1
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Xu K, Du Y, Xu B, Huang Y, Feng W, Yu D, Chen Y, Wang X. Gelatin-Encapsulated Tetrahedral DNA Nanostructure Enhances Cellular Internalization for Treating Noise-Induced Hearing Loss. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310604. [PMID: 38329190 DOI: 10.1002/smll.202310604] [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: 11/18/2023] [Revised: 12/23/2023] [Indexed: 02/09/2024]
Abstract
Nanoparticle-based drug delivery strategies have emerged as a crucial avenue for comprehensive sensorineural hearing loss treatment. Nevertheless, developing therapy vectors crossing both biological and cellular barriers has encountered significant challenges deriving from various external factors. Herein, the rational integration of gelatin nanoparticles (GNPs) with tetrahedral DNA nanostructures (TDNs) to engineer a distinct drug-delivery nanosystem (designed as TDN@GNP) efficiently enhances the biological permeability and cellular internalization, further resolving the dilemma of noise-induced hearing loss via loading epigallocatechin gallate (EGCG) with anti-lipid peroxidation property. Rationally engineering of TDN@GNP demonstrates dramatic alterations in the physicochemical key parameters of TDNs that are pivotal in cell-particle interactions and promote cellular uptake through multiple endocytic pathways. Furthermore, the EGCG-loaded nanosystem (TDN-EGCG@GNP) facilitates efficient inner ear drug delivery by superior permeability through the biological barrier (round window membrane), maintaining high drug concentration within the inner ear. The TDN-EGCG@GNP actively overcomes the cell membrane, exhibiting hearing protection from noise insults via reduced lipid peroxidation in outer hair cells and spiral ganglion neurons. This work exemplifies how integrating diverse vector functionalities can overcome biological and cellular barriers in the inner ear, offering promising applications for inner ear disorders.
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Affiliation(s)
- Ke Xu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200100, P. R. China
| | - Yiwei Du
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200100, P. R. China
| | - Baoying Xu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yuqi Huang
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Wei Feng
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Dehong Yu
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yu Chen
- Materdicine Lab, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Xueling Wang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200100, P. R. China
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2
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Kalra S, Donnelly A, Singh N, Matthews D, Del Villar-Guerra R, Bemmer V, Dominguez C, Allcock N, Cherny D, Revyakin A, Rusling DA. Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-Linking. J Am Chem Soc 2024; 146:13617-13628. [PMID: 38695163 PMCID: PMC11100008 DOI: 10.1021/jacs.4c03413] [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: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates "superstaples" that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.
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Affiliation(s)
- Shantam Kalra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Amber Donnelly
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Nishtha Singh
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Daniel Matthews
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Rafael Del Villar-Guerra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Victoria Bemmer
- Centre
for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, U.K.
| | - Cyril Dominguez
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Natalie Allcock
- Core
Biotechnology Services Electron Microscopy Facility, University of Leicester, Leicester LE1 7RH, U.K.
| | - Dmitry Cherny
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Andrey Revyakin
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - David A. Rusling
- School
of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K.
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Safarkhani M, Ahmadi S, Ipakchi H, Saeb MR, Makvandi P, Ebrahimi Warkiani M, Rabiee N, Huh Y. Advancements in Aptamer-Driven DNA Nanostructures for Precision Drug Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401617. [PMID: 38713753 DOI: 10.1002/advs.202401617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/08/2024] [Indexed: 05/09/2024]
Abstract
DNA nanostructures exhibit versatile geometries and possess sophisticated capabilities not found in other nanomaterials. They serve as customizable nanoplatforms for orchestrating the spatial arrangement of molecular components, such as biomolecules, antibodies, or synthetic nanomaterials. This is achieved by incorporating oligonucleotides into the design of the nanostructure. In the realm of drug delivery to cancer cells, there is a growing interest in active targeting assays to enhance efficacy and selectivity. The active targeting approach involves a "key-lock" mechanism where the carrier, through its ligand, recognizes specific receptors on tumor cells, facilitating the release of drugs. Various DNA nanostructures, including DNA origami, Tetrahedral, nanoflower, cruciform, nanostar, nanocentipede, and nanococklebur, can traverse the lipid layer of the cell membrane, allowing cargo delivery to the nucleus. Aptamers, easily formed in vitro, are recognized for their targeted delivery capabilities due to their high selectivity for specific targets and low immunogenicity. This review provides a comprehensive overview of recent advancements in the formation and modification of aptamer-modified DNA nanostructures within drug delivery systems.
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Affiliation(s)
- Moein Safarkhani
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
- School of Chemistry, Damghan University, Damghan, 36716-45667, Iran
| | - Sepideh Ahmadi
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
| | - Hossein Ipakchi
- Department of Chemical Engineering, McMaster University, Hamilton, L8S 4L8, Canada
| | - Mohammad Reza Saeb
- Department of Pharmaceutical Chemistry, Medical University of Gdańsk, J. Hallera 107, Gdańsk, 80-416, Poland
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, 324000 Quzhou, Zhejiang, China
- Centre of Research Impact and Outreach, Chitkara University, Rajpura, Punjab, 140417, India
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai, 600077, India
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Institute for Biomedical Materials and Devices (IBMD), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Navid Rabiee
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai, 600077, India
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6150, Australia
| | - YunSuk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
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4
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Qin B, Wang Q, Wang Y, Han F, Wang H, Jiang S, Yu H. Enzymatic Synthesis of TNA Protects DNA Nanostructures. Angew Chem Int Ed Engl 2024; 63:e202317334. [PMID: 38323479 DOI: 10.1002/anie.202317334] [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: 11/14/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/08/2024]
Abstract
Xeno-nucleic acids (XNAs) are synthetic genetic polymers with improved biological stabilities and offer powerful molecular tools such as aptamers and catalysts. However, XNA application has been hindered by a very limited repertoire of tool enzymes, particularly those that enable de novo XNA synthesis. Here we report that terminal deoxynucleotide transferase (TdT) catalyzes untemplated threose nucleic acid (TNA) synthesis at the 3' terminus of DNA oligonucleotide, resulting in DNA-TNA chimera resistant to exonuclease digestion. Moreover, TdT-catalyzed TNA extension supports one-pot batch preparation of biostable chimeric oligonucleotides, which can be used directly as staple strands during self-assembly of DNA origami nanostructures (DONs). Such TNA-protected DONs show enhanced biological stability in the presence of exonuclease I, DNase I and fetal bovine serum. This work not only expands the available enzyme toolbox for XNA synthesis and manipulation, but also provides a promising approach to fabricate DONs with improved stability under the physiological condition.
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Affiliation(s)
- Bohe Qin
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Qi Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Yuang Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Feng Han
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Haiyan Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Shuoxing Jiang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu, 210023, China
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5
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Youssef S, Tsang E, Samanta A, Kumar V, Gothelf KV. Reversible Protection and Targeted Delivery of DNA Origami with a Disulfide-Containing Cationic Polymer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2301058. [PMID: 37916910 DOI: 10.1002/smll.202301058] [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: 02/06/2023] [Revised: 10/08/2023] [Indexed: 11/03/2023]
Abstract
DNA nanostructures have considerable biomedical potential as intracellular delivery vehicles as they are highly homogeneous and can be functionalized with high spatial resolution. However, challenges like instability under physiological conditions, limited cellular uptake, and lysosomal degradation limit their use. This paper presents a bio-reducible, cationic polymer poly(cystaminebisacrylamide-1,6-diaminohexane) (PCD) as a reversible DNA origami protector. PCD displays a stronger DNA affinity than other cationic polymers. DNA nanostructures with PCD protection are shielded from low salt conditions and DNase I degradation and show a 40-fold increase in cell-association when linked to targeting antibodies. Confocal microscopy reveals a potential secondary cell uptake mechanism, directly delivering the nanostructures to the cytoplasm. Additionally, PCD can be removed by cleaving its backbone disulfides using the intracellular reductant, glutathione. Finally, the application of these constructs is demonstrated for targeted delivery of a cytotoxic agent to cancer cells, which efficiently decreases their viability. The PCD protective agent that is reported here is a simple and efficient method for the stabilization of DNA origami structures. With the ability to deprotect the DNA nanostructures upon entry of the intracellular space, the possibility for the use of DNA origami in pharmaceutical applications is enhanced.
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Affiliation(s)
- Sarah Youssef
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt
| | - Emily Tsang
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Anirban Samanta
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Vipin Kumar
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, 8000, Denmark
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6
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [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: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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7
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Vogt M, List J, Langecker M, Santiago I, Simmel FC, Kopperger E. Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis. J Phys Chem B 2023; 127:10710-10722. [PMID: 38060372 DOI: 10.1021/acs.jpcb.3c05959] [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: 12/22/2023]
Abstract
DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.
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Affiliation(s)
- Matthias Vogt
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Jonathan List
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Martin Langecker
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Ibon Santiago
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Enzo Kopperger
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
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8
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Nixon SR, Phukan IK, Armijo BJ, Ebrahimi SB, Samanta D. Proximity-Driven DNA Nanosensors. ECS SENSORS PLUS 2023; 2:030601. [PMID: 37424706 PMCID: PMC10323711 DOI: 10.1149/2754-2726/ace068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/12/2023] [Indexed: 07/11/2023]
Abstract
In proximity-driven sensing, interactions between a probe and an analyte produce a detectable signal by causing a change in distance of two probe components or signaling moieties. By interfacing such systems with DNA-based nanostructures, platforms that are highly sensitive, specific, and programmable can be designed. In this Perspective, we delineate the advantages of using DNA building blocks in proximity-driven nanosensors and provide an overview of recent progress in the field, from sensors that rapidly detect pesticides in food to probes that identify rare cancer cells in blood. We also discuss current challenges and identify key areas that need further development.
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Affiliation(s)
- Sara R. Nixon
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Imon Kanta Phukan
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
| | - Brian J. Armijo
- Department of Chemistry, Southwestern University, Georgetown, TX 78626, United States of America
| | - Sasha B. Ebrahimi
- Drug Product Development—Steriles, GlaxoSmithKline, Collegeville, PA 19426, United States of America
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, United States of America
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9
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Alexander S, Moghadam MG, Rothenbroker M, Y T Chou L. Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics. Adv Drug Deliv Rev 2023; 199:114898. [PMID: 37230305 DOI: 10.1016/j.addr.2023.114898] [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: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.
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Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
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10
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He Z, Shi K, Li J, Chao J. Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage. iScience 2023; 26:106638. [PMID: 37187699 PMCID: PMC10176269 DOI: 10.1016/j.isci.2023.106638] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. It obeys the strict Watson-Crick base pairing principle to create intricate structures with nanoscale accuracy, which greatly enriches the complexity, dimension, and functionality of DNA nanostructures. Benefiting from its high programmability and addressability, DNA origami has emerged as versatile nanomachines for transportation, sensing, and computing. This review will briefly summarize the recent progress of DNA origami, two-dimensional pattern, and three-dimensional assembly based on DNA origami, followed by introduction of its application in nanofabrication, biosensing, drug delivery, and computational storage. The prospects and challenges of assembly and application of DNA origami are also discussed.
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Affiliation(s)
- Zhimei He
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Kejun Shi
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jinggang Li
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Corresponding author
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11
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Mosley RJ, Rucci B, Byrne ME. Recent advancements in design of nucleic acid nanocarriers for controlled drug delivery. J Mater Chem B 2023; 11:2078-2094. [PMID: 36806872 DOI: 10.1039/d2tb02325c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Research of nanoscale nucleic acid carriers has garnered attention in recent years due to their distinctive and controllable properties. However, current knowledge is limited in how we can efficiently utilize these systems for clinical applications. Several researchers have pioneered new and innovative nanocarrier drug delivery systems, but understanding physiochemical properties and behavior in vivo is vital to implementing them as clinical drug delivery platforms. In this review, we outline the most significant innovations in the synthesis, physical properties, and utilization of nucleic acid nanocarriers in the past 5 years, addressing the crucial properties which improve nanocarrier characteristics, delivery, and drug release. The challenges of controlling the transport of nucleic acid nanocarriers and therapeutic release for biological applications are outlined. Barriers which inhibit effective transport into tissue are discussed with emphasis on the modifications needed to overcome such obstacles. The novel strategies discussed in this work summarize the pivotal features of modern nucleic nanocarriers and postulate where future developments could revolutionize the translation of these tools into a clinical setting.
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Affiliation(s)
- Robert J Mosley
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA.
| | - Brendan Rucci
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA.
| | - Mark E Byrne
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA. .,Department of Chemical Engineering, Rowan University, Glassboro, NJ, 08028, USA
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12
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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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13
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Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
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Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
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14
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Mathur D, Galvan AR, Green CM, Liu K, Medintz IL. Uptake and stability of DNA nanostructures in cells: a cross-sectional overview of the current state of the art. NANOSCALE 2023; 15:2516-2528. [PMID: 36722508 PMCID: PMC10407680 DOI: 10.1039/d2nr05868e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The physical and chemical properties of synthetic DNA have transformed this prototypical biopolymer into a versatile nanoscale building block material in the form of DNA nanotechnology. DNA nanotechnology is, in turn, providing unprecedented precision bioengineering for numerous biomedical applications at the nanoscale including next generation immune-modulatory materials, vectors for targeted delivery of nucleic acids, drugs, and contrast agents, intelligent sensors for diagnostics, and theranostics, which combines several of these functionalities into a single construct. Assembling a DNA nanostructure to be programmed with a specific number of targeting moieties on its surface to imbue it with concomitant cellular uptake and retention capabilities along with carrying a specific therapeutic dose is now eminently feasible due to the extraordinary self-assembling properties and high formation efficiency of these materials. However, what remains still only partially addressed is how exactly this class of materials is taken up into cells in both the native state and as targeted or chemically facilitated, along with how stable they are inside the cellular cytosol and other cellular organelles. In this minireview, we summarize what is currently reported in the literature about how (i) DNA nanostructures are taken up into cells along with (ii) what is understood about their subsequent stability in the complex multi-organelle environment of the cellular milieu along with biological fluids in general. This allows us to highlight the many challenges that still remain to overcome in understanding DNA nanostructure-cellular interactions in order to fully translate these exciting new materials.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Angelica Rose Galvan
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Christopher M Green
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
| | - Kevin Liu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA
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15
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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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16
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Singh M, Sharma D, Garg M, Kumar A, Baliyan A, Rani R, Kumar V. Current understanding of biological interactions and processing of DNA origami nanostructures: Role of machine learning and implications in drug delivery. Biotechnol Adv 2022; 61:108052. [DOI: 10.1016/j.biotechadv.2022.108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/02/2022]
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17
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
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18
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Lee JY, Yang Q, Chang X, Wisniewski H, Olivera TR, Saji M, Kim S, Perumal D, Zhang F. Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications. J Mater Chem B 2022; 10:7460-7472. [PMID: 35912570 DOI: 10.1039/d2tb00605g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.
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Affiliation(s)
- Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
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19
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Zhu K, Wang Y, Sarlus H, Geng K, Nutma E, Sun J, Kung SY, Bay C, Han J, Min JH, Benito-Cuesta I, Lund H, Amor S, Wang J, Zhang XM, Kutter C, Guerreiro-Cacais AO, Högberg B, Harris RA. Myeloid cell-specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation. EMBO Rep 2022; 23:e54499. [PMID: 35593064 PMCID: PMC9253741 DOI: 10.15252/embr.202154499] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/01/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
Targeting myeloid cells, especially microglia, for the treatment of neuroinflammatory diseases such as multiple sclerosis (MS), is underappreciated. Our in silico drug screening reveals topoisomerase 1 (TOP1) inhibitors as promising drug candidates for microglial modulation. We show that TOP1 is highly expressed in neuroinflammatory conditions, and TOP1 inhibition using camptothecin (CPT) and its FDA-approved analog topotecan (TPT) reduces inflammatory responses in microglia/macrophages and ameliorates neuroinflammation in vivo. Transcriptomic analyses of sorted microglia from LPS-challenged mice reveal an altered transcriptional phenotype following TPT treatment. To target myeloid cells, we design a nanosystem using β-glucan-coated DNA origami (MyloGami) loaded with TPT (TopoGami). MyloGami shows enhanced specificity to myeloid cells while preventing the degradation of the DNA origami scaffold. Myeloid-specific TOP1 inhibition using TopoGami significantly suppresses the inflammatory response in microglia and mitigates MS-like disease progression. Our findings suggest that TOP1 inhibition in myeloid cells represents a therapeutic strategy for neuroinflammatory diseases and that the myeloid-specific nanosystems we designed may also benefit the treatment of other diseases with dysfunctional myeloid cells.
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Affiliation(s)
- Keying Zhu
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Yang Wang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Heela Sarlus
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Keyi Geng
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Erik Nutma
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jingxian Sun
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai, China.,Shanghai Medical College, Fudan University, Shanghai, China
| | - Shin-Yu Kung
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Cindy Bay
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jinming Han
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Jin-Hong Min
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Irene Benito-Cuesta
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Harald Lund
- Department of Physiology and Pharmacology, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Sandra Amor
- Department of Pathology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jun Wang
- Department of Integrative Medicine and Neurobiology, School of Basic Medical Sciences, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai, China.,Shanghai Medical College, Fudan University, Shanghai, China
| | - Xing-Mei Zhang
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - André Ortlieb Guerreiro-Cacais
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robert A Harris
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
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20
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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21
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Cao S, Wang F, Wang L, Fan C, Li J. DNA nanotechnology-empowered finite state machines. NANOSCALE HORIZONS 2022; 7:578-588. [PMID: 35502877 DOI: 10.1039/d2nh00060a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A finite state machine (FSM, or automaton) is an abstract machine that can switch among a finite number of states in response to temporally ordered inputs, which allows storage and processing of information in an order-sensitive manner. In recent decades, DNA molecules have been actively exploited to develop information storage and nanoengineering materials, which hold great promise for smart nanodevices and nanorobotics under the framework of FSM. In this review, we summarize recent progress in utilizing DNA self-assembly and DNA nanostructures to implement FSMs. We describe basic principles for representative DNA FSM prototypes and highlight their advantages and potential in diverse applications. The challenges in this field and future directions have also been discussed.
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Affiliation(s)
- Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200127, 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.
| | - Jiang 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.
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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22
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Yao S, Chang Y, Zhai Z, Sugiyama H, Endo M, Zhu W, Xu Y, Yang Y, Qian X. DNA-Based Daisy Chain Rotaxane Nanocomposite Hydrogels as Dual-Programmable Dynamic Scaffolds for Stem Cell Adhesion. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20739-20748. [PMID: 35485950 DOI: 10.1021/acsami.2c03265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Interlocked DNA nanostructures perform programmable movements in nanoscales such as sliding, contraction, and expansion. However, utilizing nanoscaled interlocked movements to regulate the functions of larger length scaled matrix and developing their applications has not yet been reported. Herein we describe the assembly of DNA-based daisy chain rotaxane nanostructure (DNA-DCR) composed of two hollow DNA nanostructures as macrocycles, two interlocked axles and two triangular prism-shaped DNA structures as stoppers, in which three mechanical states─fixed extended state (FES), sliding state (SS), and fixed contracted state (FCS)─are characterized by using toehold-mediated strand displacement reaction (SDR). The DNA-DCRs are further used as nanocomposites and introduced into hydrogel matrix to produce interlocked hydrogels, which shows modulable stiffness by elongating the interlocked axles to regulate the hydrogel swelling with hybridization chain reaction (HCR) treatment. Then the DCR-hydrogels are employed as dynamic biointerfaces for human mesenchymal stem cells (hMSCs) adhesion studies. First, hMSCs showed lower cell density on bare DCR-hydrogel treated with HCR-initiated swelling for stiffness decreasing. Second, the cell adhesion ligand (RGD) modified DNA-DCRs are constructed for hydrogel functionalization. DCR(RGD) hydrogel endows the mobility of RGDs by switching the mechanical states of DNA-DCR. HMSCs showed increased cell density on DCRSS(RGD) hydrogel than on DCRFCS(RGD) hydrogel. Therefore, our DNA-DCR nanocomposite hydrogel exhibit dual-programmable performances including swelling adjustment and offering sliding for incorporated ligands, which can be both utilized as dynamic scaffolds for regulating the stem cell adhesion. The dual-programmable cross-scale regulation from interlocked DNA nanostructures to hydrogel matrix was achieved, demonstrating a new pathway of DNA-based materials.
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Affiliation(s)
- Shengtao Yao
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yongyun Chang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Zanjing Zhai
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai200011, China
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto606-8502, Japan
| | - Weiping Zhu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Yangyang Yang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai200237, China
- State Key Laboratory of Bioreactor, East China University of Science and Technology, Shanghai200237, China
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23
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Aye SL, Sato Y. Therapeutic Applications of Programmable DNA Nanostructures. MICROMACHINES 2022; 13:mi13020315. [PMID: 35208439 PMCID: PMC8876680 DOI: 10.3390/mi13020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
Deoxyribonucleic acid (DNA) nanotechnology, a frontier in biomedical engineering, is an emerging field that has enabled the engineering of molecular-scale DNA materials with applications in biomedicine such as bioimaging, biodetection, and drug delivery over the past decades. The programmability of DNA nanostructures allows the precise engineering of DNA nanocarriers with controllable shapes, sizes, surface chemistries, and functions to deliver therapeutic and functional payloads to target cells with higher efficiency and enhanced specificity. Programmability and control over design also allow the creation of dynamic devices, such as DNA nanorobots, that can react to external stimuli and execute programmed tasks. This review focuses on the current findings and progress in the field, mainly on the employment of DNA nanostructures such as DNA origami nanorobots, DNA nanotubes, DNA tetrahedra, DNA boxes, and DNA nanoflowers in the biomedical field for therapeutic purposes. We will also discuss the fate of DNA nanostructures in living cells, the major obstacles to overcome, that is, the stability of DNA nanostructures in biomedical applications, and the opportunities for DNA nanostructure-based drug delivery in the future.
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Sakai Y, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Topogami: Topologically Linked DNA Origami. ACS NANOSCIENCE AU 2022; 2:57-63. [PMID: 35211697 PMCID: PMC8861903 DOI: 10.1021/acsnanoscienceau.1c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
DNA origami is a widely used DNA nanotechnology that allows construction of two-dimensional and three-dimensional nanometric shapes. The designability and rigidity of DNA origami make it an ideal material for construction of topologically linked molecules such as catenanes, which are attractive for their potential as motors and molecular machines. However, a general method for production of topologically linked DNA origami has been lacking. Here, we show that catenated single-stranded DNA circles can be produced and used as a universal scaffold for the production of topologically linked (catenated) DNA origami structures where the individual linked structures can be of any arbitrary design. Assembly of these topologically linked DNA origami structures is achieved via a simple one-pot annealing protocol.
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Affiliation(s)
- Yusuke Sakai
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Gerrit D Wilkens
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine, Żwirki I Wigury 61, 02-091 Warsaw, Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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25
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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26
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Chen YR, Sun S, Yin H, Wang W, Liu R, Xu H, Yang Y, Wu ZS. Tumor-targeting [2]catenane-based grid-patterned periodic DNA monolayer array for in vivo theranostic application. J Mater Chem B 2022; 10:1969-1979. [PMID: 35014661 DOI: 10.1039/d1tb01978c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology is often used to build various nano-structures for signaling and/or drug delivery, but it essentially suffers from several major limitations, such as a large number of DNA strands and limited targeting ligands. Moreover, there is no report on in vivo two-dimensional DNA arrays because of various technical challenges. By cross-catenating two palindromic DNA rings, herein, we demonstrate a catenane-based grid-patterned periodic DNA monolayer array ([2]GDA) capable of preferentially accumulating in tumor tissues without any targeting ligands, with a thickness equal to the double-helical DNA monolayer (nearly 2 nm). The structural flexibility of [2]GDA enabled it to fold into a spherical object in solution, favoring cellular uptake. Thus, its cellular internalization activity was comparable with that of the commercial lipofectamine 3000. Moreover, [2]GDA retained the structural integrity over 24 h incubation in biological solutions, achieving a 360-fold improvement in in vivo stability. Significantly, anticancer drug-loaded [2]GDA exhibits desirable therapeutic efficacy in tumor-bearing animals without detectable side effects.
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Affiliation(s)
- Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Shujuan Sun
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ran Liu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ya Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
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27
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Wang J, Wang DX, Liu B, Jing X, Chen DY, Tang AN, Cui YX, Kong DM. Recent advances in constructing high-order DNA structures. Chem Asian J 2022; 17:e202101315. [PMID: 34989140 DOI: 10.1002/asia.202101315] [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: 11/22/2021] [Revised: 01/04/2022] [Indexed: 11/07/2022]
Abstract
Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.
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Affiliation(s)
- Jing Wang
- Nankai University, Department of Chemistry, CHINA
| | | | - Bo Liu
- Nankai University, College of Chemistry, CHINA
| | - Xiao Jing
- Nankai University, College of Chemistry, CHINA
| | - Dan-Ye Chen
- Nankai University, College of Chemistry, CHINA
| | - An-Na Tang
- Nankai University, College of Chemistry, CHINA
| | - Yun-Xi Cui
- Nankai University, College of Chemistry, CHINA
| | - De Ming Kong
- Nankai University, Key Laboratory of Functional Polymer Materials, Weijin road 94, 30071, Tianjin, CHINA
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Weizenmann N, Scheidgen-Kleyboldt G, Ye J, Krause CB, Kauert D, Helmi S, Rouillon C, Seidel R. Chemical ligation of an entire DNA origami nanostructure. NANOSCALE 2021; 13:17556-17565. [PMID: 34657945 DOI: 10.1039/d1nr04225d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Within the field of DNA nanotechnology, numerous methods were developed to produce complex two- and three-dimensional DNA nanostructures for many different emerging applications. These structures typically suffer from a low tolerance against non-optimal environmental conditions including elevated temperatures. Here, we apply a chemical ligation method to covalently seal the nicks between adjacent 5' phosphorylated and 3' amine-modified strands within the DNA nanostructures. Using a cost-effective enzymatic strand modification procedure, we are able to batch-modify all DNA strands even of large DNA objects, such as origami nanostructures. The covalent strand linkage increases the temperature stability of the structures by ∼10 K. Generally, our method also allows a 'surgical' introduction of covalent strand linkages at preselected positions. It can also be used to map the strand ligation into chains throughout the whole nanostructure and identify assembly defects. We expect that our method can be applied to a large variety of DNA nanostructures, in particular when full control over the introduced covalent linkages and the absence of side adducts and DNA damages are required.
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Affiliation(s)
- Nicole Weizenmann
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.
| | - Gerda Scheidgen-Kleyboldt
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Jingjing Ye
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.
| | - Cordula B Krause
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.
| | - Dominik Kauert
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.
| | - Seham Helmi
- Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Christophe Rouillon
- Institute of Structural Biology, Biomedical Center (BMZ), Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany.
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Chen X, Jia B, Lu Z, Liao L, Yu H, Li Z. Aptamer-Integrated Scaffolds for Biologically Functional DNA Origami Structures. ACS APPLIED MATERIALS & INTERFACES 2021; 13:39711-39718. [PMID: 34402304 DOI: 10.1021/acsami.1c09307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The manufacture of DNA origami nanostructures with highly ordered functional motifs is of great significance for biomedical applications. Here, we present a robust strategy to produce customized scaffolds with integrated aptamer sequences, which enables direct construction of functional DNA origami structures. As we demonstrated, aptamers of various numbers and types were efficiently and stably integrated in user-defined positions of the scaffolds. Specifically, two different thrombin aptamer sequences were simultaneously inserted into the M13mp18 phage genome. The assembled functional DNA origami structures from this aptamer-integrated scaffold exhibited increased binding efficiency to thrombin and displayed more than 10-fold stronger resistance to exonuclease degradation than that produced using the traditional staple extension method. Additionally, a scaffold integrated with the platelet-derived growth factor aptamer was produced, and the assembled DNA origami structures showed significant inhibitory effect on breast cancer cells MDA-MB-231. This scalable method of creating design-specific scaffolds opens up a new way to construct more stable and functionally robust DNA origami structures and thus provides an important basis for their broader applications.
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Affiliation(s)
- Xiaoxing Chen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Jia
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Zhangwei Lu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Libing Liao
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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30
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Hu X, Huang Y, Yin H, Dai L, Tian Y. DNA‐Based
Architectures for
in situ
Target Biomolecule Analysis in Confined Nano‐space
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaoxue Hu
- Shenzhen Research Institute Nanjing University Shenzhen Guangdong 518000 China
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Yide Huang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Hao Yin
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
| | - Ye Tian
- Shenzhen Research Institute Nanjing University Shenzhen Guangdong 518000 China
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing Jiangsu 210093 China
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31
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Agrahari AK, Bose P, Jaiswal MK, Rajkhowa S, Singh AS, Hotha S, Mishra N, Tiwari VK. Cu(I)-Catalyzed Click Chemistry in Glycoscience and Their Diverse Applications. Chem Rev 2021; 121:7638-7956. [PMID: 34165284 DOI: 10.1021/acs.chemrev.0c00920] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Copper(I)-catalyzed 1,3-dipolar cycloaddition between organic azides and terminal alkynes, commonly known as CuAAC or click chemistry, has been identified as one of the most successful, versatile, reliable, and modular strategies for the rapid and regioselective construction of 1,4-disubstituted 1,2,3-triazoles as diversely functionalized molecules. Carbohydrates, an integral part of living cells, have several fascinating features, including their structural diversity, biocompatibility, bioavailability, hydrophilicity, and superior ADME properties with minimal toxicity, which support increased demand to explore them as versatile scaffolds for easy access to diverse glycohybrids and well-defined glycoconjugates for complete chemical, biochemical, and pharmacological investigations. This review highlights the successful development of CuAAC or click chemistry in emerging areas of glycoscience, including the synthesis of triazole appended carbohydrate-containing molecular architectures (mainly glycohybrids, glycoconjugates, glycopolymers, glycopeptides, glycoproteins, glycolipids, glycoclusters, and glycodendrimers through regioselective triazole forming modular and bio-orthogonal coupling protocols). It discusses the widespread applications of these glycoproducts as enzyme inhibitors in drug discovery and development, sensing, gelation, chelation, glycosylation, and catalysis. This review also covers the impact of click chemistry and provides future perspectives on its role in various emerging disciplines of science and technology.
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Affiliation(s)
- Anand K Agrahari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Priyanka Bose
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Manoj K Jaiswal
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Sanchayita Rajkhowa
- Department of Chemistry, Jorhat Institute of Science and Technology (JIST), Jorhat, Assam 785010, India
| | - Anoop S Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Srinivas Hotha
- Department of Chemistry, Indian Institute of Science and Engineering Research (IISER), Pune, Maharashtra 411021, India
| | - Nidhi Mishra
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Vinod K Tiwari
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
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32
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Bertosin E, Stömmer P, Feigl E, Wenig M, Honemann MN, Dietz H. Cryo-Electron Microscopy and Mass Analysis of Oligolysine-Coated DNA Nanostructures. ACS NANO 2021; 15:9391-9403. [PMID: 33724780 PMCID: PMC8223477 DOI: 10.1021/acsnano.0c10137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cationic coatings can enhance the stability of synthetic DNA objects in low ionic strength environments such as physiological fluids. Here, we used single-particle cryo-electron microscopy (cryo-EM), pseudoatomic model fitting, and single-molecule mass photometry to study oligolysine and polyethylene glycol (PEG)-oligolysine-coated multilayer DNA origami objects. The coatings preserve coarse structural features well on a resolution of multiple nanometers but can also induce deformations such as twisting and bending. Higher-density coatings also led to internal structural deformations in the DNA origami test objects, in which a designed honeycomb-type helical lattice was deformed into a more square-lattice-like pattern. Under physiological ionic strength, where the uncoated objects disassembled, the coated objects remained intact but they shrunk in the helical direction and expanded in the direction perpendicular to the helical axis. Helical details like major/minor grooves and crossover locations were not discernible in cryo-EM maps that we determined of DNA origami coated with oligolysine and PEG-oligolysine, whereas these features were visible in cryo-EM maps determined from the uncoated reference objects. Blunt-ended double-helical interfaces remained accessible underneath the coating and may be used for the formation of multimeric DNA origami assemblies that rely on stacking interactions between blunt-ended helices. The ionic strength requirements for forming multimers from coated DNA origami differed from those needed for uncoated objects. Using single-molecule mass photometry, we found that the mass of coated DNA origami objects prior to and after incubation in low ionic strength physiological conditions remained unchanged. This finding indicated that the coating effectively prevented strand dissociation but also that the coating itself remained stable in place. Our results validate oligolysine coatings as a powerful stabilization method for DNA origami but also reveal several potential points of failure that experimenters should watch to avoid working with false premises.
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Huang N, Chen M, Chen S, Dang K, Guo H, Wang X, Yan S, Tian J, Liu Y, Ye Q. A Specific Nucleic Acid Microfluidic Capture Device Based on Stable DNA Nanostructure. ACS APPLIED MATERIALS & INTERFACES 2021; 13:24487-24492. [PMID: 34014634 DOI: 10.1021/acsami.1c04157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Benefiting from superior programmability and good biocompatibility, DNA nanomaterials have received considerable attention with promising prospects in biological detection applications. However, their poor stability and operability severely impede further development of the applications of DNA nanomaterials. Here, a thermally stable DNA nanomesh structure is integrated into a microfluidic chip. The specificity of the nucleic acid microfluidic capture device could reach the single-base mismatch level while capturing the ssDNA sample. The microfluidic chip provides a closed environment for the DNA nanomesh, giving the device excellent storage stability. After 6 months of storage at room temperature, the device still has a specific capture function on ssDNA samples with low concentration. The specific nucleic acid microfluidic capture device can be applied to the enrichment of ctDNA in the future and contribute to the early diagnosis of cancer.
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34
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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35
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36
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Li C, Luo S, Wang J, Shen Z, Wu ZS. Nuclease-resistant signaling nanostructures made entirely of DNA oligonucleotides. NANOSCALE 2021; 13:7034-7051. [PMID: 33889882 DOI: 10.1039/d1nr00197c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleic acid probes have the advantages of excellent biocompatibility, biodegradability, versatile functionalities and remarkable programmability. However, the low biostability of nucleic acid probes under complex physiological conditions limits their in vivo application. Despite impressive progress in the development of inorganic material-mediated biostable nucleic acid nanostructures, uncertain systemic toxicity of composite nanocarriers has hindered their application in living organisms. In the field of biomedicine, as a promising alternative capable of avoiding potential cytotoxicity, biologically stable nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in recent years, offering an exciting in vivo tool for cancer diagnosis and clinical treatment. In this review, we summarize the recent advances in the development of nuclease-resistant DNA nanostructures with different geometrical shapes, such as tetrahedron, octahedron, DNA triangular prism (DTP), DNA nanotubes and DNA origami, introduce innovative assembly strategies, and discuss unique structural advantages and especially biological applications in cellular imaging and targeted drug delivery in an organism. Finally, we conclude with the challenges in the clinical development of DNA nanostructures and present an outlook of the future of this rapidly expanding field.
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Affiliation(s)
- Congcong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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37
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Jia Y, Chen L, Liu J, Li W, Gu H. DNA-catalyzed efficient production of single-stranded DNA nanostructures. Chem 2021. [DOI: 10.1016/j.chempr.2020.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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38
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Dass M, Gür FN, Kołątaj K, Urban MJ, Liedl T. DNA Origami-Enabled Plasmonic Sensing. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:5969-5981. [PMID: 33828635 PMCID: PMC8016175 DOI: 10.1021/acs.jpcc.0c11238] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Indexed: 05/02/2023]
Abstract
The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.
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Affiliation(s)
- Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Fatih N. Gür
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Karol Kołątaj
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Maximilian J. Urban
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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Dai L, Liu P, Hu X, Zhao X, Shao G, Tian Y. DNA origami: an outstanding platform for functions in nanophotonics and cancer therapy. Analyst 2021; 146:1807-1819. [PMID: 33595553 DOI: 10.1039/d0an02160a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to the proposal and evolution of the DNA origami technique over the past decade, DNA molecules have been utilized as building blocks for the precise construction of nanoscale architectures. Benefiting from the superior programmability of DNA molecules, the sequence-dependent recognition mechanism and robust complementation among DNA strands make it possible to customize almost arbitrary structures. Such an assembly strategy bypasses some of the limits of conventional fabrication methods; the fabrication accuracy and complexity of the target product are unprecedentedly promoted as well. Furthermore, due to the spatial addressability of the final products, nanostructures assembled through the DNA origami technique can also serve as a versatile platform for the spatial positioning of functional elements, represented by colloidal nanoparticles (NPs). The subsequent fabrication of heterogeneous functional nanoarchitectures is realized via modifying colloidal NPs with DNA strands and manipulating them to anchor into DNA origami templates. This has given rise to investigations of their novel properties in nanophotonics and therapeutic effects towards some diseases. In this review, we survey the crucial progress in the development of DNA origami design, assembly and structural analysis and summarize available applications in nanophotonics and cancer therapy based on the object-dressed DNA origami complex. Moreover, we elucidate the development of this field and discuss the potential directions of this kind of application-oriented nanomanufacturing.
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Affiliation(s)
- Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210093, 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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Wang Q, Chen X, Li X, Song D, Yang J, Yu H, Li Z. 2'-Fluoroarabinonucleic Acid Nanostructures as Stable Carriers for Cellular Delivery in the Strongly Acidic Environment. ACS APPLIED MATERIALS & INTERFACES 2020; 12:53592-53597. [PMID: 33206496 DOI: 10.1021/acsami.0c11684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA nanotechnology is powerful in constructing programmable nanostructures with distinct dimensions, sizes, and shapes. However, natural DNA molecules are prone to nuclease degradation, thus limiting the in vivo applications of such DNA nanostructures. 2'-Fluoroarabinonucleic acid (FANA) is a chemically modified oligonucleotide with similar base pairing properties to DNA and exhibits superior physical and chemical stabilities. In this work, FANA molecules were used to construct double crossover nanostructures, and it was demonstrated that incorporation of FANA conferred nucleic acid nanostructures with increased thermal stability and stronger nuclease resistance. More importantly, FANA nanostructures were able to maintain the structural integrity in the strongly acidic environment (pH 1.2). Last, such FANA nanostructures functioned well in acting as stable carriers of small-molecule cargoes for cellular delivery in simulated gastric fluid, while the DNA counterparts were mostly degraded. Collectively, these results demonstrated that FANA self-assembly was not only a substantial complement to the structural DNA nanotechnology but also an appealing molecular tool for in vivo biomedical applications.
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Affiliation(s)
- Qian Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoxing Chen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xintong Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jintao Yang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, China
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Nicolson F, Ali A, Kircher MF, Pal S. DNA Nanostructures and DNA-Functionalized Nanoparticles for Cancer Theranostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001669. [PMID: 33304747 PMCID: PMC7709992 DOI: 10.1002/advs.202001669] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/27/2020] [Indexed: 05/12/2023]
Abstract
In the last two decades, DNA has attracted significant attention toward the development of materials at the nanoscale for emerging applications due to the unparalleled versatility and programmability of DNA building blocks. DNA-based artificial nanomaterials can be broadly classified into two categories: DNA nanostructures (DNA-NSs) and DNA-functionalized nanoparticles (DNA-NPs). More importantly, their use in nanotheranostics, a field that combines diagnostics with therapy via drug or gene delivery in an all-in-one platform, has been applied extensively in recent years to provide personalized cancer treatments. Conveniently, the ease of attachment of both imaging and therapeutic moieties to DNA-NSs or DNA-NPs enables high biostability, biocompatibility, and drug loading capabilities, and as a consequence, has markedly catalyzed the rapid growth of this field. This review aims to provide an overview of the recent progress of DNA-NSs and DNA-NPs as theranostic agents, the use of DNA-NSs and DNA-NPs as gene and drug delivery platforms, and a perspective on their clinical translation in the realm of oncology.
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Affiliation(s)
- Fay Nicolson
- Department of ImagingDana‐Farber Cancer Institute & Harvard Medical SchoolBostonMA02215USA
- Center for Molecular Imaging and NanotechnologyMemorial Sloan Kettering Cancer CenterNew YorkNY10065USA
| | - Akbar Ali
- Department of ChemistryIndian Institute of Technology‐ BhilaiRaipurChhattisgarh492015India
| | - Moritz F. Kircher
- Department of ImagingDana‐Farber Cancer Institute & Harvard Medical SchoolBostonMA02215USA
- Center for Molecular Imaging and NanotechnologyMemorial Sloan Kettering Cancer CenterNew YorkNY10065USA
- Department of RadiologyBrigham and Women's Hospital & Harvard Medical SchoolBostonMA02215USA
| | - Suchetan Pal
- Department of ChemistryIndian Institute of Technology‐ BhilaiRaipurChhattisgarh492015India
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Kimna C, Lieleg O. Molecular micromanagement: DNA nanotechnology establishes spatio-temporal control for precision medicine. BIOPHYSICS REVIEWS 2020; 1:011305. [PMID: 38505628 PMCID: PMC10903406 DOI: 10.1063/5.0033378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/08/2020] [Indexed: 03/21/2024]
Abstract
Current advances in DNA nanotechnology pinpoint exciting perspectives for the design of customized, patient-specific treatments. This advance is made possible by the exceptionally high precision and specificity that are typical for DNA base pairing on the one hand and our growing ability to harness those features in synthetic, DNA-based constructs on the other hand. Modern medicine may soon benefit from recent developments in this field, especially regarding the targeted delivery of drugs and the rational interference of synthetic DNA strands with cellular oligonucleotides. In this Review, we summarize selected examples from the area of DNA nanotechnology, where the development of precisely controlled, advanced functional mechanisms was achieved. To demonstrate the high versatility of these rationally designed structures, we categorize the dynamic DNA-based materials suggested for precision medicine according to four fundamental tasks: "hold & release," "heal," "detect & measure," as well as "guide & direct." In all the biomedical applications we highlight, DNA strands not only constitute structural building blocks but allow for creating stimuli-responsive objects, serve as an active cargo, or act as molecular control/guidance tools. Moreover, we discuss several issues that need to be considered when DNA-based structures are designed for applications in the field of precision medicine. Even though the majority of DNA-based objects have not been used in clinical settings yet, recent progress regarding the stability, specificity, and control over the dynamic behavior of synthetic DNA structures has advanced greatly. Thus, medical applications of those nanoscopic objects should be feasible in the near future.
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Hu X, Xu Z, Min Q, Teng C, Tian Y. Endogenous Stimuli-Responsive DNA Nanostructures Toward Cancer Theranostics. FRONTIERS IN NANOTECHNOLOGY 2020. [DOI: 10.3389/fnano.2020.574328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nanostructures specifically responsive to endogenous biomolecules hold great potential in accurate diagnosis and precision therapy of cancers. In the pool of nanostructures with responsiveness to unique triggers, nanomaterials derived from DNA self-assembly have drawn particular attention due to their intrinsic biocompatibility and structural programmability, enabling the selective bioimaging, and site-specific drug delivery in cancer cells and tumor tissues. In this mini review, we summarize the most recent advances in the development of endogenous stimuli-responsive DNA nanostructures featured with precise self-assembly, targeted delivery, and controlled drug release for cancer theranostics. This mini review briefly discusses the diverse dynamic DNA nanostructures aiming at bioimaging and biomedicine, including DNA self-assembling materials, DNA origami structures, DNA hydrogels, etc. We then elaborate the working principles of DNA nanostructures activated by biomarkers (e.g., miRNA, mRNA, and proteins) in tumor cells and microenvironments of tumor tissue (e.g., pH, ATP, and redox gradient). Subsequently, applications of the endogenous stimuli-responsive DNA nanostructures in biological imaging probes for detecting cancer hallmarks as well as intelligent carriers for drug release in vivo are discussed. In the end, we highlight the current challenges of DNA nanotechnology and the further development of this promising research direction.
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Xu F, Xia Q, Wang P. Rationally Designed DNA Nanostructures for Drug Delivery. Front Chem 2020; 8:751. [PMID: 33195016 PMCID: PMC7542244 DOI: 10.3389/fchem.2020.00751] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
DNA is an excellent biological material that has received growing attention in the field of nanotechnology due to its unique capability for precisely engineering materials via sequence specific interactions. Self-assembled DNA nanostructures of prescribed physicochemical properties have demonstrated potent drug delivery efficiency in vitro and in vivo. By using various conjugation techniques, DNA nanostructures may be precisely integrated with a large diversity of functional moieties, such as targeting ligands, proteins, and inorganic nanoparticles, to enrich their functionalities and to enhance their performance. In this review, we start with introducing strategies on constructing DNA nanostructures. We then summarize the biological barriers ahead of drug delivery using DNA nanostructures, followed by introducing existing rational solutions to overcome these biological barriers. Lastly, we discuss challenges and opportunities for DNA nanostructures toward real applications in clinical settings.
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Affiliation(s)
- Fan Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Xia
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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Keller A, Linko V. Challenges and Perspectives of DNA Nanostructures in Biomedicine. Angew Chem Int Ed Engl 2020; 59:15818-15833. [PMID: 32112664 PMCID: PMC7540699 DOI: 10.1002/anie.201916390] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Indexed: 01/12/2023]
Abstract
DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.
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Affiliation(s)
- Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Strasse 10033098PaderbornGermany
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
- HYBER CentreDepartment of Applied PhysicsAalto UniversityP. O. Box 1510000076AaltoFinland
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Chandrasekaran AR, Halvorsen K. Nuclease Degradation Analysis of DNA Nanostructures Using Gel Electrophoresis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2020; 82:e115. [PMID: 32931657 PMCID: PMC8034824 DOI: 10.1002/cpnc.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Custom-built DNA nanostructures are now used in applications such as biosensing, molecular computation, biomolecular analysis, and drug delivery. While the functionality and biocompatibility of DNA makes DNA nanostructures useful in such applications, the field faces a challenge in making biostable DNA nanostructures. Being a natural material, DNA is most suited for biological applications, but is also easily degraded by nucleases. Several methods have been employed to study the nuclease degradation rates and enhancement of nuclease resistance. This protocol describes the use of gel electrophoresis to analyze the extent of nuclease degradation of DNA nanostructures and to report degradation times, kinetics of nuclease digestion, and evaluation of biostability enhancement factors. © 2020 Wiley Periodicals LLC. Basic Protocol: Timed analysis of nuclease degradation of DNA nanostructures Support Protocol: Calculating biostability enhancement factors.
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Affiliation(s)
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York
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Arroyo-Currás N, Sadeia M, Ng AK, Fyodorova Y, Williams N, Afif T, Huang CM, Ogden N, Andresen Eguiluz RC, Su HJ, Castro CE, Plaxco KW, Lukeman PS. An electrochemical biosensor exploiting binding-induced changes in electron transfer of electrode-attached DNA origami to detect hundred nanometer-scale targets. NANOSCALE 2020; 12:13907-13911. [PMID: 32578652 DOI: 10.1039/d0nr00952k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The specific detection in clinical samples of analytes with dimensions in the tens to hundreds of nanometers, such as viruses and large proteins, would improve disease diagnosis. Detection of these "mesoscale" analytes (as opposed to their nanoscale components), however, is challenging as it requires the simultaneous binding of multiple recognition sites often spaced over tens of nanometers. In response, we have adapted DNA origami, with its unparalleled customizability to precisely display multiple target-binding sites over the relevant length scale, to an electrochemical biosensor platform. Our proof-of-concept employs triangular origami covalently attached to a gold electrode and functionalized with redox reporters. Electrochemical interrogation of this platform successfully monitors mesoscale, target-binding-induced changes in electron transfer in a manner consistent with coarse-grained molecular dynamics simulations. Our approach enables the specific detection of analytes displaying recognition sites that are separated by ∼40 nm, a spacing significantly greater than that achieved in similar sensor architectures employing either antibodies or aptamers.
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Affiliation(s)
- Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Keller A, Linko V. Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adrian Keller
- Technische und Makromolekulare Chemie Universität Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finnland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finnland
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