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Peng X, Liu Y, Peng F, Wang T, Cheng Z, Chen Q, Li M, Xu L, Man Y, Zhang Z, Tan Y, Liu Z. Aptamer-controlled stimuli-responsive drug release. Int J Biol Macromol 2024; 279:135353. [PMID: 39245104 DOI: 10.1016/j.ijbiomac.2024.135353] [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: 06/12/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024]
Abstract
Aptamers have been widely researched and applied in nanomedicine due to their programmable, activatable, and switchable properties. However, there are few reviews on aptamer-controlled stimuli-responsive drug delivery. This article highlights the mechanisms and advantages of aptamers in the construction of stimuli-responsive drug delivery systems. We summarize the assembly/reconfiguration mechanisms of aptamers in controlled release systems. The assembly and drug release strategies of drug delivery systems are illustrated. Specifically, we focus on the binding mechanisms to the target and the factors that induce/inhibit the binding to the stimuli, such as strand, pH, light, and temperature. The applications of aptamer-based stimuli-responsive drug release are elaborated. The challenges are discussed, and the future directions are proposed.
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Affiliation(s)
- Xingxing Peng
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Feicheng Peng
- Hunan Institute for Drug Control, Changsha 410001, Hunan Province, PR China
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhongyu Cheng
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Qiwen Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Mingfeng Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Lishang Xu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yunqi Man
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhirou Zhang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yifu Tan
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China; Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, PR China.
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2
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Hasanzadeh A, Ebadati A, Saeedi S, Kamali B, Noori H, Jamei B, Hamblin MR, Liu Y, Karimi M. Nucleic acid-responsive smart systems for controlled cargo delivery. Biotechnol Adv 2024; 74:108393. [PMID: 38825215 DOI: 10.1016/j.biotechadv.2024.108393] [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: 08/21/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Stimulus-responsive delivery systems allow controlled, highly regulated, and efficient delivery of various cargos while minimizing side effects. Owing to the unique properties of nucleic acids, including the ability to adopt complex structures by base pairing, their easy synthesis, high specificity, shape memory, and configurability, they have been employed in autonomous molecular motors, logic circuits, reconfigurable nanoplatforms, and catalytic amplifiers. Moreover, the development of nucleic acid (NA)-responsive intelligent delivery vehicles is a rapidly growing field. These vehicles have attracted much attention in recent years due to their programmable, controllable, and reversible properties. In this work, we review several types of NA-responsive controlled delivery vehicles based on locks and keys, including DNA/RNA-responsive, aptamer-responsive, and CRISPR-responsive, and summarize their advantages and limitations.
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arefeh Ebadati
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Department of Molecular and Cell Biology, University of California, Merced, Merced, USA
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kamali
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Behnam Jamei
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran, Iran.
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3
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Li S, Tian T, Zhang T, Lin Y, Cai X. A bioswitchable delivery system for microRNA therapeutics based on a tetrahedral DNA nanostructure. Nat Protoc 2024:10.1038/s41596-024-01050-7. [PMID: 39215132 DOI: 10.1038/s41596-024-01050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 07/11/2024] [Indexed: 09/04/2024]
Abstract
As microRNAs (miRNA) regulate almost all physiopathological activities in the human body, miRNA therapeutics that deliver miRNA regulators have attracted considerable attention in the field of nucleic acid drug development. The use of tetrahedral DNA nanostructures to deliver miRNA regulators is promising because of their simple fabrication, enhanced cell entry, effective tissue penetration, biocompatibility and functional editability. This protocol extension builds on our previous protocol for the use of tetrahedral DNA nanostructures and was designed to establish an updated bioswitchable delivery system (BDS) for achieving controlled cargo loading and release. A ribonuclease H-sensitive sequence is designed as a bioswitchable apparatus for the targeted release of the miRNA regulator. The functional sequence of the miRNA regulator and minimal secondary structure formation tendency during annealing are two key points in cargo design. We provide two BDS design strategies; BDS-A comprises an intact DNA tetrahedron with the RNA cargo hanging outside, offering the merits of lower cost, simplicity, and more direct structural design. In the BDS-B design, the RNA regulators are embedded into the DNA tetrahedron, which is beneficial for dermal tissue permeation applications. Following sequence design in Oligo 7 and Tiamat, the BDS assembly is completed and then ribonuclease H achieves controlled release of the miRNA regulator by triggering the bioswitchable apparatus. This is verified via polyacrylamide and agarose gel electrophoresis or fluorophore modifications. Both BDSs show promising cellular membrane permeability, tissue permeability and target inhibition in vitro and in vivo. The assembly and characterization of the BDS can be completed in 4 d, and the validation time for biostability and biological applications will depend on the specific use.
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Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
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4
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Le QV, Shim G. Biorobotic Drug Delivery for Biomedical Applications. Molecules 2024; 29:3663. [PMID: 39125066 PMCID: PMC11314275 DOI: 10.3390/molecules29153663] [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: 04/30/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 08/12/2024] Open
Abstract
Despite extensive efforts, current drug-delivery systems face biological barriers and difficulties in bench-to-clinical use. Biomedical robotic systems have emerged as a new strategy for drug delivery because of their innovative diminutive engines. These motors enable the biorobots to move independently rather than relying on body fluids. The main components of biorobots are engines controlled by external stimuli, chemical reactions, and biological responses. Many biorobot designs are inspired by blood cells or microorganisms that possess innate swimming abilities and can incorporate living materials into their structures. This review explores the mechanisms of biorobot locomotion, achievements in robotic drug delivery, obstacles, and the perspectives of translational research.
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Affiliation(s)
- Quoc-Viet Le
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam;
| | - Gayong Shim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea
- Integrative Institute of Basic Sciences, Soongsil University, Seoul 06978, Republic of Korea
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5
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Martins ASG, Reis SD, Benson E, Domingues MM, Cortinhas J, Vidal Silva JA, Santos SD, Santos NC, Pêgo AP, Moreno PMD. Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309140. [PMID: 38342712 DOI: 10.1002/smll.202309140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/22/2023] [Indexed: 02/13/2024]
Abstract
The successful translation of therapeutic nucleic acids (NAs) for the treatment of neurological disorders depends on their safe and efficient delivery to neural cells, in particular neurons. DNA nanostructures can be a promising NAs delivery vehicle. Nonetheless, the potential of DNA nanostructures for neuronal cell delivery of therapeutic NAs is unexplored. Here, tetrahedral DNA nanostructures (TDN) as siRNA delivery scaffolds to neuronal cells, exploring the influence of functionalization with two different reported neuronal targeting ligands: C4-3 RNA aptamer and Tet1 peptide are investigated. Nanostructures are characterized in vitro, as well as in silico using molecular dynamic simulations to better understand the overall TDN structural stability. Enhancement of neuronal cell uptake of TDN functionalized with the C4-3 Aptamer (TDN-Apt), not only in neuronal cell lines but also in primary neuronal cell cultures is demonstrated. Additionally, TDN and TDN-Apt nanostructures carrying siRNA are shown to promote silencing in a process aided by chloroquine-induced endosomal disruption. This work presents a thorough workflow for the structural and functional characterization of the proposed TDN as a nano-scaffold for neuronal delivery of therapeutic NAs and for targeting ligands evaluation, contributing to the future development of new neuronal drug delivery systems based on DNA nanostructures.
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Affiliation(s)
- Ana S G Martins
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, s/n, Porto, 4200-465, Portugal
| | - Sara D Reis
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Erik Benson
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Tomtebodavägen 23, Solna, 171 65, Sweden
| | - Marco M Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, 1649-028, Portugal
| | - João Cortinhas
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Joana A Vidal Silva
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Sofia D Santos
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, 1649-028, Portugal
| | - Ana P Pêgo
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto, 4050-313, Portugal
| | - Pedro M D Moreno
- i3S (Instituto de Investigação e Inovação em Saúde), Universidade do Porto, INEB (Instituto Nacional de Engenharia Biomédica), Rua Alfredo Allen, 208, Porto, 4200-135, Portugal
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Chen Y, Xu J, Shi S, Ma W, Cui W, Yan R, Lin Y. A DNA nanostructure-Hif-1α inducer complex as novel nanotherapy against cisplatin-induced acute kidney injury. Cell Prolif 2024; 57:e13601. [PMID: 38221742 DOI: 10.1111/cpr.13601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Since its discovery in 1978, cisplatin-based chemotherapy regimens have served a pivotal role in human cancer treatment, saving millions of lives. However, its high risk still poses a significant challenge for cisplatin-induced acute kidney injury (AKI), which occurs in 30% of cisplatin-treated patients. Unfortunately, no effective solution for preventing or managing this severe complication, which greatly impacts its clinical administration. Kidney is the main organ injured by cisplatin, and the injury is related to cisplatin-induced cell apoptosis and DNA injury. Therefore, to achieve the safe use of cisplatin in tumour treatment, the key lies in identifying a kidney treatment that can effectively minimize cisplatin nephrotoxicity. Here, we successfully synthesized and applied a DNA-nanostructure complex, named TFG, which contains tetrahedral framework nucleic acids (tFNAs) and FG-4592, a novel Hif-1α inducer. As cargo, TFG is composed entirely of DNA strands. It possesses low nephrotoxicity and renal aggregation properties while FG-4592 is able to relieve renal injury by downregulating the apoptosis signal pathways. And it can relieve cisplatin-induced renal injury when taken cisplatin treatment. This work aims to enhance chemotherapy protection in tumour patients by using TFG, a DNA-based nanomedicines to kidney. This work has the potential to revolutionize the treatment of renal diseases, particularly drug-induced kidney injury, leading to improved clinical outcomes.
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Affiliation(s)
- Yuanchong Chen
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| | - Jiangshan Xu
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| | - Weitong Cui
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| | - Ran Yan
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
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7
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Kashani GK, Naghib SM, Soleymani S, Mozafari MR. A review of DNA nanoparticles-encapsulated drug/gene/protein for advanced controlled drug release: Current status and future perspective over emerging therapy approaches. Int J Biol Macromol 2024; 268:131694. [PMID: 38642693 DOI: 10.1016/j.ijbiomac.2024.131694] [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: 01/14/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
In the last ten years, the field of nanomedicine has experienced significant progress in creating novel drug delivery systems (DDSs). An effective strategy involves employing DNA nanoparticles (NPs) as carriers to encapsulate drugs, genes, or proteins, facilitating regulated drug release. This abstract examines the utilization of DNA NPs and their potential applications in strategies for controlled drug release. Researchers have utilized the distinctive characteristics of DNA molecules, including their ability to self-assemble and their compatibility with living organisms, to create NPs specifically for the purpose of delivering drugs. The DNA NPs possess numerous benefits compared to conventional drug carriers, such as exceptional stability, adjustable dimensions and structure, and convenient customization. Researchers have successfully achieved a highly efficient encapsulation of different therapeutic agents by carefully designing their structure and composition. This advancement enables precise and targeted delivery of drugs. The incorporation of drugs, genes, or proteins into DNA NPs provides notable advantages in terms of augmenting therapeutic effectiveness while reducing adverse effects. DNA NPs serve as a protective barrier for the enclosed payloads, preventing their degradation and extending their duration in the body. The protective effect is especially vital for delicate biologics, such as proteins or gene-based therapies that could otherwise be vulnerable to enzymatic degradation or quick elimination. Moreover, the surface of DNA NPs can be altered to facilitate specific targeting towards particular tissues or cells, thereby augmenting the accuracy of delivery. A significant benefit of DNA NPs is their capacity to regulate the kinetics of drug release. Through the manipulation of the DNA NPs structure, scientists can regulate the rate at which the enclosed cargo is released, enabling a prolonged and regulated dispensation of medication. This control is crucial for medications with limited therapeutic ranges or those necessitating uninterrupted administration to attain optimal therapeutic results. In addition, DNA NPs have the ability to react to external factors, including alterations in temperature, pH, or light, which can initiate the release of the payload at precise locations or moments. This feature enhances the precision of drug release control. The potential uses of DNA NPs in the controlled release of medicines are extensive. The NPs have the ability to transport various therapeutic substances, for example, drugs, peptides, NAs (NAs), and proteins. They exhibit potential for the therapeutic management of diverse ailments, including cancer, genetic disorders, and infectious diseases. In addition, DNA NPs can be employed for targeted drug delivery, traversing biological barriers, and surpassing the constraints of conventional drug administration methods.
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Affiliation(s)
- Ghazal Kadkhodaie Kashani
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran.
| | - Sina Soleymani
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran; Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia; Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Iran University of Science and Technology (IUST), Tehran, Iran
| | - M R Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
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Postigo A, Martínez-Vicente P, Baumann KN, Del Barrio J, Hernández-Ainsa S. Assessing the influence of small structural modifications in simple DNA-based nanostructures on their role as drug nanocarriers. Biomater Sci 2024; 12:1549-1557. [PMID: 38305143 DOI: 10.1039/d3bm01987j] [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: 02/03/2024]
Abstract
DNA nanotechnology leverages Watson-Crick-Franklin base-pairing interactions to build complex DNA-based nanostructures (DNS). Due to DNA specific self-assembly properties, DNS can be designed with a total control of their architecture, which has been demonstrated to have an impact on the overall DNS features. Indeed, structural properties such as the shape, size and flexibility of DNS can influence their biostability as well as their ability to internalise into cells. We present here two series of simple DNS with small and precise variations related to their length or flexibility and study the influence that these structural changes have on their overall properties as drug nanocarriers. Results indicate that shorter and more flexible DNS present higher stability towards nuclease degradation. These structural changes also have a certain effect on their cell internalisation ability and drug release rate. Consequently, drug-loaded DNS cytotoxicity varies according to the design, with lower cell viability values obtained in the DNS exhibiting faster drug release and larger cell interaction rates. In summary, small changes in the structure of simple DNS can have an influence on their overall capabilities as drug nanocarriers. The effects reported here could guide the design of simple DNS for future therapeutic uses.
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Affiliation(s)
- Alejandro Postigo
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
| | - Pablo Martínez-Vicente
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
| | | | - Jesús Del Barrio
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
| | - Silvia Hernández-Ainsa
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
- ARAID Foundation, Government of Aragon, Zaragoza 50018, Spain
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9
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He S, Deng H, Li P, Tian Q, Yang Y, Hu J, Li H, Zhao T, Ling H, Liu Y, Liu S, Guo Q. Bimodal DNA self-origami material with nucleic acid function enhancement. J Nanobiotechnology 2024; 22:39. [PMID: 38279115 PMCID: PMC10821560 DOI: 10.1186/s12951-024-02296-9] [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: 10/12/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND The design of DNA materials with specific nanostructures for biomedical tissue engineering applications remains a challenge. High-dimensional DNA nanomaterials are difficult to prepare and are unstable; moreover, their synthesis relies on heavy metal ions. Herein, we developed a bimodal DNA self-origami material with good biocompatibility and differing functions using a simple synthesis method. We simulated and characterized this material using a combination of oxDNA, freeze-fracture electron microscopy, and atomic force microscopy. Subsequently, we optimized the synthesis procedure to fix the morphology of this material. RESULTS Using molecular dynamics simulation, we found that the bimodal DNA self-origami material exhibited properties of spontaneous stretching and curling and could be fixed in a single morphology via synthesis control. The application of different functional nucleic acids enabled the achievement of various biological functions, and the performance of functional nucleic acids was significantly enhanced in the material. Consequently, leveraging the various functional nucleic acids enhanced by this material will facilitate the attainment of diverse biological functions. CONCLUSION The developed design can comprehensively reveal the morphology and dynamics of DNA materials. We thus report a novel strategy for the construction of high-dimensional DNA materials and the application of functional nucleic acid-enhancing materials.
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Affiliation(s)
- Songlin He
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Haotian Deng
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Peiqi Li
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Qinyu Tian
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Yongkang Yang
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jingjing Hu
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
- Department of Gastroenterology, the Second Medical Center and National Clinical Research Center of Geriatric Diseases, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Hao Li
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Tianyuan Zhao
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Hongkun Ling
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin, 300071, China.
- Nankai University Eye Institute, Nankai University, Tianjin, 300071, China.
| | - Shuyun Liu
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China.
- School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Quanyi Guo
- Institute of Orthopedics, First Medical Center, Chinese PLA General Hospital; Beijing Key Laboratory of Regenerative Medicine in Orthopedics; Key Laboratory of Musculoskeletal Trauma and War Injuries PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China.
- School of Medicine, Nankai University, Tianjin, 300071, China.
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10
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Teodori L, Omer M, Kjems J. RNA nanostructures for targeted drug delivery and imaging. RNA Biol 2024; 21:1-19. [PMID: 38555519 PMCID: PMC10984137 DOI: 10.1080/15476286.2024.2328440] [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] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
The RNA molecule plays a pivotal role in many biological processes by relaying genetic information, regulating gene expression, and serving as molecular machines and catalyzers. This inherent versatility of RNA has fueled significant advancements in the field of RNA nanotechnology, driving the engineering of complex nanoscale architectures toward biomedical applications, including targeted drug delivery and bioimaging. RNA polymers, serving as building blocks, offer programmability and predictability of Watson-Crick base pairing, as well as non-canonical base pairing, for the construction of nanostructures with high precision and stoichiometry. Leveraging the ease of chemical modifications to protect the RNA from degradation, researchers have developed highly functional and biocompatible RNA architectures and integrated them into preclinical studies for the delivery of payloads and imaging agents. This review offers an educational introduction to the use of RNA as a biopolymer in the design of multifunctional nanostructures applied to targeted delivery in vivo, summarizing physical and biological barriers along with strategies to overcome them. Furthermore, we highlight the most recent progress in the development of both small and larger RNA nanostructures, with a particular focus on imaging reagents and targeted cancer therapeutics in pre-clinical models and provide insights into the prospects of this rapidly evolving field.
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Affiliation(s)
- Laura Teodori
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
| | - Marjan Omer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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11
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Yu L, Xu Y, Al-Amin M, Jiang S, Sample M, Prasad A, Stephanopoulos N, Šulc P, Yan H. CytoDirect: A Nucleic Acid Nanodevice for Specific and Efficient Delivery of Functional Payloads to the Cytoplasm. J Am Chem Soc 2023; 145:27336-27347. [PMID: 38055928 PMCID: PMC10789493 DOI: 10.1021/jacs.3c07491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Direct and efficient delivery of functional payloads such as chemotherapy drugs, siRNA, or small-molecule inhibitors into the cytoplasm, bypassing the endo/lysosomal trapping, is a challenging task for intracellular medicine. Here, we take advantage of the programmability of DNA nanotechnology to develop a DNA nanodevice called CytoDirect, which incorporates disulfide units and human epidermal growth factor receptor 2 (HER2) affibodies into a DNA origami nanostructure, enabling rapid cytosolic uptake into targeted cancer cells and deep tissue penetration. We further demonstrated that therapeutic oligonucleotides and small-molecule chemotherapy drugs can be easily delivered by CytoDirect and showed notable effects on gene knockdown and cell apoptosis, respectively. This study demonstrates the synergistic effect of disulfide and HER2 affibody modifications on the rapid cytosolic delivery of DNA origami and its payloads to targeted cells and deep tissues, thereby expanding the delivery capabilities of DNA nanostructures in a new direction for disease treatment.
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Affiliation(s)
- Lu Yu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Yang Xu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Md Al-Amin
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Shuoxing Jiang
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Matthew Sample
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Abhay Prasad
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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12
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Yang GQ, Cai W, Zhang Z, Wang Y. Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System. ACS APPLIED BIO MATERIALS 2023; 6:5125-5144. [PMID: 38011318 DOI: 10.1021/acsabm.3c00636] [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: 11/29/2023]
Abstract
Every year cancer causes approximately 10 million deaths globally. Researchers have developed numerous targeted drug delivery systems (DDSs) with nanoparticles, polymers, and liposomes, but these synthetic materials have poor degradability and low biocompatibility. Because DNA nanostructures have good degradability and high biocompatibility, extensive studies have been performed to construct DDSs with DNA nanostructures as the molecular-layer master frame (MF) assembled via programmable DNA-aided self-assembly for targeted drug release. To learn the progressing trend of self-assembly techniques and keep pace with their recent rapid advancements, it is crucial to provide an overview of their past and recent progress. In this review article, we first present the techniques to assemble the MF of a DDS with solely DNA strands; to assemble MFs with one or more additional type of construction materials, e.g., polymers (including RNA and protein), inorganic nanoparticle, or metal ions, in addition to DNA strands; and to assemble the more complex DNA nanocomplexes. It is observed that both the techniques used and the MFs constructed have become increasingly complex and that the DDS constructed has an increasing number of advanced functions. From our focused review, we anticipate that DDSs with the MF of multiple building materials and DNA nanocomplexes will attract an increasing number of researchers' interests. On the basis of knowledge about materials and functional components (e.g., targeting aptamers/peptides/antibodies and stimuli for drug release) obtained from previously performed studies, researchers can combine more materials with DNA strands to assemble more powerful MFs and incorporate more components to endow DDSs with improved or additional properties/functions, thereby subsequently contributing to cancer prevention.
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Affiliation(s)
- Gary Q Yang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Weibin Cai
- School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083, P. R. China
| | - Zhiwen Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Yujun Wang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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13
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Kim JE, Kang JH, Kwon WH, Lee I, Park SJ, Kim CH, Jeong WJ, Choi JS, Kim K. Self-assembling biomolecules for biosensor applications. Biomater Res 2023; 27:127. [PMID: 38053161 PMCID: PMC10696764 DOI: 10.1186/s40824-023-00466-8] [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: 10/01/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
Molecular self-assembly has received considerable attention in biomedical fields as a simple and effective method for developing biomolecular nanostructures. Self-assembled nanostructures can exhibit high binding affinity and selectivity by displaying multiple ligands/receptors on their surface. In addition, the use of supramolecular structure change upon binding is an intriguing approach to generate binding signal. Therefore, many self-assembled nanostructure-based biosensors have been developed over the past decades, using various biomolecules (e.g., peptides, DNA, RNA, lipids) and their combinations with non-biological substances. In this review, we provide an overview of recent developments in the design and fabrication of self-assembling biomolecules for biosensing. Furthermore, we discuss representative electrochemical biosensing platforms which convert the biochemical reactions of those biomolecules into electrical signals (e.g., voltage, ampere, potential difference, impedance) to contribute to detect targets. This paper also highlights the successful outcomes of self-assembling biomolecules in biosensor applications and discusses the challenges that this promising technology needs to overcome for more widespread use.
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Affiliation(s)
- Ji-Eun Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jeon Hyeong Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Woo Hyun Kwon
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Inseo Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Sang Jun Park
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Chun-Ho Kim
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
- Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea.
| | - Jun Shik Choi
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea.
| | - Kyobum Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea.
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14
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McCarthy DR, Remington JM, Ferrell JB, Schneebeli ST, Li J. Nano-Bio Interactions between DNA Nanocages and Human Serum Albumin. J Chem Theory Comput 2023; 19:7873-7881. [PMID: 37877553 PMCID: PMC11070245 DOI: 10.1021/acs.jctc.3c00720] [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] [Indexed: 10/26/2023]
Abstract
DNA nanostructures have emerged as promising nanomedical tools due to their biocompatibility and tunable behavior. Recent work has shown that DNA nanocages decorated with organic dendrimers strongly bind human serum albumin (HSA), yet the dynamic structures of these complexes remain uncharacterized. This theoretical and computational investigation elucidates the fuzzy interactions between dendritically functionalized cubic DNA nanocages and HSA. The dendrimer-HSA interactions occur via nonspecific binding with the protein thermodynamically and kinetically free to cross the open faces of the cubic scaffold. However, the rigidity of the DNA scaffold prevents the binding energetics from scaling with the number of dendrimers. These discoveries not only provide a useful framework by which to model general interactions of DNA nanostructures complexed with serum proteins but also give valuable molecular insight into the design of next-generation DNA nanomedicines.
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Affiliation(s)
| | | | | | - Severin T. Schneebeli
- Department of Chemistry, University of Vermont, Burlington, VT 05405
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT 05405
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
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15
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Zhao Y, Li S, Feng M, Zhang M, Liu Z, Yao Y, Zhang T, Jiang Y, Lin Y, Cai X. Effects of Puerarin-Loaded Tetrahedral Framework Nucleic Acids on Osteonecrosis of the Femoral Head. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302326. [PMID: 37317020 DOI: 10.1002/smll.202302326] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/30/2023] [Indexed: 06/16/2023]
Abstract
Osteonecrosis of the femoral head (ONFH) is recognized as a common refractory orthopedic disease that causes severe pain and poor quality of life in patients. Puerarin (Pue), a natural isoflavone glycoside, can promote osteogenesis and inhibit apoptosis of bone mesenchymal stem cells (BMSCs), demonstrating its great potential in the treatment of osteonecrosis. However, its low aqueous solubility, fast degradation in vivo, and inadequate bioavailability, limit its clinical application and therapeutic efficacy. Tetrahedral framework nucleic acids (tFNAs) are promising novel DNA nanomaterials in drug delivery. In this study, tFNAs as Pue carriers is used and synthesized a tFNA/Pue complex (TPC) that exhibited better stability, biocompatibility, and tissue utilization than free Pue. A dexamethasone (DEX)-treated BMSC model in vitro and a methylprednisolone (MPS)-induced ONFH model in vivo is also established, to explore the regulatory effects of TPC on osteogenesis and apoptosis of BMSCs. This findings showed that TPC can restore osteogenesis dysfunction and attenuated BMSC apoptosis induced by high-dose glucocorticoids (GCs) through the hedgehog and Akt/Bcl-2 pathways, contributing to the prevention of GC-induced ONFH in rats. Thus, TPC is a promising drug for the treatment of ONFH and other osteogenesis-related diseases.
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Affiliation(s)
- Yuxuan Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Maogeng Feng
- The Affiliated Stomatological Hospital of Southwest Medical University, Luzhou, 646000, P. R. China
| | - Mei Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Zhiqiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yangxue Yao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Tianxu Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yueying Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
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16
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Zhang Y, Tian X, Wang Z, Wang H, Liu F, Long Q, Jiang S. Advanced applications of DNA nanostructures dominated by DNA origami in antitumor drug delivery. Front Mol Biosci 2023; 10:1239952. [PMID: 37609372 PMCID: PMC10440542 DOI: 10.3389/fmolb.2023.1239952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
DNA origami is a cutting-edge DNA self-assembly technique that neatly folds DNA strands and creates specific structures based on the complementary base pairing principle. These innovative DNA origami nanostructures provide numerous benefits, including lower biotoxicity, increased stability, and superior adaptability, making them an excellent choice for transporting anti-tumor agents. Furthermore, they can considerably reduce side effects and improve therapy success by offering precise, targeted, and multifunctional drug delivery system. This comprehensive review looks into the principles and design strategies of DNA origami, providing valuable insights into this technology's latest research achievements and development trends in the field of anti-tumor drug delivery. Additionally, we review the key function and major benefits of DNA origami in cancer treatment, some of these approaches also involve aspects related to DNA tetrahedra, aiming to provide novel ideas and effective solutions to address drug delivery challenges in cancer therapy.
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Affiliation(s)
- Yiming Zhang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Zijian Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Haochen Wang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Qipeng Long
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
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17
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Oktay E, Bush J, Vargas M, Scarton DV, O'Shea B, Hartman A, Green CM, Neyra K, Gomes CM, Medintz IL, Mathur D, Veneziano R. Customized Scaffolds for Direct Assembly of Functionalized DNA Origami. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37267624 DOI: 10.1021/acsami.3c05690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Functional DNA origami nanoparticles (DNA-NPs) are used as nanocarriers in a variety of biomedical applications including targeted drug delivery and vaccine development. DNA-NPs can be designed into a broad range of nanoarchitectures in one, two, and three dimensions with high structural fidelity. Moreover, the addressability of the DNA-NPs enables the precise organization of functional moieties, which improves targeting, actuation, and stability. DNA-NPs are usually functionalized via chemically modified staple strands, which can be further conjugated with additional polymers and proteins for the intended application. Although this method of functionalization is extremely efficient to control the stoichiometry and organization of functional moieties, fewer than half of the permissible sites are accessible through staple modifications. In addition, DNA-NP functionalization rapidly becomes expensive when a high number of functionalizations such as fluorophores for tracking and chemical modifications for stability that do not require spatially precise organization are used. To facilitate the synthesis of functional DNA-NPs, we propose a simple and robust strategy based on an asymmetric polymerase chain reaction (aPCR) protocol that allows direct synthesis of custom-length scaffolds that can be randomly modified and/or precisely modified via sequence design. We demonstrated the potential of our strategy by producing and characterizing heavily modified scaffold strands with amine groups for dye functionalization, phosphorothioate bonds for stability, and biotin for surface immobilization. We further validated our sequence design approach for precise conjugation of biomolecules by synthetizing scaffolds including binding loops and aptamer sequences that can be used for direct hybridization of nucleic acid tagged biomolecules or binding of protein targets.
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Affiliation(s)
- Esra Oktay
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Joshua Bush
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Merlyn Vargas
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Dylan Valerio Scarton
- College of Science, Interdisciplinary Program in Neuroscience, George Mason University, Fairfax, Virginia 22030-4444, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Bailey O'Shea
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Amber Hartman
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Carolina M Gomes
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington DC 20375-0001, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078, United States
| | - Remi Veneziano
- College of Engineering and Computing, Department of Bioengineering, George Mason University, Manassas, Virginia 20110-2201, United States
- Institute for Advanced Biomedical Research, Manassas, Virginia 20110-2201, United States
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18
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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19
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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20
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Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y, Zhang Z, Ding J, Shi S. Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 2023; 13:916-941. [PMID: 36970219 PMCID: PMC10031267 DOI: 10.1016/j.apsb.2022.10.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.
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Affiliation(s)
- Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Rujing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kunmeng Yang
- The First Norman Bethune College of Clinical Medicine, Jilin University, Changchun 130061, China
| | - Yuhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yachen Peng
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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21
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Prajapati A, Srivastava A, Sankaranarayanan SA, Pebam M, Buddhiraju HS, Patra P, Yadav P, Joshi H, Rengan AK. High-Affinity DNA Nanomatrix: A Platform Technology for Synergistic Drug Delivery and Photothermal Therapy. ACS Macro Lett 2023; 12:255-262. [PMID: 36723076 DOI: 10.1021/acsmacrolett.2c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With the advent of nucleosome/nucleotide intercalating drugs, DNA-based nanocarriers have recently gained impetus. However, most of the newly proposed DNA nanosystems are rather complex, thereby having low scalability and translatability. In this study, we propose a simple DNA nanomatrix core encapsulated within a chitosan shell, which is expected to enhance the encapsulation efficiency of intercalating drugs. This has been demonstrated using proflavine hemisulfate (PfHS), a model intercalating agent that shows improved ROS generation, among other anticancerous properties. The release of the drug from the nanomatrix is triggered by providing a heat trigger using IR-792 perchlorate, a known NIR photothermal sensitizer.
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Affiliation(s)
- Akshit Prajapati
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Aditya Srivastava
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Sri Amruthaa Sankaranarayanan
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Monika Pebam
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Hima Sree Buddhiraju
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Paloma Patra
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Priyanka Yadav
- Department of Biotechnology, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Himanshu Joshi
- Department of Biotechnology, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Aravind Kumar Rengan
- Department of Biomedical Engineering, Indian institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502284, India
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22
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Cao M, Vial A, Minder L, Guédin A, Fribourg S, Azéma L, Feuillie C, Molinari M, Di Primo C, Barthélémy P, Jeanne LC. Aptamer-based nanotrains and nanoflowers as quinine delivery systems. Int J Pharm X 2023; 5:100172. [PMID: 36861067 PMCID: PMC9969250 DOI: 10.1016/j.ijpx.2023.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
In this study, we designed aptamer-based self-assemblies for the delivery of quinine. Two different architectures were designed by hybridizing quinine binding aptamers and aptamers targeting Plasmodium falciparum lactate dehydrogenase (PfLDH): nanotrains and nanoflowers. Nanotrains consisted in controlled assembly of quinine binding aptamers through base-pairing linkers. Nanoflowers were larger assemblies obtained by Rolling Cycle Amplification of a quinine binding aptamer template. Self-assembly was confirmed by PAGE, AFM and cryoSEM. The nanotrains preserved their affinity for quinine and exhibited a higher drug selectivity than nanoflowers. Both demonstrated serum stability, hemocompatibility, low cytotoxicity or caspase activity but nanotrains were better tolerated than nanoflowers in the presence of quinine. Flanked with locomotive aptamers, the nanotrains maintained their targeting ability to the protein PfLDH as analyzed by EMSA and SPR experiments. To summarize, nanoflowers were large assemblies with high drug loading ability, but their gelating and aggregating properties prevent from precise characterization and impaired the cell viability in the presence of quinine. On the other hand, nanotrains were assembled in a selective way. They retain their affinity and specificity for the drug quinine, and their safety profile as well as their targeting ability hold promise for their use as drug delivery systems.
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Affiliation(s)
- Mengyuan Cao
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France,Corresponding authors.
| | - Anthony Vial
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Laetitia Minder
- Univ. Bordeaux, INSERM, CNRS, IECB, US001, UAR 3033, Pessac, France
| | - Aurore Guédin
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Laurent Azéma
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Cécile Feuillie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Carmelo Di Primo
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Leblond Chain Jeanne
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France,Corresponding authors.
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23
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Cao M, Vial A, Minder L, Guédin A, Fribourg S, Azéma L, Feuillie C, Molinari M, Di Primo C, Barthélémy P, Leblond Chain J. WITHDRAWN: Aptamer-based nanotrains and nanoflowers as quinine delivery systems. Int J Pharm 2023; 632:122552. [PMID: 36587777 DOI: 10.1016/j.ijpharm.2022.122552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022]
Abstract
This article has been withdrawn: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been withdrawn at the request of the author, editor and publisher. The publisher regrets that an error occurred during the publication of this paper, which was intended to be published in International Journal of Pharmaceutics: X (not International Journal of Pharmaceutics). This error bears no reflection on the scientific content of this article or its authors. The publisher apologizes to the readers for this unfortunate error.
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Affiliation(s)
- Mengyuan Cao
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Anthony Vial
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Laetitia Minder
- Univ. Bordeaux, INSERM, CNRS, IECB, US001, UAR 3033, Pessac, France
| | - Aurore Guédin
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Laurent Azéma
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Cécile Feuillie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Carmelo Di Primo
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
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24
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Tian T, Zhang T, Shi S, Gao Y, Cai X, Lin Y. A dynamic DNA tetrahedron framework for active targeting. Nat Protoc 2023; 18:1028-1055. [PMID: 36670289 DOI: 10.1038/s41596-022-00791-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/03/2022] [Indexed: 01/22/2023]
Abstract
An active targeting strategy-enabled DNA tetrahedron delivery vehicle could facilitate stable drug encapsulation and stimuli-responsive on-demand release, building a universal platform for different drug delivery requirements. Owing to the excellent biocompatible nature, programmability and remarkable cell and tissue permeability, the tetrahedral DNA nanostructure (TDN) has proven its value in the delivery of various bioactive molecules. We previously described this as a static multifunctional complex in our earlier protocol. However, static structures and passive targeting behavior might introduce off-target effects under complicated biological conditions. Therefore, in this Protocol Extension, we present a major update of the TDN delivery vehicle enabling an active targeting strategy to be used for stimuli-sensitive conformation changes and on-site cargo release, which could avoid drawbacks, including complex and time-consuming fabrication processes and undetermined cell penetration ability of other DNA-based delivery vehicles. Upon exquisite design of TDN size based on cargo type, one-pot annealing is applied to fabricate the Tiamat-designed TDN exoskeleton. Then the design of the dynamic DNA apparatus can be based on the target and environmental stimuli, including DNA strand hybridization-based and pH-sensitive DNA apparatus, and careful titration of strand lengths and mismatches is achieved using polyacrylamide and agarose gel electrophoresis, or fluorophore modifications. Finally, cargo loading strategies are designed, including site and stand titration and cargo encapsulation verification. The dynamic structures show promising targetability and effectiveness in antitumor and anti-inflammatory treatment in vitro and in vivo. Assembly and characterization in the lab takes ~5 d, and the timing for the verification of biostability and biological applications depends on the uses.
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Affiliation(s)
- Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yang Gao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
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25
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Chandrasekaran AR. DNA nanotechnology in the undergraduate laboratory: Electrophoretic analysis of DNA nanostructure biostability. JOURNAL OF CHEMICAL EDUCATION 2023; 100:316-320. [PMID: 37193549 PMCID: PMC10168010 DOI: 10.1021/acs.jchemed.2c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The field of DNA nanotechnology has grown rapidly in the last decade and has expanded to multiple laboratories. While lectures in DNA nanotechnology have been introduced in some institutions, laboratory components at the undergraduate level are still lacking. Undergraduate students predominantly learn about DNA nanotechnology through their involvement as interns in research laboratories. The DNA nanostructure biostability analysis experiment presented here can be used as a hands-on introductory laboratory exercise for discussing concepts in DNA nanotechnology in an undergraduate setting. This experiment discusses biostability, gel electrophoresis and quantitative analysis of nuclease degradation of a model DNA nanostructure, the paranemic crossover (PX) DNA motif. The experiment can be performed in a chemistry, biology or a biochemistry laboratory with minimal costs and can be adapted in undergraduate institutions using the instructor and student manuals provided here. Laboratory courses based on cutting edge research not only provide students a direct hands-on approach to the subject, but can also increase undergraduate student participation in research. Moreover, laboratory courses that reflect the increasingly multidisciplinary nature of research add value to undergraduate education.
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26
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A Biophysical Study of DNA Condensation Mediated by Histones and Protamines. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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28
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Programmable Assembly of Multivalent DNA‐Protein Superstructures for Tumor Imaging and Targeted Therapy. Angew Chem Int Ed Engl 2022; 61:e202211505. [DOI: 10.1002/anie.202211505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/07/2022]
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29
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Xu Z, Shi T, Mo F, Yu W, Shen Y, Jiang Q, Wang F, Liu X. Programmable Assembly of Multivalent DNA‐Protein Superstructures for Tumor Imaging and Targeted Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhen Xu
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Tianhui Shi
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Fengye Mo
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Wenqian Yu
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Yu Shen
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Qunying Jiang
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Fuan Wang
- Wuhan University College of Chemistry and Molecular Sciences 430072 Wuhan City CHINA
| | - Xiaoqing Liu
- Wuhan University College of Chemistry and Molecular Sciences No. 299 Bayi Road, Wuchang District 430072 Wuhan CHINA
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30
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Li S, Liu Y, Zhang T, Lin S, Shi S, He J, Xie Y, Cai X, Tian T, Lin Y. A Tetrahedral Framework DNA-Based Bioswitchable miRNA Inhibitor Delivery System: Application to Skin Anti-Aging. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204287. [PMID: 35901292 DOI: 10.1002/adma.202204287] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/21/2022] [Indexed: 02/05/2023]
Abstract
MicroRNA (miR)-based therapy shows strong potential; however, structural limitations pose a challenge in fully exploiting its biomedical functionality. Tetrahedral framework DNA (tFNA) has proven to be an ideal vehicle for miR therapy. Inspired by the ancient Chinese myth "Sun and Immortal Birds," a novel bioswitchable miR inhibitor delivery system (BiRDS) is designed with three miR inhibitors (the three immortal birds) and a nucleic acid core (the central sun). The BiRDS fuses miR inhibitors within the framework, maximizing their loading capacity, while allowing the system to retain the characteristics of small-sized tFNA and avoiding uncertainty associated with RNA exposure in traditional loading protocols. The RNase H-responsive sequence at the tail of each "immortal bird" enables the BiRDS to transform from a 3D to a 2D structure upon entering cells, promoting the delivery of miR inhibitors. To confirm the application potential, the BiRDS is used to deliver the miR-31 inhibitor, with antiaging effects on hair follicle stem cells, into a skin aging model. Superior skin penetration ability and RNA delivery are observed with significant anti-aging effects. These findings demonstrate the capability and editability of the BiRDS to improve the stability and delivery efficacy of miRs for future innovations.
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Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yuhao Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shiyu Lin
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiajun He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
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31
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Baumann KN, Schröder T, Ciryam PS, Morzy D, Tinnefeld P, Knowles TPJ, Hernández-Ainsa S. DNA-Liposome Hybrid Carriers for Triggered Cargo Release. ACS APPLIED BIO MATERIALS 2022; 5:3713-3721. [PMID: 35838663 PMCID: PMC9382633 DOI: 10.1021/acsabm.2c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
The design of simple and versatile synthetic routes to
accomplish
triggered-release properties in carriers is of particular interest
for drug delivery purposes. In this context, the programmability and
adaptability of DNA nanoarchitectures in combination with liposomes
have great potential to render biocompatible hybrid carriers for triggered
cargo release. We present an approach to form a DNA mesh on large
unilamellar liposomes incorporating a stimuli-responsive DNA building
block. Upon incubation with a single-stranded DNA trigger sequence,
a hairpin closes, and the DNA building block is allowed to self-contract.
We demonstrate the actuation of this building block by single-molecule
Förster resonance energy transfer (FRET), fluorescence recovery
after photobleaching, and fluorescence quenching measurements. By
triggering this process, we demonstrate the elevated release of the
dye calcein from the DNA–liposome hybrid carriers. Interestingly,
the incubation of the doxorubicin-laden active hybrid carrier with
HEK293T cells suggests increased cytotoxicity relative to a control
carrier without the triggered-release mechanism. In the future, the
trigger could be provided by peritumoral nucleic acid sequences and
lead to site-selective release of encapsulated chemotherapeutics.
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Affiliation(s)
- Kevin N Baumann
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Prashanth S Ciryam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Diana Morzy
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Silvia Hernández-Ainsa
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.,Government of Aragon, ARAID Foundation, Zaragoza 50018, Spain
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32
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Scalable purification of single stranded DNA scaffolds for biomanufacturing DNA-origami nanostructures: exploring anion-exchange and multimodal chromatography. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Luo D, Lin X, Zhao Y, Hu J, Mo F, Song G, Zou Z, Wang F, Liu X. A dynamic DNA nanosponge for triggered amplification of gene-photodynamic modulation. Chem Sci 2022; 13:5155-5163. [PMID: 35655573 PMCID: PMC9093187 DOI: 10.1039/d2sc00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/18/2022] [Indexed: 12/19/2022] Open
Abstract
Nucleic acid therapeutics has reached clinical utility through modulating gene expression. As a potential oligonucleotide drug, DNAzyme has RNA-cleaving activity for gene silencing, but faces challenges due to the lack of a safe and effective delivery vehicle and low in vivo catalytic activity. Here we describe DNAzyme-mediated gene regulation using dynamic DNA nanomaterials with intrinsic biocompatibility, stability, tumor-targeted delivery and uptake, and self-enhanced efficacy. We assemble programmable DNA nanosponges to package and deliver diverse nucleic acid drugs and therapeutic agents such as aptamer, DNAzyme and its cofactor precursor, and photosensitizer in one pot through the rolling circle amplification reaction, formulating a controllable nanomedicine using encoded instructions. Upon environmental stimuli, DNAzyme activity increases and RNA cleavage accelerates by a supplementary catalytic cofactor. In addition, this approach induces elevated O2 and 1O2 generation as auxiliary treatment, achieving simultaneously self-enhanced gene-photodynamic cancer therapy. These findings may advance the clinical trial of oligonucleotide drugs as tools for gene modulation.
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Affiliation(s)
- Dan Luo
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Xue Lin
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Yun Zhao
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Jialing Hu
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Fengye Mo
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Gege Song
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Zhiqiao Zou
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University 430072 Wuhan P. R. China
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34
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Wu Q, Yang L, Xie L, Shang J, He S, Liu J, Wang F. Modular Assembly of a Concatenated DNA Circuit for In Vivo Amplified Aptasensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200983. [PMID: 35460185 DOI: 10.1002/smll.202200983] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Probing endogenous molecular profiles in living entities is of fundamental significance to decipher biological functions and exploit novel theranostics. Despite programmable nucleic acid-based aptasensing systems across the breadth of molecular imaging, an aptasensing system enabling in vivo imaging with high sensitivity, accuracy, and adaptability is highly required yet is still in its infancy. Artificial catalytic DNA circuits that can modularly integrate to generate multiple outputs from a single input in an isothermal autonomous manner, have supplemented powerful toolkits for intracellular biosensing research. Herein, a multilayer nonenzymatic catalytic DNA circuits-based aptasensing system is devised for in situ imaging of a bioactive molecule in living mice by assembling branched DNA copolymers with high-molecular-weight and high-signal-gain based on avalanche-mimicking hybridization chain reactions (HCRs). The HCRs aptasensing circuit performs as a general and powerful sensing platform for precise analysis of a series of bioactive molecules due to its inherent rich recognition repertoire and hierarchical reaction accelerations. With tumor-targeting capsule encapsulation, the HCRs aptasensing circuit is specifically delivered into tumor cells and allowed the high-contrast imaging of intracellular adenosine triphosphate in living mice, highlighting its potential for visualizing these clinically important biomolecules and for studying the associated physiological processes.
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Affiliation(s)
- Qiong Wu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Medical College, Wuhan University of Science and Technology, Wuhan, 430065, P. R. China
| | - Lei Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Lingling Xie
- Medical College, Wuhan University of Science and Technology, Wuhan, 430065, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Shizhen He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Jing Liu
- Department of Gastroenterology, Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan, 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
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Asakiya C, Zhu L, Yuhan J, Zhu L, Huang K, Xu W. Current progress of miRNA-derivative nucleotide drugs: Modifications, delivery systems, applications. Expert Opin Drug Deliv 2022; 19:435-450. [PMID: 35387533 DOI: 10.1080/17425247.2022.2063835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION miRNA-derivative clinical nucleotide drugs (mdCNDs) effectively treat several diseases, with numerous undergoing clinical trials. In early-stage trials in disease therapeutics such as malignant pleural mesothelioma and hepatic virus C infection, mdCND's therapeutic potency is undeniably good for effectiveness and safety. AREAS COVERED 15 mdCNDs undergoing clinical trials are introduced in this review. MiRNA modifications methods have been summarized including phosphorothioate, cholesterol, locked nucleic acid, 2'-O-methyl, N,N-diethyl-4-(4-nitronaphthalen1-ylazo)-phenylamine modifications and many more. Moreover, delivery systems, including self-assembled, inorganic ions nanoparticles, exosomes, and lipid-based nanosystems for mdCNDs targeted delivery, are presented. Among that, EnGeneIC, N-Acetylgalactosamine, liposomal nanoparticles, and cholesterol-conjugated for mdCNDs delivery are currently undergoing clinical trials. The pH, light, temperature, redox-responsive, enzyme, and specific-substance modes to trigger the release of miRNAs to target sites on-demand and the prospects of mdCNDs are discussed in this review. EXPERT OPINION mdNCDs are one type of promising clinical drugs, however, it is still in the infancy. During the development process, it is imperative to advance in modifying miRNAs, especially at the 5'-end, to enhance targetability and stability against nucleases, develop a stimuli-responsive mode to control the release of mdCNDs to tissue cell-type-specific sites.
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Affiliation(s)
- Charles Asakiya
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jieyu Yuhan
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA. CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Res 2022; 50:1256-1268. [PMID: 35104875 PMCID: PMC8860605 DOI: 10.1093/nar/gkac049] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/22/2022] Open
Abstract
DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.
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Affiliation(s)
- Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wolfgang G Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Brian R Shy
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mohammad Saffari Doost
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Evelyn Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vivasvan S Vykunta
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jennifer R Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diana M Lopez
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Cindy R Sandoval Espinoza
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexander E Deyanov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel J Lew
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Michael G Poirer
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Alexander Marson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley 94720, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA
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Chen L, Zhang J, Lin Z, Zhang Z, Mao M, Wu J, Li Q, Zhang Y, Fan C. Pharmaceutical applications of framework nucleic acids. Acta Pharm Sin B 2022; 12:76-91. [PMID: 35127373 PMCID: PMC8799870 DOI: 10.1016/j.apsb.2021.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/08/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023] Open
Abstract
DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.
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Affiliation(s)
- Liang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhun Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziyan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Miao Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiacheng Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, 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
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuanqing Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, 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
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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Chen K, Zhang Y, Zhu L, Chu H, Huang K, Shao X, Asakiya C, Huang K, Xu W. Insights into nucleic acid-based self-assembling nanocarriers for targeted drug delivery and controlled drug release. J Control Release 2021; 341:869-891. [PMID: 34952045 DOI: 10.1016/j.jconrel.2021.12.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022]
Abstract
Over the past few decades, rapid advances of nucleic acid nanotechnology always drive the development of nanoassemblies with programmable design, powerful functionality, excellent biocompatibility and outstanding biosafety. Nowadays, nucleic acid-based self-assembling nanocarriers (NASNs) play an increasingly greater role in the research and development in biomedical studies, particularly in drug delivery, release and targeting. In this review, NASNs are systematically summarized the strategies cooperated with their broad applications in drug delivery. We first discuss the self-assembling methods of nanocarriers comprised of DNA, RNA and composite materials, and summarize various categories of targeting media, including aptamers, small molecule ligands and proteins. Furthermore, drug release strategies by smart-responding multiple kinds of stimuli are explained, and various applications of NASNs in drug delivery are discussed, including protein drugs, nucleic acid drugs, small molecule drugs and nanodrugs. Lastly, we propose limitations and potential of NASNs in the future development, and expect that NASNs enable facilitate the development of new-generation drug vectors to assist in solving the growing demands on disease diagnosis and therapy or other biomedicine-related applications in the real world.
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Affiliation(s)
- Keren Chen
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Yangzi Zhang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Longjiao Zhu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Huashuo Chu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Xiangli Shao
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Charles Asakiya
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China.
| | - Wentao Xu
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17, Qinghua East Road, Beijing 100083, China.
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Zhou L, Hayden A, Chandrasekaran AR, Vilcapoma J, Cavaliere C, Dey P, Mao S, Sheng J, Dey BK, Rangan P, Halvorsen K. Sequence-selective purification of biological RNAs using DNA nanoswitches. CELL REPORTS METHODS 2021; 1:100126. [PMID: 35072148 PMCID: PMC8782281 DOI: 10.1016/j.crmeth.2021.100126] [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] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/07/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022]
Abstract
Nucleic acid purification is a critical aspect of biomedical research and a multibillion-dollar industry. Here we establish sequence-selective RNA capture, release, and isolation using conformationally responsive DNA nanoswitches. We validate purification of specific RNAs ranging in size from 22 to 401 nt with up to 75% recovery and 99.98% purity in a benchtop process with minimal expense and equipment. Our method compared favorably with bead-based extraction of an endogenous microRNA from cellular total RNA, and can be programmed for multiplexed purification of multiple individual RNA targets from one sample. Coupling our approach with downstream LC/MS, we analyzed RNA modifications in 5.8S ribosomal RNA, and found 2'-O-methylguanosine, 2'-O-methyluridine, and pseudouridine in a ratio of ~1:7:22. The simplicity, low cost, and low sample requirements of our method make it suitable for easy adoption, and the versatility of the approach provides opportunities to expand the strategy to other biomolecules.
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Affiliation(s)
- Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Cassandra Cavaliere
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Song Mao
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Bijan K. Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Prashanth Rangan
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biology, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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40
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Pitz ME, Nukovic AM, Elpers MA, Alexander-Bryant AA. Factors Affecting Secondary and Supramolecular Structures of Self-Assembling Peptide Nanocarriers. Macromol Biosci 2021; 22:e2100347. [PMID: 34800001 DOI: 10.1002/mabi.202100347] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Indexed: 01/12/2023]
Abstract
Self-assembling peptides are a popular vector for therapeutic cargo delivery due to their versatility, tunability, and biocompatibility. Accurately predicting secondary and supramolecular structures of self-assembling peptides is essential for de novo peptide design. However, computational modeling of such assemblies is not yet able to accurately predict structure formation for many peptide sequences. This review identifies patterns in literature between secondary and supramolecular structures, primary sequences, and applications to provide a guide for informed peptide design. An overview of peptide structures, their applications as nanocarriers, and analytical methods for characterizing secondary and supramolecular structure is examined. A top-down approach is then used to identify trends between peptide sequence and assembly structure from the current literature, including an analysis of the drivers at work, such as local and nonlocal sequence effects and solution conditions.
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Affiliation(s)
- Megan E Pitz
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Alexandra M Nukovic
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Margaret A Elpers
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
| | - Angela A Alexander-Bryant
- Department of Bioengineering, 301 Rhodes Research Center, Clemson University, Clemson, SC, 29634-0905, USA
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Fu W, Ma L, Ju Y, Xu J, Li H, Shi S, Zhang T, Zhou R, Zhu J, Xu R, You C, Lin Y. Therapeutic siCCR2 Loaded by Tetrahedral Framework DNA Nanorobotics in Therapy for Intracranial Hemorrhage. ADVANCED FUNCTIONAL MATERIALS 2021. [DOI: 10.1002/adfm.202101435] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Wei Fu
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Lu Ma
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Yan Ju
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Jianguo Xu
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Hao Li
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
| | - Ronghui Zhou
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
| | - Jianwei Zhu
- Department of Neurosurgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu 610072 China
| | - Ruxiang Xu
- Department of Neurosurgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu 610072 China
| | - Chao You
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
- Department of Neurosurgery West China Hospital of Sichuan University China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
- Department of Neurosurgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu 610072 China
- College of Biomedical Engineering Sichuan University Chengdu Sichuan 610041 China
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Hivare P, Rajwar A, Gupta S, Bhatia D. Spatiotemporal Dynamics of Endocytic Pathways Adapted by Small DNA Nanocages in Model Neuroblastoma Cell-Derived Differentiated Neurons. ACS APPLIED BIO MATERIALS 2021; 4:3350-3359. [PMID: 35014420 DOI: 10.1021/acsabm.0c01668] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multiple endocytic pathways operate on the plasma membrane of cells at any moment with diverse but specific cellular functions. Knowledge of uptake of synthetic nanoparticles and ligands with respect to endocytic pathways is crucial to device the appropriate ligands for therapeutic delivery into differentiated neurons for targeting neuronal diseases. We herein explore the mechanisms of cellular uptake of 3D tetrahedral DNA nanocages at different stages of differentiating neurons. We monitored the uptake, kinetics, and dynamics of DNA cages of different geometries, and interestingly we find a specific pattern and adaptability of the uptake of DNA devices with respect to the geometry of the ligand and specific endocytic pathways. We find that tetrahedral DNA nanocages get endocytosed mostly via clathrin-mediated endocytosis in fully mature neurons. This endocytic uptake and intracellular choreography of DNA nanodevices will help us design the smartly targeted biotherapeutics for targeting neuronal disorders.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Anjali Rajwar
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications. Angew Chem Int Ed Engl 2021; 60:6890-6918. [PMID: 31729826 PMCID: PMC9205421 DOI: 10.1002/anie.201909927] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/29/2019] [Indexed: 01/01/2023]
Abstract
Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.
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Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana, Illinois 61801 (USA)
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
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Vázquez-González M, Willner I. Aptamer-Functionalized Micro- and Nanocarriers for Controlled Release. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9520-9541. [PMID: 33395247 DOI: 10.1021/acsami.0c17121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sequence-specific nucleic acids recognizing low-molecular-weight ligands or macromolecules (aptamers) have found growing interest for biomedical applications. The present review article summarizes recent applications of aptamers as stimuli-responsive gating units of drug (or dye)-loaded nano- or microcarriers for controlled and targeted drug release. In the presence of cellular biomarkers, the nano-/microcarriers are unlocked by forming aptamer-ligand complexes. Different aptamer-functinalized nano-/microcarriers are presented, including inorganic nanomaterials, metal-organic framework nanoparticles, and soft materials. The chemistries associated with the preparation of the carriers and the mechanisms to unlock the carriers are discussed. Stimuli-responsive gated drug-loaded micro-/nanocarriers hold great promise as functional sense-and-treat materials for the targeted and selective release of drugs.
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Affiliation(s)
- Margarita Vázquez-González
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Kim N, Kim E, Kim H, Thomas MR, Najer A, Stevens MM. Tumor-Targeting Cholesterol-Decorated DNA Nanoflowers for Intracellular Ratiometric Aptasensing. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007738. [PMID: 33554370 PMCID: PMC7610848 DOI: 10.1002/adma.202007738] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/31/2020] [Indexed: 05/24/2023]
Abstract
Probing endogenous molecular profiles is of fundamental importance to understand cellular function and processes. Despite the promise of programmable nucleic-acid-based aptasensors across the breadth of biomolecular detection, target-responsive aptasensors enabling intracellular detection are as of yet infrequently realized. Several challenges remain, including the difficulties in quantification/normalization of quencher-based intensiometric signals, stability issues of the probe architecture, and complex sensor operations often necessitating extensive structural modeling. Here, the biomimetic crystallization-empowered self-assembly of a tumor-targetable DNA-inorganic hybrid nanocomposite aptasensor is presented, which enables Förster resonance energy transfer (FRET)-based quantitative interpretation of changes in the cellular target abundance. Leveraging the design programmability and high-throughput fabrication of rolling circle amplification-driven DNA nanoarchitecture, this designer platform offers a method to self-assemble a robust nanosensor from a multifunctionality-encoded template that includes a cell-targeting aptamer, a ratiometric aptasensor, and a cholesterol-decorating element. Taking prostate cancer cells and intracellular adenosine triphosphate molecules as a model system, a synergistic effect in the targeted delivery by cholesterol and aptamers, and the feasibility of quantitative intracellular aptasensing are demonstrated. It is envisioned that this approach provides a highly generalizable strategy across wide-ranging target systems toward a biologically deliverable nanosensor that enables quantitative monitoring of the abundance of endogenous biomolecules.
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Affiliation(s)
- Nayoung Kim
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, SW7 2AZ London, UK
| | | | - Hyemin Kim
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, SW7 2AZ London, UK
| | | | - Adrian Najer
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, SW7 2AZ London, UK
| | - Molly M. Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, SW7 2AZ London, UK
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Mollarasouli F, Badilli U, Bakirhan NK, Ozkan SA, Ozkan Y. Advanced DNA nanomachines: Strategies and bioapplications. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2020.102290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Xiao D, Li Y, Tian T, Zhang T, Shi S, Lu B, Gao Y, Qin X, Zhang M, Wei W, Lin Y. Tetrahedral Framework Nucleic Acids Loaded with Aptamer AS1411 for siRNA Delivery and Gene Silencing in Malignant Melanoma. ACS APPLIED MATERIALS & INTERFACES 2021; 13:6109-6118. [PMID: 33497198 DOI: 10.1021/acsami.0c23005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
siRNA is found to effectively knock down the target gene in cells, which is considered a promising strategy for gene therapy. However, the application of siRNA is limited due to its low efficiency of the cellular uptake. Tetrahedral framework nucleic acids (tFNAs) are synthesized by four single-stranded DNAs and show multiple biological functions in recent studies, especially suitable for drug delivery. More than 60% of malignant melanomas are associated with Braf gene mutation, an attractive therapeutic target for RNA interference. In this study, we modified anti-Braf siRNA (siBraf) with tFNAs to downregulate the target gene. Meanwhile, we directly incorporated AS1411 (a DNA aptamer) to our nanostructure, which assists tFNAs to improve the cellular uptake efficacy of siBraf significantly. The results indicated that tFNAs-AS1411-siBraf exhibited more potent activity to cleave Braf mRNA than free siBraf. This study may provide a new idea for the combination therapy of siRNA and aptamers via DNA nanomaterials to achieve gene silencing.
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Affiliation(s)
- Dexuan Xiao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yanjing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Tianxu Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Boyao Lu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Yang Gao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Xin Qin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Mei Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China
| | - Wei Wei
- Department of Emergency, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, P. R. China.,College of Biomedical Engineering, Sichuan University, Chengdu 610041, China
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Abstract
DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.
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Affiliation(s)
- Arun Richard Chandrasekaran
- grid.265850.c0000 0001 2151 7947The RNA Institute, University at Albany, State University of New York, Albany, NY USA
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Huang X, Blum NT, Lin J, Shi J, Zhang C, Huang P. Chemotherapeutic drug-DNA hybrid nanostructures for anti-tumor therapy. MATERIALS HORIZONS 2021; 8:78-101. [PMID: 34821291 DOI: 10.1039/d0mh00715c] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Compared to traditional drug delivery systems, DNA nanostructure-based drug delivery systems have several advantages including programmable sequences, precise size and shape, high drug payloads, excellent biocompatibility and biodegradability. To date, a wide range of chemotherapeutic drug-DNA hybrid nanostructures have been developed for anti-tumor therapy. In this review, the constructions of various DNA nanostructures for anticancer drug delivery are firstly summarized. Next, the anticancer drug loading methods for DNA nanostructures are presented. Then, the recent applications of chemotherapeutic drug-DNA hybrid nanostructures for drug delivery are highlighted. In the end, the challenges and opportunities of the chemotherapeutic drug-DNA hybrid nanostructure-based delivery system are discussed. The designs of drug-DNA hybrid systems, including the constructions of nanostructures and the strategies for drug loading, largely influence the efficiency of drug delivery. Recent studies have focused on the development of novel drug-DNA hybrid systems to acquire more precise and efficient therapy for various diseases. A systematic review of the design strategies of chemotherapeutic drug-DNA hybrid nanostructures will benefit the innovation and development of the chemotherapeutic drug-based chemotherapy in clinics.
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Affiliation(s)
- Xiangang Huang
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China.
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