. J Mater Chem B 2022; 10:7460-7472. [PMID: 35912570 DOI: 10.1039/d2tb00605g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.
Collapse
Affiliation(s)
- Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| |
Collapse
|
8
|
Liu S, Xiang K, Wang C, Zhang Y, Fan GC, Wang W, Han H. DNA Nanotweezers for Biosensing Applications: Recent Advances and Future Prospects. ACS Sens 2022; 7:3-20. [PMID: 34989231 DOI: 10.1021/acssensors.1c01647] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA nanotweezers (DTs) are reversible DNA nanodevices that can optionally switch between opened and closed states. Due to their excellent flexibility and high programmability, they have been recognized as a promising platform for constructing a diversity of biosensors and logic gates, as well as a versatile tool for molecular biology studies. In this review, we provide an overview of biosensing applications using DTs. First, the design and working principle of DTs are introduced. Next, the signal producing principles of DTs are summarized. Furthermore, biosensing applications of DTs for varying targets and purposes, both in buffers and complex biological environments, are highlighted. Finally, we provide potential opportunities and challenges for the further development of DTs.
Collapse
Affiliation(s)
- Shanshan Liu
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Kaikai Xiang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Chunyan Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Yutian Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| | - Gao-Chao Fan
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, Shandong, People’s Republic of China
| | - Wenjing Wang
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, People’s Republic of China
| | - Heyou Han
- The State Key Laboratory of Agricultural Microbiology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, People’s Republic of China
| |
Collapse
|
9
|
Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
Collapse
Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| |
Collapse
|
10
|
Lachance-Brais C, Hennecker CD, Alenaizan A, Luo X, Toader V, Taing M, Sherrill CD, Mittermaier AK, Sleiman HF. Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics. J Am Chem Soc 2021; 143:19824-19833. [PMID: 34783562 DOI: 10.1021/jacs.1c08972] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.
Collapse
Affiliation(s)
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Violeta Toader
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Monica Taing
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| |
Collapse
|
11
|
Henry SJ, Stephanopoulos N. Functionalizing DNA nanostructures for therapeutic applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1729. [PMID: 34008347 PMCID: PMC8526372 DOI: 10.1002/wnan.1729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022]
Abstract
Recent advances in nanotechnology have enabled rapid progress in many areas of biomedical research, including drug delivery, targeted therapies, imaging, and sensing. The emerging field of DNA nanotechnology, in which oligonucleotides are designed to self-assemble into programmable 2D and 3D nanostructures, offers great promise for further advancements in biomedicine. DNA nanostructures present highly addressable and functionally diverse platforms for biological applications due to their ease of construction, controllable architecture and size/shape, and multiple avenues for chemical modification. Both supramolecular and covalent modification with small molecules and polymers have been shown to expand or enhance the functions of DNA nanostructures in biological contexts. These alterations include the addition of small molecule, protein, or nucleic acid moieties that enable structural stability under physiological conditions, more efficient cellular uptake and targeting, delivery of various molecular cargos, stimulus-responsive behaviors, or modulation of a host immune response. Herein, various types of DNA nanostructure modifications and their functional consequences are examined, followed by a brief discussion of the future opportunities for functionalized DNA nanostructures as well as the barriers that must be overcome before their translational use. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.
Collapse
Affiliation(s)
- Skylar J.W. Henry
- School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ
| |
Collapse
|
12
|
|
13
|
Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| |
Collapse
|
14
|
Vázquez-González M, Willner I. Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications. Int J Mol Sci 2021; 22:1803. [PMID: 33670386 PMCID: PMC7918352 DOI: 10.3390/ijms22041803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 01/05/2023] Open
Abstract
Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions "nucleoapzymes". In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.
Collapse
Affiliation(s)
- Margarita Vázquez-González
- Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Center for Nanoscience and Nanotechnology, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| |
Collapse
|
15
|
Mollarasouli F, Badilli U, Bakirhan NK, Ozkan SA, Ozkan Y. Advanced DNA nanomachines: Strategies and bioapplications. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2020.102290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
16
|
Ma Y, Centola M, Keppner D, Famulok M. Interlocked DNA Nanojoints for Reversible Thermal Sensing. Angew Chem Int Ed Engl 2020; 59:12455-12459. [PMID: 32567796 PMCID: PMC7384075 DOI: 10.1002/anie.202003991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/12/2020] [Indexed: 01/12/2023]
Abstract
The ability to precisely measure and monitor temperature at high resolution at the nanoscale is an important task for better understanding the thermodynamic properties of functional entities at the nanoscale in complex systems, or at the level of a single cell. However, the development of high-resolution and robust thermal nanosensors is challenging. The design, assembly, and characterization of a group of thermal-responsive deoxyribonucleic acid (DNA) joints, consisting of two interlocked double-stranded DNA (dsDNA) rings, is described. The DNA nanojoints reversibly switch between the static and mobile state at different temperatures without a special annealing process. The temperature response range of the DNA nanojoint can be easily tuned by changing the length or the sequence of the hybridized region in its structure, and because of its interlocked structure the temperature response range of the DNA nanojoint is largely unaffected by its own concentration; this contrasts with systems that consist of separated components.
Collapse
Affiliation(s)
- Yinzhou Ma
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Mathias Centola
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
| | - Daniel Keppner
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Michael Famulok
- LIMES Chemical Biology UnitUniversität BonnGerhard-Domagk-Straße 153121BonnGermany
- Center of Advanced European Studies and ResearchLudwig-Erhard-Allee 253175BonnGermany
| |
Collapse
|
17
|
Ma Y, Centola M, Keppner D, Famulok M. Interlocked DNA Nanojoints for Reversible Thermal Sensing. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yinzhou Ma
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Mathias Centola
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
| | - Daniel Keppner
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2 53175 Bonn Germany
| |
Collapse
|
18
|
Hahn J, Shih WM. Thermal cycling of DNA devices via associative strand displacement. Nucleic Acids Res 2019; 47:10968-10975. [PMID: 31584082 PMCID: PMC6847259 DOI: 10.1093/nar/gkz844] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/23/2022] Open
Abstract
DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce 'recovery' strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of 'recovery' strands is favored at higher temperatures due to the primacy of a net release of strands. The temperature responses of the devices could be modulated by adjustment of design parameters such as the net increase of base pairs and the concentrations of strands. Degradation of function was not observable even after 500 thermal cycles. We experimentally demonstrated simple digital-logic circuits that evaluate at 35°C and reset after transient heating to 65°C. Thus associative strand displacement enables robust thermal cycling of DNA-based devices in a closed system.
Collapse
Affiliation(s)
- Jaeseung Hahn
- Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA.,Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - William M Shih
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA.,Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| |
Collapse
|
19
|
Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
Collapse
Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| |
Collapse
|
20
|
Valsangkar VA, Chandrasekaran AR, Zhuo L, Mao S, Lee GW, Kizer M, Wang X, Halvorsen K, Sheng J. Click and photo-release dual-functional nucleic acid nanostructures. Chem Commun (Camb) 2019; 55:9709-9712. [PMID: 31353371 PMCID: PMC6687541 DOI: 10.1039/c9cc03806j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We functionalize nucleic acid nanostructures with click chemistry (for attachment of cargos) and a photocleavable linker (for release). We demonstrate cargo attachment using a fluorescein dye and release using UV trigger from an RNA three-way junction, a DNA star motif and a DNA tetrahedron. Such multifunctional nucleic acid nanostructures have potential in targeted drug delivery.
Collapse
Affiliation(s)
- Vibhav A Valsangkar
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | | | - Lifeng Zhuo
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Song Mao
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Goh Woon Lee
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| |
Collapse
|
21
|
Tam DY, Zhuang X, Wong SW, Lo PK. Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805481. [PMID: 30861628 DOI: 10.1002/smll.201805481] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/30/2019] [Indexed: 05/23/2023]
Abstract
Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.
Collapse
Affiliation(s)
- Dick Yan Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xinyu Zhuang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| |
Collapse
|
22
|
Yang W, Shen Y, Zhang D, Li C, Yuan R, Xu W. Programmed Dual-Functional DNA Tweezer for Simultaneous and Recognizable Fluorescence Detection of microRNA and Protein. Anal Chem 2019; 91:7782-7789. [DOI: 10.1021/acs.analchem.9b01266] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Wenting Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yu Shen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Danyang Zhang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Wenju Xu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| |
Collapse
|
23
|
Chandrasekaran AR, Abraham Punnoose J, Valsangkar V, Sheng J, Halvorsen K. Integration of a photocleavable element into DNA nanoswitches. Chem Commun (Camb) 2019; 55:6587-6590. [PMID: 31116197 DOI: 10.1039/c9cc03069g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Reconfigurable DNA nanostructures can be designed to respond to external stimuli such as nucleic acids, pH, small molecules and enzymes. In this study, we incorporated photocleavable linkers in DNA strands that trigger a conformational change in binary DNA nanoswitches. We demonstrate control of the output using UV light, with potential applications in biosensing and molecular computation.
Collapse
Affiliation(s)
| | - Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Vibhav Valsangkar
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| |
Collapse
|
24
|
Wang SS, Ellington AD. Pattern Generation with Nucleic Acid Chemical Reaction Networks. Chem Rev 2019; 119:6370-6383. [DOI: 10.1021/acs.chemrev.8b00625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Siyuan S. Wang
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
25
|
Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
Collapse
Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
| |
Collapse
|
26
|
Cheng B, Kashida H, Shimada N, Maruyama A, Asanuma H. Photo-regulatable DNA isothermal amplification by template-mediated ligation. Chem Commun (Camb) 2019; 55:1080-1083. [PMID: 30617360 DOI: 10.1039/c8cc09218d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By combining azobenzene-tethered oligonucleotides as modulators and poly(l-lysine)-graft-dextran (PLL-g-Dex), a chaperone polymer, to facilitate strand displacement, we successfully developed a photo-regulatable DNA isothermal amplification method. By alternating UV and visible irradiation, linear amplification was achieved. The method enables photo-regulatability and mismatch discrimination in linear amplification of the DNA target.
Collapse
Affiliation(s)
- Bohao Cheng
- Department of Bio molecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Hiromu Kashida
- Department of Bio molecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa 266-8501, Japan.
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57 Nagatsuta, Midori-ku, Yokohama, Kanagawa 266-8501, Japan.
| | - Hiroyuki Asanuma
- Department of Bio molecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| |
Collapse
|
27
|
Kim J, Jang D, Park H, Jung S, Kim DH, Kim WJ. Functional-DNA-Driven Dynamic Nanoconstructs for Biomolecule Capture and Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707351. [PMID: 30062803 DOI: 10.1002/adma.201707351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The discovery of sequence-specific hybridization has allowed the development of DNA nanotechnology, which is divided into two categories: 1) structural DNA nanotechnology, which utilizes DNA as a biopolymer; and 2) dynamic DNA nanotechnology, which focuses on the catalytic reactions or displacement of DNA structures. Recently, numerous attempts have been made to combine DNA nanotechnologies with functional DNAs such as aptamers, DNAzymes, amplified DNA, polymer-conjugated DNA, and DNA loaded on functional nanoparticles for various applications; thus, the new interdisciplinary research field of "functional DNA nanotechnology" is initiated. In particular, a fine-tuned nanostructure composed of functional DNAs has shown immense potential as a programmable nanomachine by controlling DNA dynamics triggered by specific environments. Moreover, the programmability and predictability of functional DNA have enabled the use of DNA nanostructures as nanomedicines for various biomedical applications, such as cargo delivery and molecular drugs via stimuli-mediated dynamic structural changes of functional DNAs. Here, the concepts and recent case studies of functional DNA nanotechnology and nanostructures in nanomedicine are reviewed, and future prospects of functional DNA for nanomedicine are indicated.
Collapse
Affiliation(s)
- Jinhwan Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
| | - Donghyun Jang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Hyeongmok Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, 57922, Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| |
Collapse
|
28
|
Neves MMPDS, Martín-Yerga D. Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging. BIOSENSORS 2018; 8:E100. [PMID: 30373209 PMCID: PMC6316691 DOI: 10.3390/bios8040100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.
Collapse
Affiliation(s)
| | - Daniel Martín-Yerga
- Department of Chemical Engineering, KTH Royal Institute of Technology, 100-44 Stockholm, Sweden.
| |
Collapse
|
29
|
Xu Y, Luo X, Geng N, Wu M, Lu Z. DNA Nanotweezers with Hydrolytic Activity for Enzyme-Free and Sensitive Detection of Fusion Gene via Logic Operation. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2018; 2018:4178045. [PMID: 30420935 PMCID: PMC6211150 DOI: 10.1155/2018/4178045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/23/2018] [Indexed: 06/09/2023]
Abstract
Gene fusion is a molecular event occurring in cellular proliferation and differentiation, and the occurrence of irregular fusion gene results in various malignant diseases. So, sensing fusion gene with high performance is an important task for integrating individual disease information. Here, we proposed a nonenzymatic and high-throughput fluorescent assay system for the detection of fusion gene by employing DNA nanotweezers with hydrolytic activity. This tweezer was assembled by three single-stranded DNAs and engineered with sensing elements and reporting subunits. In the absence of the fusion gene, the engineered tweezer remained opened and inactive which led to no signal output. However, the addition of fusion genes would cause structure alterations of the tweezer from open to close and further DNAzyme activation with the assembly of two reporting subunits. Then, the activated DNAzyme catalyzed fluorescence substrates for signal conversion. Taking BCR/ABL fusion gene as an example, the tweezer-based assay system showed not only excellent distinguishing capability towards different input targets but also high sensitivity with a detection limit of 5.29 pM. In addition to good detection performance, this system was simple and enzyme-free, offering a powerful nanometer tool as a smart nanodevice for sensing fusion detection.
Collapse
Affiliation(s)
- Yongjie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, College of Basic Medicine, Guizhou University, Guiyang 550002, Guizhou, China
| | - Xiangrong Luo
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, College of Basic Medicine, Guizhou University, Guiyang 550002, Guizhou, China
| | - Nana Geng
- Special Key Laboratory of Oral Diseases Research, Higher Education Institutions of Guizhou Province, Zunyi Medical University, Zunyi 563099, Guizhou, China
| | - Mingsong Wu
- Special Key Laboratory of Oral Diseases Research, Higher Education Institutions of Guizhou Province, Zunyi Medical University, Zunyi 563099, Guizhou, China
| | - Zhishun Lu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, College of Basic Medicine, Guizhou University, Guiyang 550002, Guizhou, China
| |
Collapse
|
30
|
Wang X, Chandrasekaran AR, Shen Z, Ohayon YP, Wang T, Kizer ME, Sha R, Mao C, Yan H, Zhang X, Liao S, Ding B, Chakraborty B, Jonoska N, Niu D, Gu H, Chao J, Gao X, Li Y, Ciengshin T, Seeman NC. Paranemic Crossover DNA: There and Back Again. Chem Rev 2018; 119:6273-6289. [PMID: 29911864 DOI: 10.1021/acs.chemrev.8b00207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.
Collapse
Affiliation(s)
- Xing Wang
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | | | - Zhiyong Shen
- College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241000 , China
| | - Yoel P Ohayon
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tong Wang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Megan E Kizer
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hao Yan
- Department of Chemistry and Biochemistry and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoping Zhang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Shiping Liao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Baoquan Ding
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Banani Chakraborty
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics , University of South Florida , Tampa , Florida 33620 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Hongzhou Gu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Jie Chao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Xiang Gao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Yuhang Li
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tanashaya Ciengshin
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10012 , United States
| |
Collapse
|
31
|
Mondal P, Granucci G, Rastädter D, Persico M, Burghardt I. Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study. Chem Sci 2018; 9:4671-4681. [PMID: 29899961 PMCID: PMC5969502 DOI: 10.1039/c8sc00072g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/25/2018] [Indexed: 12/21/2022] Open
Abstract
Azobenzene covalently attached to RNA undergoes trans-to-cis photo-switching on a time scale of ∼15 picoseconds – 30 times slower than in vacuo.
The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA–azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ∼10–15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA–azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.
Collapse
Affiliation(s)
- Padmabati Mondal
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany . ;
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , v. Moruzzi 13 , I-56124 Pisa , Italy .
| | - Dominique Rastädter
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany . ;
| | - Maurizio Persico
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , v. Moruzzi 13 , I-56124 Pisa , Italy .
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany . ;
| |
Collapse
|
32
|
Angell C, Kai M, Xie S, Dong X, Chen Y. Bioderived DNA Nanomachines for Potential Uses in Biosensing, Diagnostics, and Therapeutic Applications. Adv Healthc Mater 2018; 7:e1701189. [PMID: 29350489 DOI: 10.1002/adhm.201701189] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/23/2017] [Indexed: 12/28/2022]
Abstract
Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed. The combination of DNA motors with other platforms is then discussed. In each section of these motors, their mechanisms and their usage in the biomedical field are described. Finally, it is believed that these DNA-based nanomachines and hybrid motifs will become an integral point-of-care diagnostics and smart, site-specific therapeutic delivery.
Collapse
Affiliation(s)
- Chava Angell
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Mingxuan Kai
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Sibai Xie
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Xiangyi Dong
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| | - Yi Chen
- Department of NanoengineeringUniversity of California San Diego, La Jolla CA 92093 USA
| |
Collapse
|
33
|
Grebenovsky N, Goldau T, Bolte M, Heckel A. Light Regulation of DNA Minicircle Dimerization by Utilizing Azobenzene C
-Nucleosides. Chemistry 2018; 24:3425-3428. [DOI: 10.1002/chem.201706003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Nikolai Grebenovsky
- Institute of Organic Chemistry and Chemical Biology; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| | - Thomas Goldau
- Institute of Organic Chemistry and Chemical Biology; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| | - Michael Bolte
- Institute for Inorganic Chemistry; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| |
Collapse
|
34
|
Kaewsomboon T, Nishizawa S, Kanamori T, Yuasa H, Ohkubo A. pH-Dependent Switching of Base Pairs Using Artificial Nucleobases with Carboxyl Groups. J Org Chem 2018; 83:1320-1327. [PMID: 29322767 DOI: 10.1021/acs.joc.7b02828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we report the synthesis of modified oligonucleotides consisting of benzoic acid or isophthalic acid residues as new nucleobases. As evaluated by UV thermal denaturation analysis at different pH conditions (5.0, 6.0, 7.0, and 8.0), these modified oligonucleotides exhibited pH-dependent recognition of natural nucleobases and one is first found to be capable of base pair switching in response to a pH change. The isophthalic acid residue incorporated into the oligonucleotide on a d-threoninol backbone could preferentially bind with adenine but with guanine in response to a change in the pH conditions from pH 5 to pH 7 (or 8) without significant difference in duplex stability. These findings would be valuable for further developing pH-responsive DNA-based molecular devices.
Collapse
Affiliation(s)
- Tanasak Kaewsomboon
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| |
Collapse
|
35
|
Adam V, Prusty DK, Centola M, Škugor M, Hannam JS, Valero J, Klöckner B, Famulok M. Expanding the Toolbox of Photoswitches for DNA Nanotechnology Using Arylazopyrazoles. Chemistry 2018; 24:1062-1066. [DOI: 10.1002/chem.201705500] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Volker Adam
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Deepak K. Prusty
- Max-Planck-Fellowship Group Chemical Biology; Center of Advanced European Studies and Research; Ludwig-Erhard-Allee 2 53175 Bonn Germany
| | - Mathias Centola
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Marko Škugor
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Jeffrey S. Hannam
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Julián Valero
- Max-Planck-Fellowship Group Chemical Biology; Center of Advanced European Studies and Research; Ludwig-Erhard-Allee 2 53175 Bonn Germany
| | - Bernhard Klöckner
- Kekulé Institut für Organische Chemie und Biochemie; Gerhard-Domagk-Str.1 53121 Bonn Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Max-Planck-Fellowship Group Chemical Biology; Center of Advanced European Studies and Research; Ludwig-Erhard-Allee 2 53175 Bonn Germany
| |
Collapse
|
36
|
Kamiya Y, Yamada Y, Muro T, Matsuura K, Asanuma H. DNA Microcapsule for Photo-Triggered Drug Release Systems. ChemMedChem 2017; 12:2016-2021. [DOI: 10.1002/cmdc.201700512] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 09/21/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Yukiko Kamiya
- Department of Biomolecular Engineering; Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
- Institute of Materials and Systems for Sustainability; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Yoshinobu Yamada
- Department of Biomolecular Engineering; Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Takahiro Muro
- Department of Biomolecular Engineering; Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology; Graduate School of Engineering; Tottori University; Koyama-Minami 4-101 Tottori 680-8552 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering; Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| |
Collapse
|
37
|
Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
| |
Collapse
|
38
|
Cheng B, Kashida H, Shimada N, Maruyama A, Asanuma H. Chaperone-Polymer-Assisted, Photodriven DNA Strand Displacement. Chembiochem 2017; 18:1568-1572. [DOI: 10.1002/cbic.201700202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Bohao Cheng
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Naohiko Shimada
- Department of Biomolecular Engineering; Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Nagatsuta 4259 Midori-ku Yokohama 266-8501 Japan
| | - Atsushi Maruyama
- Department of Biomolecular Engineering; Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Nagatsuta 4259 Midori-ku Yokohama 266-8501 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| |
Collapse
|
39
|
Dai Z, Leung HM, Lo PK. Stimuli-Responsive Self-Assembled DNA Nanomaterials for Biomedical Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602881. [PMID: 28005298 DOI: 10.1002/smll.201602881] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/31/2016] [Indexed: 05/23/2023]
Abstract
Stimuli-responsive DNA-based materials represent a major class of remarkable functional nanomaterials for nano-biotechnological applications. In this review, recent progress in the development of stimuli-responsive systems based on self-assembled DNA nanostructures is introduced and classified. Representative examples are presented in terms of their design, working principles and mechanisms to trigger the response of the stimuli-responsive DNA system upon expose to a large variety of stimuli including pH, metal ions, oligonucleotides, small molecules, enzymes, heat, and light. Substantial in vitro studies have clearly revealed the advantages of the use of stimuli-responsive DNA nanomaterials in different biomedical applications, particularly for biosensing, drug delivery, therapy and diagnostic purposes in addition to bio-computing. Some of the challenges faced and suggestions for further development are also highlighted.
Collapse
Affiliation(s)
- Ziwen Dai
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Hoi Man Leung
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| |
Collapse
|
40
|
Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds. Polym J 2016. [DOI: 10.1038/pj.2016.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
41
|
Long-range movement of large mechanically interlocked DNA nanostructures. Nat Commun 2016; 7:12414. [PMID: 27492061 PMCID: PMC4980458 DOI: 10.1038/ncomms12414] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023] Open
Abstract
Interlocked molecules such as catenanes and rotaxanes, connected only via mechanical bonds have the ability to perform large-scale sliding and rotational movements, making them attractive components for the construction of artificial molecular machines and motors. We here demonstrate the realization of large, rigid rotaxane structures composed of DNA origami subunits. The structures can be easily modified to carry a molecular cargo or nanoparticles. By using multiple axle modules, rotaxane constructs are realized with axle lengths of up to 355 nm and a fuel/anti-fuel mechanism is employed to switch the rotaxanes between a mobile and a fixed state. We also create extended pseudo-rotaxanes, in which origami rings can slide along supramolecular DNA filaments over several hundreds of nanometres. The rings can be actively moved and tracked using atomic force microscopy. Rotaxanes are interlocked molecules that can undergo sliding and rotational movements and can be used in artificial molecular machines and motors. Here, Simmel and co-workers show a rigid rotaxane structures consisting of DNA origami subunits that can slide over several hundreds of nanometres.
Collapse
|
42
|
Kingsland A, Samai S, Yan Y, Ginger DS, Maibaum L. Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA. J Phys Chem Lett 2016; 7:3027-3031. [PMID: 27428569 DOI: 10.1021/acs.jpclett.6b00956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Azobenzene incorporated into DNA has a photoisomerization quantum yield that depends on the DNA sequence near the azobenzene attachment site. We use Molecular Dynamics computer simulations to elucidate which physical properties of the modified DNA determine the quantum yield. We show for a wide range of DNA sequences that the photoisomerization quantum yield is strongly correlated with the variance of the number of atoms in close proximity to the outer phenyl ring of the azobenzene group. We infer that quantum yield is controlled by the availability of fluctuations that enable the conformational change. We demonstrate that these simulations can be used as a qualitative predictive tool by calculating the quantum yield for several novel DNA sequences, and confirming these predictions using UV-vis spectroscopy. Our results will be useful for the development of a wide range of applications of photoresponsive DNA nanotechnology.
Collapse
Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Soumyadyuti Samai
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Yunqi Yan
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - David S Ginger
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| |
Collapse
|
43
|
Nakasone Y, Ooi H, Kamiya Y, Asanuma H, Terazima M. Dynamics of Inter-DNA Chain Interaction of Photoresponsive DNA. J Am Chem Soc 2016; 138:9001-4. [DOI: 10.1021/jacs.6b02525] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Nakasone
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | | | - Masahide Terazima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
44
|
Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chemistry 2016; 22:10533-8. [DOI: 10.1002/chem.201602006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- PRESTO (Japan) Science and Technology Agency; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| |
Collapse
|
45
|
Bergen A, Rudiuk S, Morel M, Le Saux T, Ihmels H, Baigl D. Photodependent Melting of Unmodified DNA Using a Photosensitive Intercalator: A New and Generic Tool for Photoreversible Assembly of DNA Nanostructures at Constant Temperature. NANO LETTERS 2016; 16:773-80. [PMID: 26652690 DOI: 10.1021/acs.nanolett.5b04762] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
External control of DNA melting and hybridization, a key step in bio- and DNA nanotechnology, is commonly achieved with temperature. The use of light to direct this process is a challenging alternative, which has been only possible with a DNA modification, such as covalent grafting or mismatch introduction, so far. Here we describe the first photocontrol of DNA melting that relies on the addition of a molecule that noncovalently interacts with unmodified DNA and affects its melting properties in a photoreversible and highly robust manner, without any prerequisite in the length or sequence of the target DNA molecule. We synthesize azobenzene-containing guanidinium derivatives and show that a bivalent molecule with a conformation-dependent binding mode, AzoDiGua, strongly increases the melting temperature (Tm) of DNA under dark conditions because its trans isomer intercalates in the DNA double helix. Upon UV irradiation at 365 nm, the trans-cis isomerization induced the ejection of AzoDiGua from the intercalation binding sites, resulting in a decrease in Tm up to 18 °C. This illumination-dependent Tm shift is observed on many types of DNA, from self-complementary single-stranded or double-stranded oligonucleotides to long genomic duplex DNA molecules. Finally, we show that simply adding AzoDiGua allows us to photoreversibly control the assembly/disassembly of a DNA nanostructure at constant temperature, as demonstrated here with a self-hybridized DNA hairpin. We anticipate that this strategy will be the key ingredient in a new and generic way of placing DNA-based bio- and nanotechnologies under dynamic control by light.
Collapse
Affiliation(s)
- Anna Bergen
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Mathieu Morel
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Thomas Le Saux
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Heiko Ihmels
- Department of Chemistry-Biology, University of Siegen , Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| |
Collapse
|
46
|
Wu J, Yu F, Zhang Z, Chen Y, Du J. Highly sensitive self-complementary DNA nanoswitches triggered by polyelectrolytes. NANOSCALE 2016; 8:464-470. [PMID: 26627445 DOI: 10.1039/c5nr05193b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dimerization of two homologous strands of genomic DNA/RNA is an essential feature of retroviral replication. Herein we show that a cationic comb-type copolymer (CCC), poly(L-lysine)-graft-dextran, accelerates the dimerization of self-complementary stem-loop DNA, frequently found in functional DNA/RNA molecules, such as aptamers. Furthermore, an anionic polymer poly(sodium vinylsulfonate) (PVS) dissociates CCC from the duplex shortly within a few seconds. Then single stem-loop DNA spontaneously transforms from its dimer. Thus we can easily control the dimer and stem-loop DNA by switching on/off CCC activity. Both polyelectrolytes and DNA concentrations are in the nanomole per liter range. The polyelectrolyte-assisted transconformation and sequences design strategy ensures the reversible state control with rapid response and effective switching under physiologically relevant conditions. A further application of this sensitive assembly is to construct an aptamer-type drug delivery system, bind or release functional molecules responding to its transconformation.
Collapse
Affiliation(s)
- Jincai Wu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Feng Yu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Zheng Zhang
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Yong Chen
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Jie Du
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| |
Collapse
|
47
|
Li XY, Huang J, Jiang HX, Du YC, Han GM, Kong DM. Molecular logic gates based on DNA tweezers responsive to multiplex restriction endonucleases. RSC Adv 2016. [DOI: 10.1039/c6ra05132d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Self-assembled DNA tweezers containing four different restriction endonuclease recognition sites were designed and a set of logic gates were constructed.
Collapse
Affiliation(s)
- Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University Tianjin
- People's Republic of China
| | - Juan Huang
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University Tianjin
- People's Republic of China
| | - Hong-Xin Jiang
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University Tianjin
- People's Republic of China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University Tianjin
- People's Republic of China
| | - Gui-Mei Han
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University Tianjin
- People's Republic of China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology
- College of Chemistry
- Nankai University Tianjin
- People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
| |
Collapse
|
48
|
Lu CH, Guo W, Hu Y, Qi XJ, Willner I. Multitriggered Shape-Memory Acrylamide-DNA Hydrogels. J Am Chem Soc 2015; 137:15723-31. [PMID: 26579882 DOI: 10.1021/jacs.5b06510] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acrylamide-acrylamide nucleic acids are cross-linked by two cooperative functional motives to form shaped acrylamide-DNA hydrogels. One of the cross-linking motives responds to an external trigger, leading to the dissociation of one of the stimuli-responsive bridges, and to the transition of the stiff shaped hydrogels into soft shapeless states, where the residual bridging units, due to the chains entanglement, provide an intrinsic memory for the reshaping of the hydrogels. Subjecting the shapeless states to counter stimuli restores the dissociated bridges, and regenerates the original shape of the hydrogels. By the cyclic dissociation and reassembly of the stimuli-responsive bridges, the reversible switchable transitions of the hydrogels between stiff shaped hydrogel structures and soft shapeless states are demonstrated. Shaped hydrogels bridged by K(+)-stabilized G-quadruplexes/duplex units, by i-motif/duplex units, or by two different duplex bridges are described. The cyclic transitions of the hydrogels between shaped and shapeless states are stimulated, in the presence of appropriate triggers and counter triggers (K(+) ion/crown ether; pH = 5.0/8.0; fuel/antifuel strands). The shape-memory hydrogels are integrated into shaped two-hydrogel or three-hydrogel hybrid structures. The cyclic programmed transitions of selective domains of the hybrid structures between shaped hydrogel and shapeless states are demonstrated. The possible applications of the shape-memory hydrogels for sensing, inscription of information, and controlled release of loads are discussed.
Collapse
Affiliation(s)
- Chun-Hua Lu
- The Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Weiwei Guo
- The Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Yuwei Hu
- The Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Xiu-Juan Qi
- The Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel.,The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University , Fuzhou 350002, China
| | - Itamar Willner
- The Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| |
Collapse
|
49
|
Kahn JS, Trifonov A, Cecconello A, Guo W, Fan C, Willner I. Integration of Switchable DNA-Based Hydrogels with Surfaces by the Hybridization Chain Reaction. NANO LETTERS 2015; 15:7773-7778. [PMID: 26488684 DOI: 10.1021/acs.nanolett.5b04101] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A novel method to assemble acrylamide/acrydite DNA copolymer hydrogels on surfaces, specifically gold-coated surfaces, is introduced. The method involves the synthesis of two different copolymer chains consisting of hairpin A, HA, modified acrylamide copolymer and hairpin B, HB, acrylamide copolymer. In the presence of a nucleic acid promoter monolayer associated with the surface, the hybridization chain reaction between the two hairpin-modified polymer chains is initiated, giving rise to the cross-opening of hairpins HA and HB and the formation of a cross-linked hydrogel on the surface. By the cofunctionalization of the HA- and HB-modified polymer chains with G-rich DNA tethers that include the G-quadruplex subunits, hydrogels of switchable stiffness are generated. In the presence of K(+)-ions, the hydrogel associated with the surface is cooperatively cross-linked by duplex units of HA and HB, and K(+)-ion-stabilized G-quadruplex units, giving rise to a stiff hydrogel. The 18-crown-6-ether-stimulated elimination of the K(+)-ions dissociates the bridging G-quadruplex units, resulting in a hydrogel of reduced stiffness. The duplex/G-quadruplex cooperatively stabilized hydrogel associated with the surface reveals switchable electrocatalytic properties. The incorporation of hemin into the G-quadruplex units electrocatalyzes the reduction of H2O2. The 18-crown-6-ether stimulated dissociation of the hemin/G-quadruplex bridging units leads to a catalytically inactive hydrogel.
Collapse
Affiliation(s)
- Jason S Kahn
- Institute of Chemistry, The Minerva Center for Complex Biohybrid Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Alexander Trifonov
- Institute of Chemistry, The Minerva Center for Complex Biohybrid Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Minerva Center for Complex Biohybrid Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Weiwei Guo
- Institute of Chemistry, The Minerva Center for Complex Biohybrid Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Chunhai Fan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Complex Biohybrid Systems, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| |
Collapse
|
50
|
Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| |
Collapse
|