1
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Ma C, Li S, Zeng Y, Lyu Y. DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications. BIOSENSORS 2024; 14:236. [PMID: 38785710 PMCID: PMC11117991 DOI: 10.3390/bios14050236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.
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Affiliation(s)
- Chunran Ma
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
- Furong Laboratory, Changsha 410082, China
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2
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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.
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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.
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3
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Shandiz SA, Leuty GM, Guo H, Mokarizadeh AH, Maia JM, Tsige M. Structure and Thermodynamics of Linear, Ring, and Catenane Polymers in Solutions and at Liquid-Liquid Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:7154-7166. [PMID: 37155243 DOI: 10.1021/acs.langmuir.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent decades, advances in the syntheses of mechanically interlocked macromolecules, such as catenanes, have led to much greater interest in the applications of these complexes, from molecular motors and actuators to nanoscale computational memory and nanoswitches. Much remains to be understood, however, regarding how catenated ring compounds behave as a result of the effects of different solvents as well as the effects of solvent/solvent interfaces. In this work, we have investigated, using molecular dynamics simulations, the effects of solvation of poly(ethylene oxide) chains of different topologies─linear, ring, and [2]catenane─in two solvents both considered favorable toward PEO (water, toluene) and at the water/toluene interface. Compared to ring and [2]catenane molecules, the linear PEO chain showed the largest increase in size at the water/toluene interface compared to bulk water or bulk toluene. Perhaps surprisingly, observations indicate that the tendency of all three topologies to extend at the water/toluene interface may have more to do with screening the interaction between the two solvents than with optimizing specific solvent-polymer contacts.
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Affiliation(s)
- Saeed Akbari Shandiz
- Department of Macromolecular Science & Engineering, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Gary M Leuty
- LinQuest Corporation, Beavercreek, Ohio 45431, United States
| | - Hao Guo
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Abdol Hadi Mokarizadeh
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Joao M Maia
- Department of Macromolecular Science & Engineering, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Mesfin Tsige
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
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4
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Mori K, Takezawa Y, Shionoya M. Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner. Chem Sci 2023; 14:1082-1088. [PMID: 36756334 PMCID: PMC9891364 DOI: 10.1039/d2sc06534g] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.
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Affiliation(s)
- Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Takezawa
- 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
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5
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Li Q, Centola M, Keppner D, Valero J, Famulok M. Reconfigurable Nanopolygons Made of DNA Catenanes. Bioconjug Chem 2023; 34:105-110. [PMID: 36595299 DOI: 10.1021/acs.bioconjchem.2c00464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The development of new types of bonds and linkages that can reversibly tune the geometry and structural features of molecules is an elusive goal in chemistry. Herein, we report the use of catenated DNA structures as nanolinkages that can reversibly switch their angle and form different kinds of polygonal nanostructures. We designed a reconfigurable catenane that can self-assemble into a triangular or hexagonal structure upon addition of programmable DNA strands that function via toehold strand-displacement. The nanomechanical and structural features of these catenated nanojoints can be applied for the construction of dynamic systems such as molecular motors with switchable functionalities.
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Affiliation(s)
- Qi Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Xianlie Middle Road 100, 510070 Guangzhou, China.,LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.,Chemical Biology Max-Planck-Fellow Group, Max-Planck Institute for Neurobiology of Behavior - Caesar, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Keppner
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany.,Chemical Biology Max-Planck-Fellow Group, Max-Planck Institute for Neurobiology of Behavior - Caesar, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
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6
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Chen S, Liu TL, Dong Y, Li J. A Wireless, Regeneratable Cocaine Sensing Scheme Enabled by Allosteric Regulation of pH Sensitive Aptamers. ACS NANO 2022; 16:20922-20936. [PMID: 36468646 DOI: 10.1021/acsnano.2c08511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A key challenge for achieving continuous biosensing with existing technologies is the poor reusability of the biorecognition interface due to the difficulty in the dissociation of analytes from the bioreceptors upon surface saturation. In this work, we introduce a regeneratable biosensing scheme enabled by allosteric regulation of a re-engineered pH sensitive anti-cocaine aptamer. The aptamer can regain its affinity with target analytes due to proton-promoted duplex-to-triplex transition in DNA configuration followed by the release of adsorbed analytes. A Pd/PdHx electrode placed next to the sensor can enable the pH regulation of the local chemical environment via electrochemical reactions. Demonstration of a "flower-shaped", stretchable, and inductively coupled electronic system with sensing and energy harvesting capabilities provides a promising route to designing wireless devices in biointegrated forms. These advances have the potential for future development of electronic sensing platforms with on-chip regeneration capability for continuous, quantitative, and real-time monitoring of chemical and biological markers.
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Affiliation(s)
- Shulin Chen
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
| | - Tzu-Li Liu
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
| | - Yan Dong
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
| | - Jinghua Li
- Department of Materials Science and Engineering, The Ohio State University, Columbus, Ohio43210, United States
- Chronic Brain Injury Program, The Ohio State University, Columbus, Ohio43210, United States
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7
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Yao S, Chang Y, Zhai Z, Sugiyama H, Endo M, Zhu W, Xu Y, Yang Y, Qian X. DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20739-20748. [PMID: 35485950 DOI: 10.1021/acsami.2c03265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interlocked DNA nanostructures perform programmable movements in nanoscales such as sliding, contraction, and expansion. However, utilizing nanoscaled interlocked movements to regulate the functions of larger length scaled matrix and developing their applications has not yet been reported. Herein we describe the assembly of DNA-based daisy chain rotaxane nanostructure (DNA-DCR) composed of two hollow DNA nanostructures as macrocycles, two interlocked axles and two triangular prism-shaped DNA structures as stoppers, in which three mechanical states─fixed extended state (FES), sliding state (SS), and fixed contracted state (FCS)─are characterized by using toehold-mediated strand displacement reaction (SDR). The DNA-DCRs are further used as nanocomposites and introduced into hydrogel matrix to produce interlocked hydrogels, which shows modulable stiffness by elongating the interlocked axles to regulate the hydrogel swelling with hybridization chain reaction (HCR) treatment. Then the DCR-hydrogels are employed as dynamic biointerfaces for human mesenchymal stem cells (hMSCs) adhesion studies. First, hMSCs showed lower cell density on bare DCR-hydrogel treated with HCR-initiated swelling for stiffness decreasing. Second, the cell adhesion ligand (RGD) modified DNA-DCRs are constructed for hydrogel functionalization. DCR(RGD) hydrogel endows the mobility of RGDs by switching the mechanical states of DNA-DCR. HMSCs showed increased cell density on DCRSS(RGD) hydrogel than on DCRFCS(RGD) hydrogel. Therefore, our DNA-DCR nanocomposite hydrogel exhibit dual-programmable performances including swelling adjustment and offering sliding for incorporated ligands, which can be both utilized as dynamic scaffolds for regulating the stem cell adhesion. The dual-programmable cross-scale regulation from interlocked DNA nanostructures to hydrogel matrix was achieved, demonstrating a new pathway of DNA-based materials.
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Affiliation(s)
- Shengtao Yao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yongyun Chang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Zanjing Zhai
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Weiping Zhu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yangyang Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
- State Key Laboratory of Bioreactor, East China University of Science and Technology, Shanghai200237, China
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8
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022; 61:e202113617. [PMID: 34889013 PMCID: PMC8854376 DOI: 10.1002/anie.202113617] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 11/15/2022]
Abstract
The main protease (Mpro ) and papain-like protease (PLpro ) play critical roles in SARS-CoV-2 replication and are promising targets for antiviral inhibitors. The simultaneous visualization of Mpro and PLpro is extremely valuable for SARS-CoV-2 detection and rapid inhibitor screening. However, such a crucial investigation has remained challenging because of the lack of suitable probes. We have now developed a dual-color probe (3MBP5) for the simultaneous detection of Mpro and PLpro by fluorescence (or Förster) resonance energy transfer (FRET). This probe produces fluorescence from both the Cy3 and Cy5 fluorophores that are cleaved by Mpro and PLpro . 3MBP5-activatable specificity was demonstrated with recombinant proteins, inhibitors, plasmid-transfected HEK 293T cells, and SARS-CoV-2-infected TMPRSS2-Vero cells. Results from the dual-color probe first verified the simultaneous detection and intracellular distribution of SARS-CoV-2 Mpro and PLpro . This is a powerful tool for the simultaneous detection of different proteases with value for the rapid screening of inhibitors.
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Affiliation(s)
- Yong Cheng
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Raina M. Borum
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Alex E. Clark
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Zhicheng Jin
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San DiegoLa JollaCA 92093USA
| | - Aaron F. Carlin
- Department of MedicineUniversity of California, San DiegoLa JollaCA 92093USA
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San DiegoLa JollaCA 92093USA
- Materials Science and Engineering ProgramUniversity of California, San DiegoLa JollaCA 92093USA
- Department of RadiologyUniversity of California, San DiegoLa JollaCA 92093USA
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9
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Sakai Y, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Topogami: Topologically Linked DNA Origami. ACS NANOSCIENCE AU 2022; 2:57-63. [PMID: 35211697 PMCID: PMC8861903 DOI: 10.1021/acsnanoscienceau.1c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
DNA origami is a widely used DNA nanotechnology that allows construction of two-dimensional and three-dimensional nanometric shapes. The designability and rigidity of DNA origami make it an ideal material for construction of topologically linked molecules such as catenanes, which are attractive for their potential as motors and molecular machines. However, a general method for production of topologically linked DNA origami has been lacking. Here, we show that catenated single-stranded DNA circles can be produced and used as a universal scaffold for the production of topologically linked (catenated) DNA origami structures where the individual linked structures can be of any arbitrary design. Assembly of these topologically linked DNA origami structures is achieved via a simple one-pot annealing protocol.
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Affiliation(s)
- Yusuke Sakai
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Gerrit D Wilkens
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine, Żwirki I Wigury 61, 02-091 Warsaw, Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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10
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Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. A Dual‐Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain‐like Proteases of SARS‐CoV‐2‐Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yong Cheng
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Raina M. Borum
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Alex E. Clark
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Zhicheng Jin
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Colman Moore
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego La Jolla CA 92093 USA
| | - Aaron F. Carlin
- Department of Medicine University of California, San Diego La Jolla CA 92093 USA
| | - Jesse V. Jokerst
- Department of NanoEngineering University of California, San Diego La Jolla CA 92093 USA
- Materials Science and Engineering Program University of California, San Diego La Jolla CA 92093 USA
- Department of Radiology University of California, San Diego La Jolla CA 92093 USA
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11
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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.
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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.
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12
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Yang S, Zhan X, Tang X, Zhao S, Yu L, Gao M, Luo D, Wang Y, Chang K, Chen M. A multiplexed circulating tumor DNA detection platform engineered from 3D-coded interlocked DNA rings. Bioact Mater 2021; 10:68-78. [PMID: 34901530 PMCID: PMC8637011 DOI: 10.1016/j.bioactmat.2021.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/24/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is a critical biomarker not only important for the early detection of tumors but also invaluable for personalized treatments. Currently ctDNA detection relies on sequencing. Here, a platform termed three-dimensional-coded interlocked DNA rings (3D-coded ID rings) was created for multiplexed ctDNA identification. The ID rings provide a ctDNA recognition ring that is physically interlocked with a reporter ring. The specific binding of ctDNA to the recognition ring initiates target-responsive cutting via a restriction endonuclease; the cutting then triggers rolling circle amplification on the reporter ring. The signals are further integrated with internal 3D codes for multiplexed readouts. ctDNAs from non-invasive clinical specimens including plasma, feces, and urine were detected and validated at a sensitivity much higher than those obtained through sequencing. This 3D-coded ID ring platform can detect any multiple DNA fragments simultaneously without sequencing. We envision that our platform will facilitate the implementation of future personalized/precision medicine. A platform termed 3D-coded ID rings was created for multiplexed ctDNA detection. This platform was integrated with two schemes: the ID ring scheme and the 3D-coded scheme. The platform could achieve multiplexed detection with detection limit of 500 copies per million in non-invasive specimens.
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Affiliation(s)
- Sha Yang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Xinyu Zhan
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Xiaoqi Tang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Lianyu Yu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Mingxuan Gao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14853-5701, USA
| | - Yunxia Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China.,College of Pharmacy and Laboratory Medicine, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China.,State Key Laboratory of Trauma, Burn and Combined Injury, Third Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
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13
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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14
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Zhou Z, Vázquez-González M, Willner I. Stimuli-responsive metal-organic framework nanoparticles for controlled drug delivery and medical applications. Chem Soc Rev 2021; 50:4541-4563. [PMID: 33625421 DOI: 10.1039/d0cs01030h] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stimuli-responsive metal-organic framework nanoparticles, NMOFs, provide a versatile platform for the controlled release of drugs and biomedical applications. The porous structure of NMOFs, their biocompatibility, low toxicity, and efficient permeability turn the NMOFs into ideal carriers for therapeutic applications. Two general methods to gate the drug-loaded NMOFs and to release the loads were developed: by one method, the loaded NMOFs are coated or surface-modified with stimuli-responsive gates being unlocked in the presence of appropriate chemical (e.g., ions or reducing agents), physical (e.g., light or heat), or biomarker (e.g., miRNA or ATP) triggers. By a second approach, the drug-loaded NMOFs include encoded structural information or co-added agents to induce the structural distortion or stimulate the degradation of the NMOFs. Different chemical triggers such as pH changes, ions, ATP, or redox agents, and physical stimuli such as light or heat are applied to degrade the NMOFs, resulting in the release of the loads. In addition, enzymes, DNAzymes, and disease-specific biomarkers are used to unlock the gated NMOFs. The triggered release of drugs for cancer therapy, anti-blood clotting, and the design of autonomous insulin-delivery systems ("artificial pancreas") are discussed. Specifically, multi-drug carrier systems and functional NMOFs exhibiting dual and cooperative therapeutic functions are introduced. The future perspectives and applications of stimuli-responsive particles are addressed.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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15
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16
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Matsuoka R, Himori S, Yamaguchi G, Nabeshima T. Kinetic and Thermodynamic Behaviors of Pseudorotaxane Formation with C3v Macrocyclic BODIPY Trimers and the Remarkable Substituent Effect on Ring-Face Selectivity. Org Lett 2020; 22:8764-8768. [PMID: 32975422 DOI: 10.1021/acs.orglett.0c02840] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The thermodynamic and kinetic behaviors of the pseudorotaxane formation between the C3v macrocyclic BODIPY trimers and unsymmetrical secondary ammonium guests are investigated. We find a remarkable substituent effect of the BODIPY trimer on the ring-face selectivity during the threading. The difference in the small substituents (H or CH3) in the macrocyclic host molecules significantly modulated the thermodynamic and kinetic selectivity of the threading direction of the unsymmetrical ammonium ions.
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Affiliation(s)
- Ryota Matsuoka
- Graduate School of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Sou Himori
- Graduate School of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Gento Yamaguchi
- Graduate School of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
| | - Tatsuya Nabeshima
- Graduate School of Pure and Applied Sciences and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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17
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Liu Y, Duan Z, Fang J, Zhang F, Xiao J, Zhang WB. Cellular Synthesis and X-ray Crystal Structure of a Designed Protein Heterocatenane. Angew Chem Int Ed Engl 2020; 59:16122-16127. [PMID: 32506656 DOI: 10.1002/anie.202005490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/24/2023]
Abstract
Herein, we report the biosynthesis of protein heterocatenanes using a programmed sequence of multiple post-translational processing events including intramolecular chain entanglement, in situ backbone cleavage, and spontaneous cyclization. The approach is general, autonomous, and can obviate the need for any additional enzymes. The catenane topology was convincingly proven using a combination of SDS-PAGE, LC-MS, size exclusion chromatography, controlled proteolytic digestion, and protein crystallography. The X-ray crystal structure clearly shows two mechanically interlocked protein rings with intact folded domains. It opens new avenues in the nascent field of protein-topology engineering.
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Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zelin Duan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
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18
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Liu Y, Duan Z, Fang J, Zhang F, Xiao J, Zhang W. Cellular Synthesis and X‐ray Crystal Structure of a Designed Protein Heterocatenane. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yajie Liu
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Zelin Duan
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking-Tsinghua Center for Life Sciences Peking University Beijing 100871 P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Fan Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
| | - Junyu Xiao
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking-Tsinghua Center for Life Sciences Peking University Beijing 100871 P. R. China
| | - Wen‐Bin Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry &, Physics of Ministry of Education Center for Soft Matter Science and Engineering College of Chemistry and Molecular Engineering Peking University Beijing 100871 P. R. China
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19
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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.
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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
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20
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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
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21
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Liao H, Huang T, Hu L, Wang M. Fluorescent aptasensors for parallel analysis of biomolecules based on interlocked DNA catenane nanomachines. Anal Chim Acta 2020; 1114:1-6. [DOI: 10.1016/j.aca.2020.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/26/2020] [Accepted: 04/03/2020] [Indexed: 10/24/2022]
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22
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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23
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Li L, An R, Tang J, Sui Z, Wang G, Komiyama M, Liang X. Facile Characterization of Topology of DNA Catenanes. Biophys J 2020; 118:1702-1708. [PMID: 32101717 DOI: 10.1016/j.bpj.2020.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/27/2020] [Accepted: 02/06/2020] [Indexed: 11/19/2022] Open
Abstract
During the preparation of single-stranded DNA catenanes, topological isomers of different linking numbers (Lk) are intrinsically produced, and they must be separated from each other to construct sophisticated nanostructures accurately. In many previous studies, however, mixtures of these isomers were directly employed to construct nanostructures without sufficient characterization. Here, we present a method that easily and clearly characterizes the isomers by polyacrylamide gel electrophoresis. To the mixtures of topological isomers of [2]catenanes, two-strut oligonucleotides, which are complementary with a part of both rings, were added to connect the rings and fix the whole conformations of isomers. As a result, the order of migration rate was always Lk3 > Lk2 > Lk1, irrespective of gel concentration. Thus, all the topological isomers were unanimously characterized by only one polyacrylamide gel electrophoresis experiment. Well-characterized DNA catenanes are obtainable by this two-strut strategy, opening the way to more advanced nanotechnology.
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Affiliation(s)
- Lin Li
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiaxuan Tang
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China
| | - Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China.
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Nucleic acids Chemistry and Biotechnology Laboratory, Shinan-qu, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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24
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Peil A, Zhan P, Liu N. DNA Origami Catenanes Templated by Gold Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905987. [PMID: 31917513 DOI: 10.1002/smll.201905987] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Mechanically interlocked molecules have marked a breakthrough in the field of topological chemistry and boosted the vigorous development of molecular machinery. As an archetypal example of the interlocked molecules, catenanes comprise macrocycles that are threaded through one another like links in a chain. Inspired by the transition metal-templated approach of catenanes synthesis, the hierarchical assembly of DNA origami catenanes templated by gold nanoparticles is demonstrated in this work. DNA origami catenanes, which contain two, three or four interlocked rings are successfully created. In particular, the origami rings within the individual catenanes can be set free with respect to one another by releasing the interconnecting gold nanoparticles. This work will set the basis for rich progress toward DNA-based molecular architectures with unique structural programmability and well-defined topology.
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Affiliation(s)
- Andreas Peil
- Max-Planck-Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
- Kirchhoff-Institute for Physics, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Pengfei Zhan
- Max-Planck-Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
| | - Na Liu
- Max-Planck-Institute for Intelligent Systems, Heisenbergstr. 3, 70569, Stuttgart, Germany
- Kirchhoff-Institute for Physics, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
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25
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Jahanban-Esfahlan A, Seidi K, Jaymand M, Schmidt TL, Majdi H, Javaheri T, Jahanban-Esfahlan R, Zare P. Dynamic DNA nanostructures in biomedicine: Beauty, utility and limits. J Control Release 2019; 315:166-185. [PMID: 31669209 DOI: 10.1016/j.jconrel.2019.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 01/16/2023]
Abstract
DNA composite materials are at the forefront, especially for biomedical science, as they can increase the efficacy and safety of current therapies and drug delivery systems. The specificity and predictability of the Watson-Crick base pairing make DNA an excellent building material for the production of programmable and multifunctional objects. In addition, the principle of nucleic acid hybridization can be applied to realize mobile nanostructures, such as those reflected in DNA walkers that sort and collect cargo on DNA tracks, DNA robots performing tasks within living cells and/or DNA tweezers as ultra-sensitive biosensors. In this review, we present the diversity of dynamic DNA nanostructures functionalized with different biomolecules/functional units, imaging smart biomaterials capable of sensing, interacting, delivery and performing complex tasks within living cells/organisms.
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Affiliation(s)
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Thorsten L Schmidt
- Physics Department, 103 Smith Hall, Kent State University, Kent, OH, 44240, USA
| | - Hasan Majdi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Javaheri
- Ludwig Boltzmann Institute for Cancer Research, 1090 Vienna, Austria.
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland.
| | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland.
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26
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Zheng J, Du Y, Wang H, Peng P, Shi L, Li T. Ultrastable Bimolecular G-Quadruplexes Programmed DNA Nanoassemblies for Reconfigurable Biomimetic DNAzymes. ACS NANO 2019; 13:11947-11954. [PMID: 31589020 DOI: 10.1021/acsnano.9b06029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The relatively low stability and polymorphism of bimolecular G-quadruplexes (bi-G4s) are big difficulties that are faced in employing them to guide DNA assembly, as they are usually subject to a transformation into more stable tetramolecular or G-wire structures favored by K+ or Mg2+. Although bi-G4s benefit by additional duplex handles, a challenge remains in tailoring their intrinsic properties to resolve the above difficulties. Toward this challenge, here we engineer several ultrastable bi-G4s via replacing their nucleotide loops with special mini-hairpins, which consist of a GAA loop and a short GC-paired stem. Such a structural alteration favors the formation of G:C:G:C tetrads in the head-to-head folding topologies of bi-G4s and improves their thermal stability, with an increase in the melting temperature by up to 25 °C. It dramatically reduces their structural conversion into G-wires, verified by atomic force microscopy. These features enable the utilization of two well-chosen bi-G4s to shape a DNA nanotriangle into the desired framework nucleic acid (FNA) architectures such as "bowknot" and "butterfly" that are reversibly switched by the bi-G4s. On this basis, we further build a reconfigurable DNAzyme device to mimic the activation of human telomerase that is modulated by the G4 dimerization. Our designed ultrastable bi-G4s will offer a promising tool for dynamically manipulating intracellular DNA nanoassemblies with endogenous K+ and exploring the relationship between dimerization and function in some physiological processes.
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Affiliation(s)
- Jiao Zheng
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Yi Du
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Huihui Wang
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Pai Peng
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Lili Shi
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
| | - Tao Li
- Department of Chemistry , University of Science and Technology of China , 96 Jinzhai Road , Hefei , Anhui 230026 , China
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27
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Design, assembly, characterization, and operation of double-stranded interlocked DNA nanostructures. Nat Protoc 2019; 14:2818-2855. [DOI: 10.1038/s41596-019-0198-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/16/2019] [Indexed: 01/03/2023]
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28
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Wang L, Gong C, Yuan X, Wei G. Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E285. [PMID: 30781679 PMCID: PMC6410314 DOI: 10.3390/nano9020285] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 02/02/2023]
Abstract
Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π⁻π stacking, DNA base pairing, and ligand⁻receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.
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Affiliation(s)
- Li Wang
- Key Laboratory of Preparation and Application of Environmental Friendly Materials (Jilin Normal University), Ministry of Education, Changchun 130103, China.
| | - Coucong Gong
- Faculty of Production Engineering, University of Bremen, D-28359 Bremen, Germany.
| | - Xinzhu Yuan
- Key Laboratory of Preparation and Application of Environmental Friendly Materials (Jilin Normal University), Ministry of Education, Changchun 130103, China.
| | - Gang Wei
- Faculty of Production Engineering, University of Bremen, D-28359 Bremen, Germany.
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29
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Zhou W, Li D, Yuan R, Xiang Y. Programmable DNA Ring/Hairpin-Constrained Structure Enables Ligation-Free Rolling Circle Amplification for Imaging mRNAs in Single Cells. Anal Chem 2019; 91:3628-3635. [DOI: 10.1021/acs.analchem.8b05613] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wenjiao Zhou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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30
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Haydell MW, Centola M, Adam V, Valero J, Famulok M. Temporal and Reversible Control of a DNAzyme by Orthogonal Photoswitching. J Am Chem Soc 2018; 140:16868-16872. [DOI: 10.1021/jacs.8b08738] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Michael W. Haydell
- 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
| | - Volker Adam
- LIMES Chemical
Biology Unit, Universität Bonn, Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Julián Valero
- 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
| | - 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
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31
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Chen J, Baker YR, Brown A, El-Sagheer AH, Brown T. Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation. Chem Sci 2018; 9:8110-8120. [PMID: 30542561 PMCID: PMC6238721 DOI: 10.1039/c8sc02952k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.
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Affiliation(s)
- Jinfeng Chen
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Ysobel R Baker
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Asha Brown
- ATDBio , Magdalen Centre , Oxford Science Park , Oxford , OX4 4GA , UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
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32
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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.
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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
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33
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Xing C, Huang Y, Dai J, Zhong L, Wang H, Lin Y, Li J, Lu CH, Yang HH. Spatial Regulation of Biomolecular Interactions with a Switchable Trident-Shaped DNA Nanoactuator. ACS APPLIED MATERIALS & INTERFACES 2018; 10:32579-32587. [PMID: 30156821 DOI: 10.1021/acsami.8b10761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA nanostructures with controllable motions and functions have been used as flexible scaffolds to precisely and spatially organize molecular reactions at the nanoscale. The construction of dynamic DNA nanostructures with site-specifically incorporated functional elements is a critical step toward building nanomachines. Artificial self-assembled DNA nanostructures have also been developed to mimic key biological processes like various small biomolecule- and protein-based functional biochemistry pathways. Here, we report a self-assembled dynamic trident-shaped DNA (TS DNA) nanoactuator, in which biomolecules can be tethered to the three "arms" of the TS DNA nanoactuator. The TS DNA nanoactuator is implemented as the mechanical scaffold for the reconfiguration of fluorescent/quenching molecules and the assembly of gold nanoparticles, which exhibit controlled spatial separation. Furthermore, two enzymes (glucose oxidase and horseradish peroxidase) are attached to the two outer arms of the TS DNA nanoactuator, which show an enhanced cascade reaction efficiency compared to free enzymes. The efficiency of the two-enzyme cascade reaction can be spatially regulated by switching the TS DNA nanoactuator between opened, semiopened, and closed states through adding the "thermodynamic drivers" (fuels or antifuels). This is the first report to precisely modulate the relative position of coupled enzyme with multiple states and only based on one dynamic DNA scaffold. The present TS DNA nanoactuator with multistage conformational transition functionality could be applied as a potential platform to precisely and dynamically control the multienzyme pathways and would broaden the scope of DNA nanostructures in single-molecule biology applications.
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Affiliation(s)
- Chao Xing
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yuqing Huang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Junduan Dai
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Lin Zhong
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Huimeng Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Yuhong Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Juan Li
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Chun-Hua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Huang-Hao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
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34
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Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane. Molecules 2018; 23:molecules23092270. [PMID: 30189687 PMCID: PMC6225352 DOI: 10.3390/molecules23092270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 11/23/2022] Open
Abstract
DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures.
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35
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Wang J, Durbeej B. Toward Fast and Efficient Visible-Light-Driven Molecular Motors: A Minimal Design. ChemistryOpen 2018; 7:583-589. [PMID: 30083493 PMCID: PMC6070775 DOI: 10.1002/open.201800089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Indexed: 12/16/2022] Open
Abstract
A key goal in the development of light-driven rotary molecular motors is to facilitate their usage in biology and medicine by shifting the required irradiation wavelengths from the UV regime to the nondestructive visible regime. Although some progress has been made toward this goal, most available visible-light-driven motors either have relatively low quantum yields or require that thermal steps follow the photoisomerizations that underlie the rotary motion. Here, a minimal design for visible-light-driven motors without these drawbacks is presented and evaluated on the basis of state-of-the-art quantum chemical calculations and molecular dynamics simulations. The design, featuring dihydropyridinium and cyclohexenylidene motifs and comprising only five conjugated double bonds, is found to produce a full 360° rotation through fast photoisomerizations (excited-state lifetimes of ≈170-250 fs) powered by photons with energies well below 3 eV.
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Affiliation(s)
- Jun Wang
- Division of Theoretical Chemistry, IFMLinköping UniversitySE-581 83LinköpingSweden
| | - Bo Durbeej
- Division of Theoretical Chemistry, IFMLinköping UniversitySE-581 83LinköpingSweden
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36
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Valero J, Pal N, Dhakal S, Walter NG, Famulok M. A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks. NATURE NANOTECHNOLOGY 2018; 13:496-503. [PMID: 29632399 PMCID: PMC5994166 DOI: 10.1038/s41565-018-0109-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/01/2018] [Indexed: 05/25/2023]
Abstract
Biological motors are highly complex protein assemblies that generate linear or rotary motion, powered by chemical energy. Synthetic motors based on DNA nanostructures, bio-hybrid designs or synthetic organic chemistry have been assembled. However, unidirectionally rotating biomimetic wheel motors with rotor-stator units that consume chemical energy are elusive. Here, we report a bio-hybrid nanoengine consisting of a catalytic stator that unidirectionally rotates an interlocked DNA wheel, powered by NTP hydrolysis. The engine consists of an engineered T7 RNA polymerase (T7RNAP-ZIF) attached to a dsDNA nanoring that is catenated to a rigid rotating dsDNA wheel. The wheel motor produces long, repetitive RNA transcripts that remain attached to the engine and are used to guide its movement along predefined ssDNA tracks arranged on a DNA nanotube. The simplicity of the design renders this walking nanoengine adaptable to other biological nanoarchitectures, facilitating the construction of complex bio-hybrid structures that achieve NTP-driven locomotion.
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Affiliation(s)
- Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn, Germany
- Center of Advanced European Studies and Research (CAESAR), Bonn, Germany
| | - Nibedita Pal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Soma Dhakal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn, Bonn, Germany.
- Center of Advanced European Studies and Research (CAESAR), Bonn, Germany.
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37
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Liu Y, Kumar S, Taylor RE. Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1518. [PMID: 29633568 DOI: 10.1002/wnan.1518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 02/14/2018] [Indexed: 01/04/2023]
Abstract
The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Sriram Kumar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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38
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Chen WH, Yang Sung S, Fadeev M, Cecconello A, Nechushtai R, Willner I. Targeted VEGF-triggered release of an anti-cancer drug from aptamer-functionalized metal-organic framework nanoparticles. NANOSCALE 2018; 10:4650-4657. [PMID: 29465130 DOI: 10.1039/c8nr00193f] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Amino-triphenyl dicarboxylate-bridged Zr4+ metal-organic framework nanoparticles (NMOFs), 100-130 nm, are modified with a nucleic acid complementary to the VEGF aptamer. The nucleic acid-functionalized NMOFs were loaded with the anti-cancer drug doxorubicin (or Rhodamine 6G as a drug model), and the loaded NMOFs were capped by hybridization with the VEGF aptamer that yielded VEGF-responsive duplex nucleic acid gates. In the presence of VEGF, a biomarker over-expressed in cancer cells, selective unlocking of the gates proceeds through the formation of VEGF/aptamer complexes, resulting in the release of the loads. In addition, the VEGF aptamer locking units were conjugated to the AS1411 aptamer sequence that binds to nucleolin receptors associated with cancer cells, resulting in the construction of cancer-cell targeted VEGF-responsive doxorubicin-loaded NMOFs. The different drug-loaded stimuli-responsive NMOFs reveal selective permeation into MDA-MB-231 breast cancer cells, compared to their incorporation into normal MCF-10A breast cells, with a two-fold enhanced incorporation into the MDA-MB-231 cells of the AS1411 aptamer-functionalized NMOFs. Cytotoxicity experiments revealed impressive selective apoptosis of the doxorubicin-loaded NMOFs towards the MDA-MB-231 cancer cells compared to the normal MCF-10A breast cells. A 55% and 70% MDA-MB-231 cell apoptosis was observed upon subjecting the cells to the VEGF aptamer and the VEGF aptamer/AS1411 aptamer conjugate-caged NMOFs, respectively, for a time-interval of three days, where only <10% apoptosis of the MCF-10A cells was observed under similar conditions.
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Affiliation(s)
- Wei-Hai Chen
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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39
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Bazargan G, Sohlberg K. Advances in modelling switchable mechanically interlocked molecular architectures. INT REV PHYS CHEM 2018. [DOI: 10.1080/0144235x.2018.1419042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Gloria Bazargan
- Department of Chemistry, Drexel University, Philadelphia, PA, USA
| | - Karl Sohlberg
- Department of Chemistry, Drexel University, Philadelphia, PA, USA
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40
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Saura-Sanmartin A, Martinez-Cuezva A, Pastor A, Bautista D, Berna J. Light-driven exchange between extended and contracted lasso-like isomers of a bistable [1]rotaxane. Org Biomol Chem 2018; 16:6980-6987. [DOI: 10.1039/c8ob02234h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A photoactive hydrogen-bonded lasso having an amide-based [1]rotaxane structure has been constructed from acyclic precursors through a self-templating approach. The stability, structural integrity and switching are described.
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Affiliation(s)
- Adrian Saura-Sanmartin
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
| | - Alberto Martinez-Cuezva
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
| | - Aurelia Pastor
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
| | | | - Jose Berna
- Departamento de Química Orgánica
- Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
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41
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Wang L, Meng Z, Martina F, Shao H, Shao F. Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor. Nucleic Acids Res 2017; 45:12090-12099. [PMID: 29126166 PMCID: PMC5716610 DOI: 10.1093/nar/gkx1045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 01/07/2023] Open
Abstract
DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements.
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Affiliation(s)
- Liying Wang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Zhenyu Meng
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Felicia Martina
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Huilin Shao
- Biomedical Institute of Global Heath Research and Technology, Departments of Biomedical Engineering and Surgery, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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42
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angew Chem Int Ed Engl 2017; 56:15210-15233. [PMID: 28444822 DOI: 10.1002/anie.201701868] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/16/2022]
Abstract
Triplex nucleic acids have recently attracted interest as part of the rich "toolbox" of structures used to develop DNA-based nanostructures and materials. This Review addresses the use of DNA triplexes to assemble sensing platforms and molecular switches. Furthermore, the pH-induced, switchable assembly and dissociation of triplex-DNA-bridged nanostructures are presented. Specifically, the aggregation/deaggregation of nanoparticles, the reversible oligomerization of origami tiles and DNA circles, and the use of triplex DNA structures as functional units for the assembly of pH-responsive systems and materials are described. Examples include semiconductor-loaded DNA-stabilized microcapsules, DNA-functionalized dye-loaded metal-organic frameworks (MOFs), and the pH-induced release of the loads. Furthermore, the design of stimuli-responsive DNA-based hydrogels undergoing reversible pH-induced hydrogel-to-solution transitions using triplex nucleic acids is introduced, and the use of triplex DNA to assemble shape-memory hydrogels is discussed. An outlook for possible future applications of triplex nucleic acids is also provided.
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Affiliation(s)
- Yuwei Hu
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Andrea Idili
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex-DNA-Nanostrukturen: von grundlegenden Eigenschaften zu Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701868] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yuwei Hu
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | | | - Andrea Idili
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Francesco Ricci
- Department of Chemistry; Universität Rom; Tor Vergata, via della Ricerca Scientifica 00133 Rom Italien
| | - Itamar Willner
- Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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44
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Wang XW, Zhang WB. Protein Catenation Enhances Both the Stability and Activity of Folded Structural Domains. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705194] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xiao-Wei Wang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education; Center for Soft Matter Science and Engineering; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 P. R. China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education; Center for Soft Matter Science and Engineering; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 P. R. China
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45
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Wang XW, Zhang WB. Protein Catenation Enhances Both the Stability and Activity of Folded Structural Domains. Angew Chem Int Ed Engl 2017; 56:13985-13989. [DOI: 10.1002/anie.201705194] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/07/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Xiao-Wei Wang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education; Center for Soft Matter Science and Engineering; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 P. R. China
| | - Wen-Bin Zhang
- Key Laboratory of Polymer Chemistry & Physics of Ministry of Education; Center for Soft Matter Science and Engineering; College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 P. R. China
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46
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Lou XY, Song N, Yang YW. Fluorescence Resonance Energy Transfer Systems in Supramolecular Macrocyclic Chemistry. Molecules 2017; 22:molecules22101640. [PMID: 28961213 PMCID: PMC6151841 DOI: 10.3390/molecules22101640] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
The fabrication of smart materials is gradually becoming a research focus in nanotechnology and materials science. An important criterion of smart materials is the capacity of stimuli-responsiveness, while another lies in selective recognition. Accordingly, supramolecular host-guest chemistry has proven a promising support for building intelligent, responsive systems; hence, synthetic macrocyclic hosts, such as calixarenes, cucurbiturils, cyclodextrins, and pillararenes, have been used as ideal building blocks. Meanwhile, manipulating and harnessing light artificially is always an intensive attempt for scientists in order to meet the urgent demands of technological developments. Fluorescence resonance energy transfer (FRET), known as a well-studied luminescent activity and also a powerful tool in spectroscopic area, has been investigated from various facets, of which the application range has been broadly expanded. In this review, the innovative collaboration between FRET and supramolecular macrocyclic chemistry will be presented and depicted with typical examples. Facilitated by the dynamic features of supramolecular macrocyclic motifs, a large variety of FRET systems have been designed and organized, resulting in promising optical materials with potential for applications in protein assembly, enzyme assays, diagnosis, drug delivery monitoring, sensing, photosynthesis mimicking and chemical encryption.
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Affiliation(s)
- Xin-Yue Lou
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
| | - Nan Song
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
| | - Ying-Wei Yang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
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47
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Fresch B, Remacle F, Levine RD. Implementation of Probabilistic Algorithms by Multi-chromophoric Molecular Networks with Application to Multiple Travelling Pathways. Chemphyschem 2017; 18:1782-1789. [DOI: 10.1002/cphc.201700228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Barbara Fresch
- Department of Chemical Science; University of Padova; Via Marzolo 1 35131 Italy
| | - Françoise Remacle
- Department of Chemistry, B6c; University of Liege; B4000 Liege Belgium
- The Fritz Haber Center for Molecular Dynamics and Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Raphael D. Levine
- The Fritz Haber Center for Molecular Dynamics and Institute of Chemistry; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
- Crump Institute for Molecular Imaging and Department of Molecular and Medical Pharmacology; David Geffen School of Medicine and Department of Chemistry and Biochemistry; University of California, Los Angeles; California 90095 USA
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48
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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49
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Valero J, Lohmann F, Famulok M. Interlocked DNA topologies for nanotechnology. Curr Opin Biotechnol 2017; 48:159-167. [PMID: 28505598 DOI: 10.1016/j.copbio.2017.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 11/19/2022]
Abstract
Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies. Therefore, the study of novel DNA-based interlocked systems is of interest for nanotechnology, synthetic biology, supramolecular chemistry, biotechnology, and for sensing purposes. Here we summarize recent developments and applications of interlocked supramolecular architectures made of DNA. Examples illustrating that these systems can be precisely controlled by switching on and off the molecular motion of its mechanically trapped components are discussed. Introducing different triggers into such systems creates molecular assemblies capable of performing logic gate operations and/or catalytic activity control. Interlocked DNA-based nanostructures thus represent promising frameworks for building increasingly complex and dynamic nanomachines with highly controllable functionality.
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Affiliation(s)
- Julián Valero
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; Center of Advanced European Studies and Research (CASEAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Finn Lohmann
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Michael Famulok
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; Center of Advanced European Studies and Research (CASEAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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50
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Heinen L, Walther A. Temporal control of i-motif switch lifetimes for autonomous operation of transient DNA nanostructures. Chem Sci 2017; 8:4100-4107. [PMID: 28580123 PMCID: PMC5439531 DOI: 10.1039/c7sc00646b] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/28/2017] [Indexed: 01/05/2023] Open
Abstract
System integration of the DNA i-motif switch with a tunable pH environment allows programmable lifetimes of DNA duplex hybridization and higher level self-assemblies in closed and autonomous systems.
Functional DNA nanotechnology creates increasingly complex behaviors useful for sensing, actuation or computation, as enabled via the integration of dynamic and responsive structural DNA motifs. However, temporally controlled and dynamic DNA structures with programmable lifetimes, that are able to operate autonomously and self-revert to the starting state are challenging to achieve due to tedious and very system-specific sequence design. Here, we present a straightforward concept to program transient lifetimes into DNA duplexes based on the pH-sensitive DNA i-motif switch. We integrate the i-motif switch with an internal, non-linear pH-resetting function using a rationally designed chemical reaction framework, by which the switch autonomously undergoes a complete “off–on–off”-cycle without the use of additional external triggers. The lifetime of the activated “on”-state (i.e. the hybridized state) can be systematically programmed over several hours. The system can be readily implemented into hybrid DNA structures on larger length scales. Focusing on autonomous materials, we demonstrate temporal control of transient fluorescence signals and temporary aggregation of gold nanoparticles.
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Affiliation(s)
- L Heinen
- Institute for Macromolecular Chemistry , University of Freiburg , Stefan-Meier-Str. 31 , 79104 Freiburg , Germany . .,Freiburg Materials Research Center , University of Freiburg , Stefan-Meier-Str. 21 , 79104 Freiburg , Germany.,Freiburg Center for Interactive Materials and Bioinspired Technologies , University of Freiburg , Georges-Köhler-Allee 105 , 79110 Freiburg , Germany
| | - A Walther
- Institute for Macromolecular Chemistry , University of Freiburg , Stefan-Meier-Str. 31 , 79104 Freiburg , Germany . .,Freiburg Materials Research Center , University of Freiburg , Stefan-Meier-Str. 21 , 79104 Freiburg , Germany.,Freiburg Center for Interactive Materials and Bioinspired Technologies , University of Freiburg , Georges-Köhler-Allee 105 , 79110 Freiburg , Germany
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