1
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Zhang TH, Yang YK, Feng YM, Luo ZJ, Wang MW, Qi PY, Zeng D, Liu HW, Liao YM, Meng J, Zhou X, Liu LW, Yang S. Engineering the novel azobenzene-based molecular photoswitches for suppressing bacterial infection through dynamic regulation of biofilm formation. PEST MANAGEMENT SCIENCE 2024. [PMID: 39373165 DOI: 10.1002/ps.8453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/05/2024] [Accepted: 09/16/2024] [Indexed: 10/08/2024]
Abstract
BACKGROUND Bacterial biofilm is a strong fortress for bacteria to resist harsh external environments, which can enhance their tolerance and exacerbate the drug/pesticide resistance risk. Currently, photopharmacology provides an advanced approach via precise spatiotemporal control for regulating biological activities by light-controlling the molecular configurations, thereby having enormous potential in the development of drug/pesticides. RESULTS To further expand the photopharmacology application for discovering new antibiofilm agents, we prepared a series of light-controlled azo-active molecules and explored their photo isomerization, fatigue resistance, and anti-biofilm performance. Furthermore, their mechanisms of inhibiting biofilm formation were systematically investigated. Overall, designed azo-derivative A11 featured excellent anti-Xoo activity with an half-maximal effective concentration (EC50) value of 5.45 μg mL-1, and the EC50 value could be further elevated to 2.19 μg mL-1 after ultraviolet irradiation (converted as cis-configuration). The photo-switching behavior showed that A11 had outstanding anti-fatigue properties. An in-depth analysis of the action mechanism showed that A11 could effectively inhibit biofilm formation and the expression of relevant virulence factors. This performance could be dynamically regulated via loading with private light-switch property. CONCLUSION In this work, designed light-controlled azo molecules provide a new model for resisting bacterial infection via dynamic regulation of bacterial biofilm formation. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Tai-Hong Zhang
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yi-Ke Yang
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yu-Mei Feng
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Zhi-Jun Luo
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Ming-Wei Wang
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Pu-Ying Qi
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Dan Zeng
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Hong-Wu Liu
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yan-Mei Liao
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Jiao Meng
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Xiang Zhou
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Li-Wei Liu
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Song Yang
- State Key Laboratory of Green Pesticides, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
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2
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Ouyang Y, Zhang P, Willner I. DNA Tetrahedra as Functional Nanostructures: From Basic Principles to Applications. Angew Chem Int Ed Engl 2024; 63:e202411118. [PMID: 39037936 DOI: 10.1002/anie.202411118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 07/24/2024]
Abstract
Self-assembled supramolecular DNA tetrahedra composed of programmed sequence-engineered complementary base-paired strands represent elusive nanostructures having key contributions to the development and diverse applications of DNA nanotechnology. By appropriate engineering of the strands, DNA tetrahedra of tuneable sizes and chemical functionalities were designed. Programmed functionalities for diverse applications were integrated into tetrahedra structures including sequence-specific recognition strands (aptamers), catalytic DNAzymes, nanoparticles, proteins, or fluorophore. The article presents a comprehensive review addressing methods to assemble and characterize the DNA tetrahedra nanostructures, and diverse applications of DNA tetrahedra framework are discussed. Topics being addressed include the application of structurally functionalized DNA tetrahedra nanostructure for the assembly of diverse optical or electrochemical sensing platforms and functionalized intracellular sensing and imaging modules. In addition, the triggered reconfiguration of DNA tetrahedra nanostructures and dynamic networks and circuits emulating biological transformations are introduced. Moreover, the functionalization of DNA tetrahedra frameworks with nanoparticles provides building units for the assembly of optical devices and for the programmed crystallization of nanoparticle superlattices. Finally, diverse applications of DNA tetrahedra in the field of nanomedicine are addressed. These include the DNA tetrahedra-assisted permeation of nanocarriers into cells for imaging, controlled drug release, active chemodynamic/photodynamic treatment of target tissues, and regenerative medicine.
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Affiliation(s)
- Yu Ouyang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Pu Zhang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Current address: Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P.R. China
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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3
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Bhattacharya A, Pandit S, Lee S, Ebrahimi SB, Samanta D. Modulating Enzyme Activity using Engineered Nanomaterials. Chembiochem 2024:e202400520. [PMID: 39117568 DOI: 10.1002/cbic.202400520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/10/2024]
Abstract
Enzymes serve as pivotal components in various biotechnological applications across several industries. Understanding enzyme inhibition sheds light on how certain compounds disrupt biochemical pathways, facilitating the design of targeted drugs for combating diseases. On the other hand, reversible inhibition or enhancement of activity can unlock new ways of controlling industrial reactions and boosting the catalytic activity of native enzymes that are taken out of their natural environments. Over the last two decades, immobilizing enzymes on nanomaterial-based solid supports has emerged as an especially promising approach for tuning enzyme activity. Nanomaterials not only inhibit enzymes but also enhance their performance, showcasing their versatility. This Concept highlights significant advancements in utilizing nanomaterials for enzyme modulation and discusses future prospects for leveraging this phenomenon in developing sophisticated molecular systems and downstream applications.
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Affiliation(s)
- Atri Bhattacharya
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Subrata Pandit
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Seungheon Lee
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
| | - Sasha B Ebrahimi
- Emerging Drug Delivery Platforms, Drug Product Development, GSK, 1250 S Collegeville Rd, Collegeville, PA-19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX, 78712, USA
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4
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Liu F, Qu P, Weiss J, Guo K, Weck M. Substrate Channeling in Compartmentalized Nanoreactors. Macromolecules 2024; 57:6805-6815. [PMID: 39071043 PMCID: PMC11270995 DOI: 10.1021/acs.macromol.4c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/28/2024] [Accepted: 06/18/2024] [Indexed: 07/30/2024]
Abstract
Thermo- and photoresponsive nanoreactors based on shell cross-linked micelles (SCMs) for the rhodium-catalyzed asymmetric transfer hydrogenation (ATH) of ketones have been developed from poly(2-oxazoline) triblock terpolymers. The nanoreactors incorporate thermoresponsive poly(2-isopropyl-2-oxazoline) as the hydrophilic corona and are covalently cross-linked with a photoswitchable spiropyran molecule. UV irradiation or changes in temperature trigger morphology switching of the polymer-based nanoreactors that alters the hydrophobicity in separate layers of the SCMs, resulting in dynamic substrate selectivity of the ATH in water. Control experiments and kinetic studies show that the thermoresponsive outer layer induces the gated behavior for more hydrophobic substrates, whereas the photoresponsive cross-linking layer induces the gated behavior for less hydrophobic substrates. The nanoreactors mimic the multichannels in Nature, transporting substrates and reagents into the catalytic core which can be controlled through external triggers such as temperature and light wavelengths. Additionally, the nanoreactors can be easily recovered and reused with continued high activity and selectivities.
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Affiliation(s)
- Fangbei Liu
- Molecular Design Institute and Department
of Chemistry, New York University, New York, New York 10003-6688, United
States
| | | | - Jeremy Weiss
- Molecular Design Institute and Department
of Chemistry, New York University, New York, New York 10003-6688, United
States
| | - Kunhao Guo
- Molecular Design Institute and Department
of Chemistry, New York University, New York, New York 10003-6688, United
States
| | - Marcus Weck
- Molecular Design Institute and Department
of Chemistry, New York University, New York, New York 10003-6688, United
States
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5
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Wang R, Kong L, Liu Y, Chai Y, Yuan R. A simple and reliable interenzyme distance regulation strategy based on a DNA quadrangular prism scaffold for ultrasensitive ochratoxin A detection. Food Chem 2024; 446:138872. [PMID: 38442680 DOI: 10.1016/j.foodchem.2024.138872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Abstract
Developing sensitive and accurate Ochratoxin A (OTA) detection methods is essential for food safety. Herein, a simple and reliable strategy for regulating interenzyme distance based on a rigid DNA quadrangular prism as a scaffold was proposed to establish a new electrochemical biosensor for ultrasensitive detection of OTA. The interenzyme distances were precisely adjusted by changing the sequences of the hybridized portions of hairpins SH1 and SH2 to the DNA quadrangular prism, avoiding the complexity and instability of the previous DNA scaffold-based enzyme spacing adjustment strategies. The electrochemical biosensor constructed at the optimal interenzyme distance (10.4 nm) achieved sensitive detection of OTA in a dynamic concentration range from 10 fg/mL to 250 ng/mL with a detection limit of 3.1 fg/mL. In addition, the biosensor was applied to quantify OTA in real samples, exhibiting great application potential in food safety.
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Affiliation(s)
- Rong Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Lingqi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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6
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Fu W, Sheng Z, Qiao Z, Xu Z, Li M, Guan Y, Li Z, Shao X. Optical Control of Insect Behavior and Receptors with Azobenzene-Bridged Fipronil and Imidacloprid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12469-12477. [PMID: 38771932 DOI: 10.1021/acs.jafc.4c00822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Photopharmacology can be implemented in a way of regulating drug activities by light-controlling the molecular configuations. Three photochromic ligands (PCLs) that bind on one or two sites of GABARs and nAChRs were reported here. These multiphoton PCLs, including FIP-AB-FIP, IMI-AB-FIP, and IMI-AB-IMI, are constructed with an azobenzene (AB) bridge that covalently connects two fipronil (FIP) and imidacloprid (IMI) molecules. Interestingly, the three PCLs as well as FIP and IMI showed great insecticidal activities against Aedes albopictus larvae and Aphis craccivora. IMI-AB-FIP in both trans/cis isomers can be reversibly interconverted depending on light, accompanied by insecticidal activity decrease or increase by 1.5-2.3 folds. In addition, IMI-AB-FIP displayed synergistic effects against A. craccivora (LC50, IMI-AB-FIP = 14.84-22.10 μM, LC50, IMI-AB-IMI = 210.52-266.63 μM, LC50, and FIP-AB-FIP = 36.25-51.04 μM), mainly resulting from a conceivable reason for simultaneous targeting on both GABARs and nAChRs. Furthermore, modulations of wiggler-swimming behaviors and cockroach neuron function were conducted and the results indirectly demonstrated the ligand-receptor interactions. In other words, real-time regulations of receptors and insect behaviors can be spatiotemporally achieved by our two-photon PCLs using light.
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Affiliation(s)
- Wen Fu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhubo Sheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhi Qiao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhiping Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Meng Li
- Joint Institute of Tobacco and Health, Kunming, Yunnan 650202, China
| | - Ying Guan
- Joint Institute of Tobacco and Health, Kunming, Yunnan 650202, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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7
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Wu Y, Luo L, Hao Z, Liu D. DNA-based nanostructures for RNA delivery. MEDICAL REVIEW (2021) 2024; 4:207-224. [PMID: 38919398 PMCID: PMC11195427 DOI: 10.1515/mr-2023-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/28/2024] [Indexed: 06/27/2024]
Abstract
RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.
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Affiliation(s)
- Yuanyuan Wu
- Beijing SupraCirc Biotechnology Co., Ltd, Beijing, China
| | - Liangzhi Luo
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Ziyang Hao
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Dongsheng Liu
- Department of Chemistry, Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Tsinghua University, Beijing, China
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8
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Luo Z, Qiao L, Chen H, Mao Z, Wu S, Ma B, Xie T, Wang A, Pei X, Sheldon RA. Precision Engineering of the Co-immobilization of Enzymes for Cascade Biocatalysis. Angew Chem Int Ed Engl 2024; 63:e202403539. [PMID: 38556813 DOI: 10.1002/anie.202403539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
The design and orderly layered co-immobilization of multiple enzymes on resin particles remain challenging. In this study, the SpyTag/SpyCatcher binding pair was fused to the N-terminus of an alcohol dehydrogenase (ADH) and an aldo-keto reductase (AKR), respectively. A non-canonical amino acid (ncAA), p-azido-L-phenylalanine (p-AzF), as the anchor for covalent bonding enzymes, was genetically inserted into preselected sites in the AKR and ADH. Employing the two bioorthogonal counterparts of SpyTag/SpyCatcher and azide-alkyne cycloaddition for the immobilization of AKR and ADH enabled sequential dual-enzyme coating on porous microspheres. The ordered dual-enzyme reactor was subsequently used to synthesize (S)-1-(2-chlorophenyl)ethanol asymmetrically from the corresponding prochiral ketone, enabling the in situ regeneration of NADPH. The reactor exhibited a high catalytic conversion of 74 % and good reproducibility, retaining 80 % of its initial activity after six cycles. The product had 99.9 % ee, which that was maintained in each cycle. Additionally, the double-layer immobilization method significantly increased the enzyme loading capacity, which was approximately 1.7 times greater than that of traditional single-layer immobilization. More importantly, it simultaneously enabled both the purification and immobilization of multiple enzymes on carriers, thus providing a convenient approach to facilitate cascade biocatalysis.
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Affiliation(s)
- Zhiyuan Luo
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Li Qiao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Haomin Chen
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Zhili Mao
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Shujiao Wu
- School of Pharmacy, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Bianqin Ma
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Anming Wang
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, China, Hangzhou, Zhejiang, 311121, China
| | - Roger A Sheldon
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand PO Wits., 2050, Johannesburg, South Africa
- Department of Biotechnology, Section BOC, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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9
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Jiang Q, Shang Y, Xie Y, Ding B. DNA Origami: From Molecular Folding Art to Drug Delivery Technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2301035. [PMID: 37715333 DOI: 10.1002/adma.202301035] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/08/2023] [Indexed: 09/17/2023]
Abstract
DNA molecules that store genetic information in living creatures can be repurposed as building blocks to construct artificial architectures, ranging from the nanoscale to the microscale. The precise fabrication of self-assembled DNA nanomaterials and their various applications have greatly impacted nanoscience and nanotechnology. More specifically, the DNA origami technique has realized the assembly of various nanostructures featuring rationally predesigned geometries, precise addressability, and versatile programmability, as well as remarkable biocompatibility. These features have elevated DNA origami from academic interest to an emerging class of drug delivery platform for a wide range of diseases. In this minireview, the latest advances in the burgeoning field of DNA-origami-based innovative platforms for regulating biological functions and delivering versatile drugs are presented. Challenges regarding the novel drug vehicle's safety, stability, targeting strategy, and future clinical translation are also discussed.
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Affiliation(s)
- Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
| | - Yiming Xie
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
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10
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Takezawa Y, Kudo N, Fuse N, Shionoya M. DNA three-way junction structures with amino acid side chains prepared via post-synthetic amide condensation. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-14. [PMID: 38359331 DOI: 10.1080/15257770.2024.2314645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
DNA three-way junction (3WJ) structures with three amino acid side chains in the core have been synthesized via post-synthetic DNA modification. Amide condensation reactions of oligonucleotides containing 2'-aminouridine with activated esters yielded DNA strands modified with His, Cys and Asp side chains to form modified 3WJs. Even a 3WJ with three negatively charged Asp side chains formed stably at room temperature. Furthermore, DNA hybridization alone placed two (His and Asp) and three (His, Cys, and Asp) side chains within the 3WJs, indicating that the DNA 3WJs are a useful platform for spatial arrangement of amino acid side chains.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naofumi Kudo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuyuki Fuse
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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11
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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12
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Zhou L, Ren L, Bai Z, Xia Q, Wang Y, Peng H, Yan Q, Shi J, Li B, Guo L, Wang L. DNA Framework Programmed Conformational Reconstruction of Antibody Complementary Determining Region. JACS AU 2023; 3:2709-2714. [PMID: 37885585 PMCID: PMC10598557 DOI: 10.1021/jacsau.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023]
Abstract
The conformation of complementary determining region (CDR) is crucial in dictating its specificity and affinity for binding with an antigen, making it a focal point in artificial antibody engineering. Although desirable, programmable scaffolds that can regulate the conformation of individual CDRs with nanometer precision are still lacking. Here, we devise a strategy to program the CDR conformation by anchoring both ends of a free CDR loop to specific sites of a DNA framework structure. This method allows us to define the span of a single CDR loop with an ∼2 nm resolution. Using this approach, we create a series of DNA framework based artificial antibodies (DNFbodies) with varied CDR loop spans, leading to different antibody-antigen binding affinities. We find that an optimized single CDR loop (∼2.3 nm span) exhibits ∼3-fold improved affinity relative to natural antibodies, confirming the critical role of the CDR conformation. This study may inspire the rational design of artificial antibodies.
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Affiliation(s)
- Liqi Zhou
- National
Laboratory of Solid State Microstructures, Jiangsu Key Laboratory
of Artificial Functional Materials, College of Engineering and Applied
Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, People’s Republic of China
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Lei Ren
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Zhiang Bai
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Qinglin Xia
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Yue Wang
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Hongzhen Peng
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Qinglong Yan
- Xiangfu
Laboratory, Jiashan 314102, People’s Republic
of China
| | - Jiye Shi
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
| | - Bin Li
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, People’s
Republic of China
| | - Linjie Guo
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
| | - Lihua Wang
- Institute
of Materiobiology, College of Science, Shanghai
University, Shanghai 200444, People’s Republic
of China
- CAS
Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, People’s Republic of China
- The
Interdisciplinary Research Center, Shanghai Synchrotron Radiation
Facility, Shanghai Advanced Research Institute,
Chinese Academy of Sciences, Shanghai 201210, People’s
Republic of China
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13
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Chen Y, Zhao M, Ouyang Y, Zhang S, Liu Z, Wang K, Zhang Z, Liu Y, Yang C, Sun W, Shen J, Zhu Z. Biotemplated precise assembly approach toward ultra-scaled high-performance electronics. Nat Protoc 2023; 18:2975-2997. [PMID: 37670036 DOI: 10.1038/s41596-023-00870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/08/2023] [Indexed: 09/07/2023]
Abstract
Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and biological materials. However, the use of DNA-templated approaches for the fabrication and performance requirements of ultra-scaled semiconductor electronics is limited by its assembly disorder and destructive interface composition. In this protocol, using carbon nanotubes (CNTs) as model semiconductors, we provide a stepwise process to build ultra-scaled, high-performance field-effect transistors (FETs) from micron-scale three-dimensional DNA templates. We apply the approach to assemble CNT arrays with uniform pitches scaled between 24.1 and 10.4 nm with yields of more than 95%, which exceeds the resolution limits of conventional lithography. To achieve highly clean CNT interfaces, we detail a rinsing-after-fixing step to remove residual DNA template and salt contaminations present around the contact and the channel regions, without modifying the alignment of the CNT arrays. The DNA-templated CNT FETs display both high on-state current (4-15 μA per CNT) and small subthreshold swing (60-100 mV per decade), which are superior to previous examples of biotemplated electronics and match the performance metrics of high-performance, silicon-based electronics. The scalable assembly of defect-free three-dimensional DNA templates requires 1 week and the CNT arrays can be synthesized within half a day. The interface engineering requires 1-2 d, while the fabrication of high-performance FET and logic gate circuits requires 2-4 d. The structural and performance characterizations of molecular-precise DNA self-assembly and high-performance electronics requires 1-2 d. The protocol is suited for users with expertise in DNA nanotechnology and semiconductor electronics.
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Affiliation(s)
- Yahong Chen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Mengyu Zhao
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Yifan Ouyang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Suhui Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zhihan Liu
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Kexin Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Zhaoxuan Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Yingxia Liu
- Department of Systems Engineering, City University of Hong Kong, Hong Kong, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China.
- Zhangjiang Laboratory, Shanghai, China.
| | - Jie Shen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China.
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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14
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Zhu L, Shen Y, Deng S, Wan Y, Luo J, Su Y, You M, Fan C, Ren K. Controllable mitochondrial aggregation and fusion by a programmable DNA binder. Chem Sci 2023; 14:8084-8094. [PMID: 37538820 PMCID: PMC10395312 DOI: 10.1039/d2sc07095b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
DNA nanodevices have been feasibly applied for various chemo-biological applications, but their functions as precise regulators of intracellular organelles are still limited. Here, we report a synthetic DNA binder that can artificially induce mitochondrial aggregation and fusion in living cells. The rationally designed DNA binder consists of a long DNA chain, which is grafted with multiple mitochondria-targeting modules. Our results indicated that the DNA binder-induced in situ self-assembly of mitochondria can be used to successfully repair ROS-stressed neuron cells. Meanwhile, this DNA binder design is highly programmable. Customized molecular switches can be easily implanted to further achieve stimuli-triggered mitochondrial aggregation and fusion inside living cells. We believe this new type of DNA regulator system will become a powerful chemo-biological tool for subcellular manipulation and precision therapy.
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Affiliation(s)
- Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology Nanjing 210094 China
| | - Yiting Shen
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology Nanjing 210094 China
| | - Shengyuan Deng
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology Nanjing 210094 China
| | - Ying Wan
- Intelligent Microsystem Technology and Engineering Center, School of Mechanical Engineering, Nanjing University of Science and Technology Nanjing 210094 China
| | - Jun Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology Nanjing 210094 China
| | - Yan Su
- Intelligent Microsystem Technology and Engineering Center, School of Mechanical Engineering, Nanjing University of Science and Technology Nanjing 210094 China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts Amherst MA 01003 USA
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200127 China
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology Nanjing 210094 China
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15
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Fernando D, Mathesh M, Cai J, Yang W. In Situ Immobilization of Multi-Enzymes for Enhanced Substrate Channeling of Enzyme Cascade Reactions: A Nanoarchitectonics Approach by Directed Metal-Organic Frameworks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37229646 DOI: 10.1021/acs.langmuir.3c00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Rationally tailoring a controlled spatial organization of enzymes in a nanoarchitecture for multi-enzyme cascade reactions can enhance the catalytic efficiency via substrate channeling. However, attaining substrate channeling is a grand challenge, requiring sophisticated techniques. Herein, we report facile polymer-directed metal-organic framework (MOF)-based nanoarchitechtonics for realizing a desirable enzyme architecture with significantly enhanced substrate channeling. The new method involves the use of poly(acrylamide-co-diallyldimethylammonium chloride) (PADD) as a modulator in a one-step process for simultaneous MOF synthesis and co-immobilization of enzymes (GOx and HRP). The resultant enzymes-PADD@MOFs constructs showed a closely packed nanoarchitecture with enhanced substrate channeling. A transient time close to 0 s was observed, owing to a short diffusion path for substrates in a 2D spindle-shaped structure and their direct transfer from one enzyme to another. This enzyme cascade reaction system showed a 3.5-fold increase in catalytic activity in comparison to free enzymes. The findings provide a new insight into using polymer-directed MOF-based enzyme nanoarchitectures to improve catalytic efficiency and selectivity.
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Affiliation(s)
- Dulini Fernando
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
| | - Motilal Mathesh
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
| | - Jackie Cai
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Wenrong Yang
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3216, Australia
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16
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O’Hagan M, Duan Z, Huang F, Laps S, Dong J, Xia F, Willner I. Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications. Chem Rev 2023; 123:6839-6887. [PMID: 37078690 PMCID: PMC10214457 DOI: 10.1021/acs.chemrev.3c00016] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/21/2023]
Abstract
This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.
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Affiliation(s)
- Michael
P. O’Hagan
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Shay Laps
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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17
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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18
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Gokulu IS, Banta S. Biotechnology applications of proteins functionalized with DNA oligonucleotides. Trends Biotechnol 2023; 41:575-585. [PMID: 36115723 DOI: 10.1016/j.tibtech.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
The functionalization of proteins with DNA through the formation of covalent bonds enables a wide range of biotechnology advancements. For example, single-molecule analytical methods rely on bioconjugated DNA as elastic biolinkers for protein immobilization. Labeling proteins with DNA enables facile protein identification, as well as spatial and temporal organization and control of protein within DNA-protein networks. Bioconjugation reactions can target native, engineered, and non-canonical amino acids (NCAAs) within proteins. In addition, further protein engineering via the incorporation of peptide tags and self-labeling proteins can also be used for conjugation reactions. The selection of techniques will depend on application requirements such as yield, selectivity, conjugation position, potential for steric hindrance, cost, commercial availability, and potential impact on protein function.
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Affiliation(s)
- Ipek Simay Gokulu
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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19
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Liu M, Wang Y, Jiang H, Han Y, Xia J. Synthetic Multienzyme Assemblies for Natural Product Biosynthesis. Chembiochem 2023; 24:e202200518. [PMID: 36625563 DOI: 10.1002/cbic.202200518] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
In nature, enzymes that catalyze sequential reactions are often assembled as clusters or complexes. The formation of multienzyme complexes, or metabolons, brings the enzyme active sites into proximity to promote intermediate transfer, decrease intermediate leakage, and streamline the metabolic flux towards the desired products. We and others have developed synthetic versions of metabolons through various strategies to enhance the catalytic rates for synthesizing valuable chemicals inside microbes. Synthetic multienzyme complexes range from static enzyme nanostructures to dynamic enzyme coacervates. Enzyme complexation optimizes the metabolic fluxes inside microbes, increases the product titer, and supplies the field with high-yield microbe strains that are amenable to large-scale fermentation. Enzyme complexes constructed inside microbial cells can be separated as independent entities and catalyze biosynthetic reactions ex vivo; such a feature gains these complexes another name, "synthetic organelles" - new subcellular entities with independent structures and functions. Still, the field is seeking new strategies to better balance dynamicity and confinement and to achieve finer control of local compartmentalization in the cells, as the natural multienzyme complexes do. Industrial applications of synthetic multienzyme complexes for the large-scale production of valuable chemicals are yet to be realized. This review focuses on synthetic multienzyme complexes that are constructed and function inside microbial cells.
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Affiliation(s)
- Min Liu
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yue Wang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hao Jiang
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yongxu Han
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry and, Center for Cell & Developmental Biology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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20
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Li Z, Wang J, Willner B, Willner I. Topologically Triggered Dynamic DNA Frameworks. Isr J Chem 2023. [DOI: 10.1002/ijch.202300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Zhenzhen Li
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Bilha Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
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21
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Peil A, Zhan P, Duan X, Krahne R, Garoli D, M Liz-Marzán L, Liu N. Transformable Plasmonic Helix with Swinging Gold Nanoparticles. Angew Chem Int Ed Engl 2023; 62:e202213992. [PMID: 36423337 DOI: 10.1002/anie.202213992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.
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Affiliation(s)
- Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Xiaoyang Duan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Roman Krahne
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Denis Garoli
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Luis M Liz-Marzán
- CIC BiomaGUNE, Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Biomedical Networking Center, Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, 43009, Bilbao, Spain
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
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22
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Tan Z, Cheng H, Chen G, Ju F, Fernández-Lucas J, Zdarta J, Jesionowski T, Bilal M. Designing multifunctional biocatalytic cascade system by multi-enzyme co-immobilization on biopolymers and nanostructured materials. Int J Biol Macromol 2023; 227:535-550. [PMID: 36516934 DOI: 10.1016/j.ijbiomac.2022.12.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/01/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
In recent decades, enzyme-based biocatalytic systems have garnered increasing interest in industrial and applied research for catalysis and organic chemistry. Many enzymatic reactions have been applied to sustainable and environmentally friendly production processes, particularly in the pharmaceutical, fine chemicals, and flavor/fragrance industries. However, only a fraction of the enzymes available has been stepped up towards industrial-scale manufacturing due to low enzyme stability and challenging separation, recovery, and reusability. In this context, immobilization and co-immobilization in robust support materials have emerged as valuable strategies to overcome these inadequacies by facilitating repeated or continuous batch operations and downstream processes. To further reduce separations, it can be advantageous to use multiple enzymes at once in one pot. Enzyme co-immobilization enables biocatalytic synergism and reusability, boosting process efficiency and cost-effectiveness. Several studies on multi-enzyme immobilization and co-localization propose kinetic advantages of the enhanced turnover number for multiple enzymes. This review spotlights recent progress in developing versatile biocatalytic cascade systems by multi-enzyme co-immobilization on environmentally friendly biopolymers and nanostructured materials and their application scope in the chemical and biotechnological industries. After a succinct overview of carrier-based and carrier-free immobilization/co-immobilizations, co-immobilization of enzymes on a range of biopolymer and nanomaterials-based supports is thoroughly compiled with contemporary and state-of-the-art examples. This study provides a new horizon in developing effective and innovative multi-enzymatic systems with new possibilities to fully harness the adventure of biocatalytic systems.
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Affiliation(s)
- Zhongbiao Tan
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, PR China.
| | - Hairong Cheng
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Gang Chen
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, PR China
| | - Fang Ju
- Sateri (Jiangsu) Fiber Co. Ltd., Suqian 221428, PR China
| | - Jesús Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, 28670 Villaviciosa de Odón, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia
| | - Jakub Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60695 Poznan, Poland
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60695 Poznan, Poland.
| | - Muhammad Bilal
- Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an 223003, PR China
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Yang XD, Zhang YJ, Zhou JH, Liu L, Sun JK. Air-Stable Radical Organic Cages as Cascade Nanozymes for Enhanced Catalysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206127. [PMID: 36440672 DOI: 10.1002/smll.202206127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/12/2022] [Indexed: 06/16/2023]
Abstract
The pursuit of single-assembled molecular cage reactors for complex tandem reactions is a long-standing target in biomimetic catalysis but still a grand challenge. Herein, nanozyme-like organic cages are reported by engineering air-stable radicals into the skeleton upon photoinduced electron transfer. The generation of radicals is accompanied by single-crystal structural transformation and exhibits superior stability over six months in air. Impressively, the radicals throughout the cage skeleton can mimic the peroxidase of natural enzymes to decompose H2 O2 into OH· and facilitate oxidation reactions. Furthermore, an integrated catalyst by encapsulating Au clusters (glucose oxidase mimics) into the cage has been developed, in which the dual active sites (Au cluster and radical) are spatially isolated and can work as cascade nanozymes to prominently promote the enzyme-like tandem reaction via a substrate channeling effect.
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Affiliation(s)
- Xiao-Dong Yang
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Ya-Jun Zhang
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
- College of Science, Hebei University of Science and Technology, Yuhua Road 70, Shijiazhuang, 050080, P. R. China
| | - Jun-Hao Zhou
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Ling Liu
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Jian-Ke Sun
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
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24
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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25
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Resveratrol Analogs and Prodrugs Differently Affect the Survival of Breast Cancer Cells Impairing Estrogen/Estrogen Receptor α/Neuroglobin Pathway. Int J Mol Sci 2023; 24:ijms24032148. [PMID: 36768470 PMCID: PMC9916867 DOI: 10.3390/ijms24032148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Breast cancer is the first leading tumor in women in terms of incidence worldwide. Seventy percent of cases are estrogen receptor (ER) α-positive. In these malignancies, 17β-estradiol (E2) via ERα increases the levels of neuroglobin (NGB), a compensatory protein that protects cancer cells from stress-induced apoptosis, including chemotherapeutic drug treatment. Our previous data indicate that resveratrol (RSV), a plant-derived polyphenol, prevents E2/ERα-induced NGB accumulation in this cellular context, making E2-dependent breast cancer cells more prone to apoptosis. Unfortunately, RSV is readily metabolized, thus preventing its effectiveness. Here, four different RSV analogs have been developed, and their effect on the ERα/NGB pathway has been compared with RSV conjugated with highly hydrophilic gold nanoparticles as prodrug to evaluate if RSV derivatives maintain the breast cancer cells' susceptibility to the chemotherapeutic drug paclitaxel as the original compound. Results demonstrate that RSV conjugation with gold nanoparticles increases RSV efficacy, with respect to RSV analogues, reducing NGB levels and enhancing the pro-apoptotic action of paclitaxel, even preventing the anti-apoptotic action exerted by E2 treatment on these cells. Overall, RSV conjugation with gold nanoparticles makes this complex a promising agent for medical application in breast cancer treatment.
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26
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Xiong M, Kong G, Liu Q, Liu L, Yin Y, Liu Y, Yuan H, Zhang XB, Tan W. DNA-Templated Anchoring of Proteins for Programmable Cell Functionalization and Immunological Response. NANO LETTERS 2023; 23:183-191. [PMID: 36577045 DOI: 10.1021/acs.nanolett.2c03928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Membrane protein engineering exhibits great potential for cell functionalization. Although genetic strategies are sophisticated for membrane protein engineering, there still exist some issues, including transgene insertional mutagenesis, laborious, complicated procedures, and low tunability. Herein, we report a DNA-templated anchoring of exogenous proteins on living cell membranes to realize programmable functionalization of living cells. Using DNA as a scaffold, the model cell membranes are readily modified with proteins, on which the density and ratio of proteins as well as their interactions can be precisely controlled through predictable DNA hybridization. Then, the natural killer (NK) cells were engineered to gain the ability to eliminate the immune checkpoint signaling at the NK-tumor synapse, which remarkably promoted NK cell activation in immunotherapy. Given the versatile functions of exogenous proteins and flexible designs of programmable DNA, this method has the potential to facilitate membrane-protein-based cell engineering and therapy.
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Affiliation(s)
- Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Qin Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Yao Yin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Ying Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Hui Yuan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha, Hunan 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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27
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Zhao Y, Gao S, Song D, Ye Z, Xu R, Luo Y, Xu Q. Lipidoid Artificial Compartments for Bidirectional Regulation of Enzyme Activity through Nanomechanical Action. J Am Chem Soc 2023; 145:551-559. [PMID: 36537880 DOI: 10.1021/jacs.2c11004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Photoresponsive inhibitor and noninhibitor systems have been developed to achieve on-demand enzyme activity control. However, inhibitors are only effective for a specific and narrow range of enzymes. Noninhibitor systems usually require mutation and modification of the enzymes, leading to irreversible loss of enzymatic activities. Inspired by biological membranes, we herein report a lipidoid-based artificial compartment composed of azobenzene (Azo) lipidoids and helper lipids, which can bidirectionally regulate the activity of the encapsulated enzymes by light. In this system, the reversible photoisomerization of Azo lipidoids triggered by UV/vis light creates a continuous rotation-inversion movement, thereby enhancing the permeability of the compartment membrane and allowing substrates to pass through. Moreover, the membrane can revert to its impermeable state when light is removed. Thus, enzyme activity can be switched on and off when encapsulating enzymes in the compartments. Importantly, since neither mutation nor modification is required, negligible loss of activity is observed for the encapsulated enzymes after repeated activation and inhibition. Furthermore, this approach provides a generic strategy for controlling multiple enzymes by forgoing the use of inhibitors and may broaden the applications of enzymes in biological mechanism research and precision medicine.
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Affiliation(s)
- Yu Zhao
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Shuliang Gao
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Donghui Song
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ruijie Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Ying Luo
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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28
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Scarpellini C, Valembois S, Goossens K, Vadi M, Lanthier C, Klejborowska G, Van Der Veken P, De Winter H, Bertrand MJM, Augustyns K. From PERK to RIPK1: Design, synthesis and evaluation of novel potent and selective necroptosis inhibitors. Front Chem 2023; 11:1160164. [PMID: 37090247 PMCID: PMC10119423 DOI: 10.3389/fchem.2023.1160164] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Receptor-Interacting serine/threonine-Protein Kinase 1 (RIPK1) emerged as an important driver of inflammation and, consequently, inflammatory pathologies. The enzymatic activity of RIPK1 is known to indirectly promote inflammation by triggering cell death, in the form of apoptosis, necroptosis and pyroptosis. Small molecule Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors have therefore recently entered clinical trials for the treatment of a subset of inflammatory pathologies. We previously identified GSK2656157 (GSK'157), a supposedly specific inhibitor of protein kinase R (PKR)-like ER kinase (PERK), as a much more potent type II Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitor. We now performed further structural optimisation on the GSK'157 scaffold in order to develop a novel class of more selective Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors. Based on a structure-activity relationship (SAR) reported in the literature, we anticipated that introducing a substituent on the para-position of the pyridinyl ring would decrease the interaction with PERK. Herein, we report a series of novel GSK'157 analogues with different para-substituents with increased selectivity for Receptor-Interacting serine/threonine-Protein Kinase 1. The optimisation led to UAMC-3861 as the best compound of this series in terms of activity and selectivity for Receptor-Interacting serine/threonine-Protein Kinase 1 over PERK. The most selective compounds were screened in vitro for their ability to inhibit RIPK1-dependent apoptosis and necroptosis. With this work, we successfully synthesised a novel series of potent and selective type II Receptor-Interacting serine/threonine-Protein Kinase 1 inhibitors based on the GSK'157 scaffold.
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Affiliation(s)
- Camilla Scarpellini
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sophie Valembois
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Mike Vadi
- Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research, Ghent, Belgium
- Laboratory Cell Death and Inflammation, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Caroline Lanthier
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Greta Klejborowska
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Mathieu J. M. Bertrand
- Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research, Ghent, Belgium
- Laboratory Cell Death and Inflammation, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- *Correspondence: Koen Augustyns,
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29
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Yan A, Sun L, Li D. Single-Molecule Imaging of Enzymatic Reactions on DNA Origami. Methods Mol Biol 2023; 2639:131-145. [PMID: 37166715 DOI: 10.1007/978-1-0716-3028-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The interaction between enzymes is very important for understanding of enzyme functions and shed light on enzymatic reaction mechanisms. With the development of DNA nanotechnology, DNA origami has become a powerful tool for analyzing the dynamic behavior of enzyme molecules. In this protocol, a method for imaging and analysis of single-molecule cascade enzyme reactions on DNA origami raft by total internal reflection fluorescence microscopy (TIRFM) is described. Through trajectory analysis and calculation, the diffusion of downstream enzymes in enzymatic reaction and chemotaxis of enzymatic reactions were elucidated at the single molecular level.
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Affiliation(s)
- An Yan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Lele Sun
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Di Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
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30
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Armstrong FA, Cheng B, Herold RA, Megarity CF, Siritanaratkul B. From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf. Chem Rev 2022; 123:5421-5458. [PMID: 36573907 PMCID: PMC10176485 DOI: 10.1021/acs.chemrev.2c00397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP+ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.
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Affiliation(s)
- Fraser A. Armstrong
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Beichen Cheng
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Ryan A. Herold
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Clare F. Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Bhavin Siritanaratkul
- Stephenson Institute for Renewable Energy and the Department of Chemistry, University of Liverpool, Liverpool L69 7ZF, United Kingdom
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31
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Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS AU 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
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Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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32
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Chen L, Liu Y, Guo W, Liu Z. Light responsive nucleic acid for biomedical application. EXPLORATION (BEIJING, CHINA) 2022; 2:20210099. [PMID: 37325506 PMCID: PMC10190984 DOI: 10.1002/exp.20210099] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/03/2022] [Indexed: 06/16/2023]
Abstract
Nucleic acids are widely used in biomedical applications because of their programmability and biocompatibility. The light responsive nucleic acids have attracted wide attention due to their remote control and high spatiotemporal resolution. In this review, we summarized the latest developments in biomedicine of light responsive molecules. The molecules which confer light responsive properties to nucleic acids were summarized. The binding sites of molecules to nucleic acids, the induced structural changes, and functional regulation of nucleic acids were reviewed. Then, the biomedical applications of light responsive nucleic acids were listed, such as drug delivery, biosensing, optogenetics, gene editing, etc. Finally, the challenges were discussed and possible future directions of light-responsive nucleic acids were proposed.
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Affiliation(s)
- Liwei Chen
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan ProvinceP. R. China
| | - Yanfei Liu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan ProvinceP. R. China
| | - Weisheng Guo
- Department of Minimally Invasive Interventional RadiologyGuangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory DiseaseSchool of Pharmaceutical Sciences & The Second Affiliated HospitalGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
| | - Zhenbao Liu
- Department of PharmaceuticsXiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan ProvinceP. R. China
- Molecular Imaging Research Center of Central South UniversityChangshaHunan ProvinceP. R. China
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33
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Lin P, Yang H, Nakata E, Morii T. Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold. Molecules 2022; 27:molecules27196309. [PMID: 36234845 PMCID: PMC9572797 DOI: 10.3390/molecules27196309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Cells have developed intelligent systems to implement the complex and efficient enzyme cascade reactions via the strategies of organelles, bacterial microcompartments and enzyme complexes. The scaffolds such as the membrane or protein in the cell are believed to assist the co-localization of enzymes and enhance the enzymatic reactions. Inspired by nature, enzymes have been located on a wide variety of carriers, among which DNA scaffolds attract great interest for their programmability and addressability. Integrating these properties with the versatile DNA–protein conjugation methods enables the spatial arrangement of enzymes on the DNA scaffold with precise control over the interenzyme distance and enzyme stoichiometry. In this review, we survey the reactions of a single type of enzyme on the DNA scaffold and discuss the proposed mechanisms for the catalytic enhancement of DNA-scaffolded enzymes. We also review the current progress of enzyme cascade reactions on the DNA scaffold and discuss the factors enhancing the enzyme cascade reaction efficiency. This review highlights the mechanistic aspects for the modulation of enzymatic reactions on the DNA scaffold.
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34
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Ouyang Y, Zhang P, Willner I. Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures. Bioconjug Chem 2022; 34:51-69. [PMID: 35973134 PMCID: PMC9853509 DOI: 10.1021/acs.bioconjchem.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.
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35
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Yu H, Feng J, Zhong F, Wu Y. Chemical Modification for the "off-/on" Regulation of Enzyme Activity. Macromol Rapid Commun 2022; 43:e2200195. [PMID: 35482602 DOI: 10.1002/marc.202200195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/14/2022] [Indexed: 11/07/2022]
Abstract
Enzymes with excellent catalytic performance play important roles in living organisms. Advances in strategies for enzyme chemical modification have enabled powerful strategies for exploring and manipulating enzyme functions and activities. Based on the development of chemical enzyme modifications, incorporating external stimuli-responsive features-for example, responsivity to light, voltage, magnetic force, pH, temperature, redox activity, and small molecules-into a target enzyme to turn "on" and "off" its activity has attracted much attention. The ability to precisely control enzyme activity using different approaches would greatly expand the chemical biology toolbox for clarification and detection of signal transduction and in vivo enzyme function and significantly promote enzyme-based disease therapy. This review summarizes the methods available for chemical enzyme modification mainly for the off-/on control of enzyme activity and particularly highlights the recent progress regarding the applications of this strategy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Huaibin Yu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Jiayi Feng
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Fangrui Zhong
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Yuzhou Wu
- Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, Ministry of Education Key Laboratory of Material Chemistry for Energy Conversion and Storage, Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
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36
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Jiao Y, Shang Y, Li N, Ding B. DNA-based enzymatic systems and their applications. iScience 2022; 25:104018. [PMID: 35313688 PMCID: PMC8933709 DOI: 10.1016/j.isci.2022.104018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA strands with unique secondary structures can catalyze various chemical reactions and mimic natural enzymes with the assistance of cofactors, which have attracted much research attention. At the same time, the emerging DNA nanotechnology provides an efficient platform to organize functional components of the enzymatic systems and regulate their catalytic performances. In this review, we summarize the recent progress of DNA-based enzymatic systems. First, DNAzymes (Dzs) are introduced, and their versatile utilities are summarized. Then, G-quadruplex/hemin (G4/hemin) Dzs with unique oxidase/peroxidase-mimicking activities and representative examples where these Dzs served as biosensors are explicitly elaborated. Next, the DNA-based enzymatic cascade systems fabricated by the structural DNA nanotechnology are depicted. In addition, the applications of catalytic DNA nanostructures in biosensing and biomedicine are included. At last, the challenges and the perspectives of the DNA-based enzymatic systems for practical applications are also discussed.
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37
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Enzyme Immobilization and Co-Immobilization: Main Framework, Advances and Some Applications. Processes (Basel) 2022. [DOI: 10.3390/pr10030494] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Enzymes are outstanding (bio)catalysts, not solely on account of their ability to increase reaction rates by up to several orders of magnitude but also for the high degree of substrate specificity, regiospecificity and stereospecificity. The use and development of enzymes as robust biocatalysts is one of the main challenges in biotechnology. However, despite the high specificities and turnover of enzymes, there are also drawbacks. At the industrial level, these drawbacks are typically overcome by resorting to immobilized enzymes to enhance stability. Immobilization of biocatalysts allows their reuse, increases stability, facilitates process control, eases product recovery, and enhances product yield and quality. This is especially important for expensive enzymes, for those obtained in low fermentation yield and with relatively low activity. This review provides an integrated perspective on (multi)enzyme immobilization that abridges a critical evaluation of immobilization methods and carriers, biocatalyst metrics, impact of key carrier features on biocatalyst performance, trends towards miniaturization and detailed illustrative examples that are representative of biocatalytic applications promoting sustainability.
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38
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Yao S, Liao Y, Pan R, Zhu W, Xu Y, Yang Y, Qian X. Programmed co-assembly of DNA-peptide hybrid microdroplets by phase separation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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39
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Cao F, Sang Y, Liu C, Bai F, Zheng L, Ren J, Qu X. Self-Adaptive Single-Atom Catalyst Boosting Selective Ferroptosis in Tumor Cells. ACS NANO 2022; 16:855-868. [PMID: 35025200 DOI: 10.1021/acsnano.1c08464] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ferroptosis, resulting from the catastrophic accumulation of lipid reactive oxygen species (ROS) and the inactivation of glutathione (GSH)-dependent peroxidase 4 (GPX4), has emerged as a form of regulated cell death for cancer therapy. Despite progress made with current ferroptosis inducers, efficient systems to trigger ferroptosis remain challenging, owing largely to their low activity, uncontrollable behavior, and even nonselective interactions. Here, we report a self-adaptive ferroptosis platform by engineering a DNA modulator onto the surface of single-atom nanozymes (SAzymes). The modulator could not only specifically intensify the ROS-generating activity but also endow the SAzymes with on-demand GSH-consuming ability in tumor cells, accelerating selective and safe ferroptosis. The self-adaptive antitumor response has been demonstrated in colon cancer and breast cancer, promoting the development of selective cancer therapy.
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Affiliation(s)
- Fangfang Cao
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Yanjuan Sang
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Chaoying Liu
- Department of Respiratory Medicine, First Affiliated Hospital, Jilin University, Jilin 130021, P. R. China
| | - Fuquan Bai
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Institute of Theoretical Chemistry, Jilin University, Jilin, Changchun 130021, P. R. China
| | - Lirong Zheng
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin, Changchun 130022, P. R. China
- University of Science and Technology of China, Hefei, Anhui 230029, P. R. China
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40
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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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41
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Papageorgiou AC. Structural Characterization of Multienzyme Assemblies: An Overview. Methods Mol Biol 2022; 2487:51-72. [PMID: 35687229 DOI: 10.1007/978-1-0716-2269-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multienzyme assemblies have attracted significant attention in recent years for use in industrial applications instead of single enzymes. Owing to their ability to catalyze cascade reactions, multienzyme assemblies have become inspirational tools for the in vitro construction of multienzyme molecular machines. The use of such molecular machines could offer several advantages such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability compared to current microbial cell catalytic systems. Besides, they can provide all the benefits found in the use of enzymes, including reusability, catalytic efficiency, and specificity. Similar to single enzymes, multienzyme assemblies could offer economical and environmentally friendly alternatives to conventional catalysts and play a central role as biocatalysts in green chemistry applications. However, detailed characterization of multienzyme assemblies and a full understanding of their mechanistic details are required for their efficient use in industrial biotransformations. Since the determination of the first enzyme structure in 1965, structural information has played a pivotal role in the characterization of enzymes and elucidation of their structure-function relationship. Among the structural biology techniques, X-ray crystallography has provided key mechanistic details into multienzyme assemblies. Here, the structural characterization of multienzyme assemblies is reviewed and several examples are provided.
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42
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Chen C, Liu Q, Yuan Y, Cai X, Ding X, Li B, Yang Y, Wang B, Wang G, Leong DT, Qian H. Protein-mediated DNA self-assembly by controlling the surface charge in a molecular crowding environment. Biomater Sci 2022; 10:2006-2013. [PMID: 35289345 DOI: 10.1039/d1bm02017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Designing and building artificial nanodevices and nanoarchitectures in living systems are extremely intriguing subjects in nanotechnology and synthetic biology. Taking advantage of cellular machinery and endogenous biomacromolecules, such as proteins,...
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Affiliation(s)
- Chunfa Chen
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Qian Liu
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
- Laboratory of Pharmacy and Chemistry, and Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing, 400016, China
| | - Yue Yuan
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Xiaolian Cai
- Department of Cardiology, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Xiaotong Ding
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Boxuan Li
- Department of Pharmacy, Changzhi Medical College, Changzhi, Shanxi 046000, China
| | - Yao Yang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Bin Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - Guansong Wang
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore.
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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43
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Song X, Wang Y, Hao Y, Zhu Q, Li Y, Song L, Deng Z. Sub-1.5 nm-gapped heterodimeric plasmonic nanomolecules. Chem Sci 2022; 13:4788-4793. [PMID: 35655881 PMCID: PMC9067581 DOI: 10.1039/d2sc01171a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022] Open
Abstract
A whole set of plasmonic nanodimers with prescribed binary compositions are constructed in solution to enable symmetry-broken strong plasmonic coupling.
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Affiliation(s)
- Xiaojun Song
- Center for Bioanalytical Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yueliang Wang
- College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing, Zhejiang 314001, China
| | - Yan Hao
- Center for Bioanalytical Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qingqing Zhu
- Center for Bioanalytical Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yanjuan Li
- Center for Bioanalytical Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lei Song
- Center for Bioanalytical Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhaoxiang Deng
- Center for Bioanalytical Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
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44
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Du Y, Shao Z, Xu Q, Li Z, Shao X. Azobenzene-Avermectin B1a Derivatives for Optical Modulation of Insect Behaviors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15530-15537. [PMID: 34914386 DOI: 10.1021/acs.jafc.1c05036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Naturally occurring avermectins are allosteric modulators of glutamate-gated chloride channels (GluCls) and possess exceptionally potent anthelmintic, acaricidal, and insecticidal activities. Here, we develop photoswitchable azobenzene-avermectin (ABAVM) derivatives, which can be photoactivated upon ultraviolet irradiation. After illumination, the best compound p-AB4″AVM had a 1.88-fold and 2.74-fold insecticidal activity enhancement toward Culex pipiens pallens and Mythimna separata larvae, respectively. p-AB4″AVM allows for optical regulation of dorsal unpaired median neuron membrane potential with a 2.15-fold fluorescence intensity decrease after illumination. p-AB4″AVM and p-AB5AVM enable optical modulation of the behavioral response of Culex pipiens pallens larvae with 1- and 4-fold reduced mobility upon irradiation, respectively. The ABAVMs could be used to reversibly manipulate GluCls with light and may be useful for the mechanistic study of macrocyclic lactone insecticides.
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Affiliation(s)
- Yaoyao Du
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhongli Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Qi Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhong Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xusheng Shao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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45
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Zheng G, Cui Y, Zhou Y, Jiang Z, Wang Q, Zhou M, Wang P, Yu Y. Photoenzymatic Activity of Artificial-Natural Bienzyme Applied in Biodegradation of Methylene Blue and Accelerating Polymerization of Dopamine. ACS APPLIED MATERIALS & INTERFACES 2021; 13:56191-56204. [PMID: 34787400 DOI: 10.1021/acsami.1c17098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzymes as biocatalysts have attracted extensive attention. In addition to immobilizing or encapsulating various enzymes for combating the easy loss of enzymatic activity, strengthening the enzymatic activity upon light irradiation is a challenge. To the best of our knowledge, the work of spatiotemporally modulating the catalytic activity of artificial-natural bienzymes with a near-infrared light irradiation has not been reported. Inspired by immobilized enzymes and nanozymes, herein a platinum nanozyme was synthesized; subsequently, the platinum nanozyme was grafted on the body of laccase, thus successfully obtaining the artificial-natural bienzyme. The three-dimensional structure of the artificial-natural bienzyme was greatly different from that of the immobilized enzyme or the encapsulated enzyme. The platinum nanozyme possessed excellent laccase-like activity, which was 3.7 times higher than that of laccase. Meanwhile, the coordination between the platinum nanozyme and laccase was proved. Besides, the cascaded catalysis of artificial-natural bienzyme was verified with hydrogen peroxide as a mediator. The enzymatic activities of artificial-natural bienzyme with and without near-infrared light irradiation were, respectively, 46.2 and 29.5% higher than that of free laccase. Moreover, the reversible catalytic activity of the coupled enzyme could be manipulated with and without a near-infrared light at 808 nm. As a result, the degradation rates of methylene blue catalyzed by the coupled enzyme and the platinum nanozyme were higher than that of laccase. Furthermore, accelerating polymerization of the dopamine was also demonstrated. Briefly, this facile strategy may provide a universal approach to control the catalytic activity of other natural enzymes.
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Affiliation(s)
- Guolin Zheng
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Yifan Cui
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Yu Zhou
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Zhe Jiang
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Qiang Wang
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Man Zhou
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Ping Wang
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
| | - Yuanyuan Yu
- Key Laboratory of Eco-Textiles, Ministry of Education, Jiangnan University, Jiangsu Province, Wuxi 214122, P. R. China
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Gong Z, Tang Y, Ma N, Cao W, Wang Y, Wang S, Tian Y. Applications of DNA-Functionalized Proteins. Int J Mol Sci 2021; 22:12911. [PMID: 34884714 PMCID: PMC8657886 DOI: 10.3390/ijms222312911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
As an important component that constitutes all the cells and tissues of the human body, protein is involved in most of the biological processes. Inspired by natural protein systems, considerable efforts covering many discipline fields were made to design artificial protein assemblies and put them into application in recent decades. The rapid development of structural DNA nanotechnology offers significant means for protein assemblies and promotes their application. Owing to the programmability, addressability and accurate recognition ability of DNA, many protein assemblies with unprecedented structures and improved functions have been successfully fabricated, consequently creating many brand-new researching fields. In this review, we briefly introduced the DNA-based protein assemblies, and highlighted the limitations in application process and corresponding strategies in four aspects, including biological catalysis, protein detection, biomedicine treatment and other applications.
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Affiliation(s)
- Zhaoqiu Gong
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
| | - Yuanyuan Tang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
| | - Ningning Ma
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
| | - Wenhong Cao
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
| | - Yong Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
| | - Shuang Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China; (Z.G.); (Y.T.); (N.M.); (W.C.); (Y.W.)
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
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47
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Li D, Xiong Q, Liang L, Duan H. Multienzyme nanoassemblies: from rational design to biomedical applications. Biomater Sci 2021; 9:7323-7342. [PMID: 34647942 DOI: 10.1039/d1bm01106e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multienzyme nanoassemblies (MENAs) that combine the functions of several enzymes into one entity have attracted widespread research interest due to their improved enzymatic performance and great potential for multiple applications. Considerable progress has been made to design and fabricate MENAs in recent years. This review begins with an introduction of the up-to-date strategies in designing MENAs, mainly including substrate channeling, compartmentalization and control of enzyme stoichiometry. The desirable properties that endow MENAs with important applications are also discussed in detail. Then, the recent advances in utilizing MENAs in the biomedical field are reviewed, with a particular focus on biosensing, tumor therapy, antioxidant and drug delivery. Finally, the challenges and perspectives for development of versatile MENAs are summarized.
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Affiliation(s)
- Di Li
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qirong Xiong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
| | - Li Liang
- State Key Lab of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore.
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Modulating the biofunctionality of enzyme-MOF nanobiocatalyst through structure-switching aptamer for continuous degradation of BPA. Colloids Surf B Biointerfaces 2021; 208:112099. [PMID: 34536675 DOI: 10.1016/j.colsurfb.2021.112099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 11/22/2022]
Abstract
Encapsulating enzyme within MOF (enzyme-MOF) gives rise to new opportunity to improve the fragility of enzyme, but practical application of enzyme-MOF composite is far from being realized. The development of a novel enzyme-MOF composite system should simultaneously guarantee the enhanced activity and controllably complete recycling, and only in this way can we efficiently and economically utilize the enzyme-MOF composite. Herein, we addressed all these fundamental limitations of current enzyme-MOF composite by establishing aptamer-functionalized enzyme-MOF composite (HRP-ZIF-8@P1). HRP-ZIF-8@P1 relied on automatic structure switch of aptamer-target binding and aptamer-cDNA (complementary DNA) hybridization, achieving effectiveness in self-enriching substrate around HRP-ZIF-8@P1 to boost enzymatic activity first, subsequently hybridizing spontaneously with magnetically controllable cDNA sequence (Fe3O4@P3) to completely recover the HRP-ZIF-8@P1, where preferentially capturing substrate could further induce the release of the hybridized HRP-ZIF-8@P1 for automatically starting the cyclic enzyme catalysis. A 5.6-fold enhancement in the catalytic efficiency for BPA degradation was endowed, and 94.7% catalytic activity was retained for 8 consecutive degradations of BPA, both of which were even more significant than HRP-ZIF-8. Additionally, remarkable stability of HRP-ZIF-8@P1 was afforded by dual-layer protection of ZIF-8 and P1 in denaturing conditions. Taking the possibility of discovering an aptamer for any target into account, the aptamer-functionalized enzyme-MOF composites provide a generic and simple guide for simultaneously boosting enzymatic activity and controllably full recycling the enzyme-MOF systems, accelerating their commercial utilizations.
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Guo R, Li M, Zuo X. DNA Framework-Mediated Geometric Renormalization of Gold Nanoparticles on a Two-Dimensional Fluidic Membrane Interface. Chempluschem 2021; 86:1472-1475. [PMID: 34520133 DOI: 10.1002/cplu.202100344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Indexed: 01/03/2023]
Abstract
The precise arrangement of single entity is a crucial objective of nanoscience and holds great promise in various fields such as biology and material science. In this work, we develop a "DNA framework-mediated geometric renormalization" (DFMGR) strategy to reassemble gold nanoparticles into specific geometric shapes on a 2-dimensional (2D) fluidic membrane interface. Cholesterol-modified AuNPs are randomly anchored on the supported lipid bilayer (SLB) via the cholesterol-lipid interaction. We demonstrate that AuNPs are laterally mobile on SLB and could be further rearranged into a specific geometric shape by DNA framework containing algebraically topological DNA arms. Using scanning electron microscope (SEM) imaging approach, simple geometric shapes, such as points assembled by monomers, line segments assembled by dimers, triangles assembled by trimers are visually presented. Interestingly, we found that the statistic angle (58.77°) and side length (12.21 nm) of triangles obtained from SEM images were both agreed well with the theoretical angle of 60° and side length of 12.58 nm. And the relative error of the angle calculated was as low as 0.33 %. These results indicated that the DFMGR strategy showed precise regulation ability for the AuNPs renormalization. We believe that DNA framework-mediated geometric renormalization strategy would be a powerful means for regulating ligand-receptor interactions in biosystems and for nanoparticle assembling in material science.
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Affiliation(s)
- Ruiyan Guo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University
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50
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Bilal M, Hussain N, Américo-Pinheiro JHP, Almulaiky YQ, Iqbal HMN. Multi-enzyme co-immobilized nano-assemblies: Bringing enzymes together for expanding bio-catalysis scope to meet biotechnological challenges. Int J Biol Macromol 2021; 186:735-749. [PMID: 34271049 DOI: 10.1016/j.ijbiomac.2021.07.064] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/23/2021] [Accepted: 07/10/2021] [Indexed: 02/06/2023]
Abstract
Co-immobilization of multi-enzymes has emerged as a promising concept to design and signify bio-catalysis engineering. Undoubtedly, the existence and importance of basic immobilization methods such as encapsulation, covalent binding, cross-linking, or even simple adsorption cannot be ignored as they are the core of advanced co-immobilization strategies. Different strategies have been developed and deployed to green the twenty-first century bio-catalysis. Moreover, co-immobilization of multi-enzymes has successfully resolved the limitations of individual enzyme loaded constructs. With an added value of this advanced bio-catalysis engineering platform, designing, and fabricating co-immobilized enzymes loaded nanostructure carriers to perform a particular set of reactions with high catalytic turnover is of supreme interest. Herein, we spotlight the emergence of co-immobilization strategies by bringing multi-enzymes together with various types of nanocarriers to expand the bio-catalysis scope. Following a brief introduction, the first part of the review focuses on multienzyme co-immobilization strategies, i.e., random co-immobilization, compartmentalization, and positional co-immobilization. The second part comprehensively covers four major categories of nanocarriers, i.e., carbon based nanocarriers, polymer based nanocarriers, silica-based nanocarriers, and metal-based nanocarriers along with their particular examples. In each section, several critical factors that can affect the performance and successful deployment of co-immobilization of enzymes are given in this work.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Nazim Hussain
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore 53700, Pakistan
| | | | - Yaaser Q Almulaiky
- University of Jeddah, College of Sciences and Arts at Khulais, Department of Chemistry, Jeddah, Saudi Arabia; Chemistry Department, Faculty of Applied Science, Taiz University, Taiz, Yemen
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
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