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Laurent Q, Bona BL, Asohan J, Rosati M, Faiad S, Bombelli FB, Metrangolo P, Sleiman HF. Self-Assembly and Biological Properties of Highly Fluorinated Oligonucleotide Amphiphiles. Angew Chem Int Ed Engl 2025; 64:e202419996. [PMID: 39636686 PMCID: PMC11811686 DOI: 10.1002/anie.202419996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 11/24/2024] [Accepted: 12/04/2024] [Indexed: 12/07/2024]
Abstract
Nucleic acids, used as therapeutics to silence disease-related genes, offer significant advantages over small molecule drugs: they provide high specificity, the ability to target "undruggable" molecules, and adaptability to a wide range of disease phenotypes. However, their instability in biological media, as well their rapid clearance from the organism limit their applicability, necessitating the use of nanocarriers to overcome these challenges. Among these strategies, spherical nucleic acids (SNA)-composed of a densely packed corona of oligonucleotides around a nanoparticle-have emerged as a powerful tool, in particular when self-assembled from DNA amphiphiles. This non-covalent strategy however has caveats, especially when it comes to stability in complex biological media, where these SNAs disassemble in contact to serum proteins. Here, we developed highly fluorinated DNA amphiphiles that readily self-assemble into SNAs and have tunable stability profiles in biological media. They are made of branched fluorinated moieties with potentially improved biodegradability as compared to their linear counterparts. Depending on the number of fluorophilic interactions, the self-assembled SNAs can have excellent serum stabilities-up to days-and readily deliver nucleic acid therapeutics for gene silencing applications. These systems show great potential as promising candidates for nucleic acid-based therapies.
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Affiliation(s)
- Quentin Laurent
- Department of ChemistryMcGill University801 Sherbrooke St. WQC-H3A 0B8MontrealCanada
| | - Beatrice L. Bona
- SupraBioNano LabDepartment of ChemistryMaterialsand Chemical Engineering “Giulio Natta”Politecnico di MilanoVia Luigi Mancinelli 7MI-20131MilanoItaly
| | - Jathavan Asohan
- Department of ChemistryMcGill University801 Sherbrooke St. WQC-H3A 0B8MontrealCanada
| | - Marta Rosati
- SupraBioNano LabDepartment of ChemistryMaterialsand Chemical Engineering “Giulio Natta”Politecnico di MilanoVia Luigi Mancinelli 7MI-20131MilanoItaly
| | - Sinan Faiad
- Department of ChemistryMcGill University801 Sherbrooke St. WQC-H3A 0B8MontrealCanada
| | - Francesca Baldelli Bombelli
- SupraBioNano LabDepartment of ChemistryMaterialsand Chemical Engineering “Giulio Natta”Politecnico di MilanoVia Luigi Mancinelli 7MI-20131MilanoItaly
| | - Pierangelo Metrangolo
- SupraBioNano LabDepartment of ChemistryMaterialsand Chemical Engineering “Giulio Natta”Politecnico di MilanoVia Luigi Mancinelli 7MI-20131MilanoItaly
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University801 Sherbrooke St. WQC-H3A 0B8MontrealCanada
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Kaviani S, Bai H, Das T, Asohan J, Elmanzalawy A, Marlyn J, Choueiri LE, Damha MJ, Laurent Q, Sleiman HF. Photochemical Stabilization of Self-Assembled Spherical Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025; 21:e2407742. [PMID: 39790078 PMCID: PMC11840461 DOI: 10.1002/smll.202407742] [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: 08/30/2024] [Revised: 11/08/2024] [Indexed: 01/12/2025]
Abstract
Oligonucleotide therapeutics, including antisense oligonucleotides and small interfering RNA, offer promising avenues for modulating the expression of disease-associated proteins. However, challenges such as nuclease degradation, poor cellular uptake, and unspecific targeting hinder their application. To overcome these obstacles, spherical nucleic acids have emerged as versatile tools for nucleic acid delivery in biomedical applications. Our laboratory has introduced sequence-defined DNA amphiphiles which self-assemble in aqueous solutions. Despite their advantages, self-assembled SNAs can be inherently fragile due to their reliance on non-covalent interactions and fall apart in biologically relevant conditions, specifically by interaction with serum proteins. Herein, this challenge is addressed by introducing two methods of covalent crosslinking of SNAs via UV irradiation. Thymine photodimerization or disulfide crosslinking at the micellar interface enhance SNA stability against human serum albumin binding. This enhanced stability, particularly for disulfide crosslinked SNAs, leads to increased cellular uptake. Furthermore, this crosslinking results in sustained activity and accessibility for release of the therapeutic nucleic acid, along with improvement in unaided gene silencing. The findings demonstrate the efficient stabilization of SNAs through UV crosslinking, influencing their cellular uptake, therapeutic release, and ultimately, gene silencing activity. These studies offer promising avenues for further optimization and exploration of pre-clinical, in vivo studies.
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Affiliation(s)
- Sepideh Kaviani
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | - Haochen Bai
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | - Trishalina Das
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | - Jathavan Asohan
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | | | - Julian Marlyn
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | - Lea El Choueiri
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | - Masad J. Damha
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
| | - Quentin Laurent
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
- University Grenoble Alpes, DCM UMR 5250Grenoble Cedex 938058France
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University801, Sherbrooke St. WestMontrealQCH3A 0B8Canada
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3
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Rafique MG, Laurent Q, Dore MD, Fakih HH, Trinh T, Rizzuto FJ, Sleiman HF. Sequence-Defined DNA Polymers: New Tools for DNA Nanotechnology and Nucleic Acid Therapy. Acc Chem Res 2025; 58:177-188. [PMID: 39772484 DOI: 10.1021/acs.accounts.4c00580] [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: 01/11/2025]
Abstract
Structural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures. Here we describe our research group's work to integrate these orthogonal interactions into DNA and its supramolecular assemblies. Using automated solid phase techniques, we synthesized sequence-defined DNA polymers (SDPs) featuring a wide range of functional groups, achieving high yields in the process. These SDPs can assemble into not only isotropic spherical morphologies─such as spherical nucleic acids (SNAs)─but also into anisotropic nanostructures such as 1D nanofibers and 2D nanosheets. Our structural and molecular modeling studies revealed new insights into intermolecular chain packing and intramolecular chain folding, influenced by phosphodiester positioning and SDP sequence. Using these new self-assembly paradigms, we created hierarchical, anisotropic assemblies and developed systems exhibiting polymorphism and chiroptical behavior dependent on the SDP sequence. We could also precisely control the size of our nanofiber assemblies via nucleation-growth supramolecular polymerization and create compartmentalized nanostructures capable of precise surface functionalization.The exquisite control over sequence, composition, and length allowed us to combine our SDPs with nanostructures including DNA wireframe assemblies such as prisms, nanotubes, and cubes to create hybrid, stimuli-responsive assemblies exhibiting emergent structural and functional modes. The spatial control of our assemblies enabled their use as nanoreactors for chemical transformations in several ways: via hybridization chain reaction within SNA coronas, through chemical conjugation within SNA cores, and through a molecular "printing" approach within wireframe assemblies for nanoscale information transfer and the creation of anisotropic "DNA-printed" polymer particles.We have also employed our SDP nanostructures toward biological and therapeutic applications. We demonstrated that our SNAs could serve as both extrinsic and intrinsic therapeutic platforms, with improved cellular internalization and biodistribution profiles, and excellent gene silencing activities. Using SDPs incorporating hydrophobic dendrons, high-affinity and highly specific oligonucleotide binding to human serum albumin was demonstrated. These structures showed an increased stability to nuclease degradation, reduced nonspecific cellular uptake, no toxicity even at high concentrations, and excellent biodistribution beyond the liver, resulting in unprecedented gene silencing activity in various tissues.Control over the sequence has thus presented us with a unique polymeric building block in the form of the SDP, which combines the chemical and structural diversity of polymers with the programmability of DNA. By linking these orthogonal assembly languages, we have discovered new self-assembly rules, created DNA-minimal nanostructures, and demonstrated their utility through a range of applications. Developing this work further will open new avenues in the fields of DNA nanomaterials, nucleic acid therapeutics, as well as block copolymer self-assembly.
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Affiliation(s)
- Muhammad Ghufran Rafique
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Quentin Laurent
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- University Grenoble Alpes, CNRS, DCM UMR 5250, 38058 Grenoble Cedex 9, France
| | - Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Evanston, Illinois 60611, United States
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Tuan Trinh
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Department of Radiology, Stanford University, Stanford, California 94304, United States
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Wang H, Xie J, Xiao M, Ke Y, Li J, Nie Z, Chen Q, Zhang Z. Spherical Nucleic Acid Probes on Floating-Gate Field-Effect Transistor Biosensors for Attomolar-Level Analyte Detection. ACS NANO 2024; 18:34391-34402. [PMID: 39609263 DOI: 10.1021/acsnano.4c14053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2024]
Abstract
Field-effect transistor (FET) sensors are attractive for the label-free detection of target biomolecules, offering ultrahigh sensitivity and a rapid response. However, conventional methods for modifying biomolecular probes on sensors often involve intricate and time-consuming procedures that require specialized training. Herein, we propose a simple and versatile approach to functionalize floating-gate (FG) FET sensors by exploiting the strong binding ability of polyvalent interactions and the three-dimensional structure of densely functionalized spherical nucleic acids (SNAs). Crucially, the SNAs can be easily deposited onto a dielectric layer under mild conditions, ensuring stable immobilization of the probes. Further, the SNAs show efficient and robust immobilization on various dielectric layers including Y2O3, Ta2O5, and HfO2, forming conjugates that resist denaturation by various agents. By modifying the DNA sequence within the SNAs, we achieved highly sensitive FG-FET biosensors for DNA, adenosine triphosphate, and viral nucleic acids at the attomolar level. For clinical samples detection, unamplified enterovirus 71 RNA at levels as low as 0.13 copies μL-1 was detected within 100 s. Moreover, the sensor attained 100% accuracy for analyte detection in both positive and negative samples. Our findings provide a general and simple method for fabricating FET-based biochemical sensors and demonstrate that the SNA-modified FG-FET biosensor is a versatile and reliable integrated platform for ultrasensitive biomarker detection.
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Affiliation(s)
- Haoran Wang
- Hunan Institute of Advanced Sensing and Information Technology, Hunan Provincial Key Laboratory of Smart Carbon Materials and Advanced Sensing, Xiangtan University, Hunan 411105, China
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing 100871, China
| | - Jing Xie
- Chinese PLA Center for Disease Control and Prevention, Beijing 100071, China
| | - Mengmeng Xiao
- Hunan Institute of Advanced Sensing and Information Technology, Hunan Provincial Key Laboratory of Smart Carbon Materials and Advanced Sensing, Xiangtan University, Hunan 411105, China
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing 100871, China
| | - Yuehua Ke
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jiawang Li
- Hunan Institute of Advanced Sensing and Information Technology, Hunan Provincial Key Laboratory of Smart Carbon Materials and Advanced Sensing, Xiangtan University, Hunan 411105, China
| | - Zongyu Nie
- Hunan Institute of Advanced Sensing and Information Technology, Hunan Provincial Key Laboratory of Smart Carbon Materials and Advanced Sensing, Xiangtan University, Hunan 411105, China
| | - Qiaoshu Chen
- Hunan Institute of Advanced Sensing and Information Technology, Hunan Provincial Key Laboratory of Smart Carbon Materials and Advanced Sensing, Xiangtan University, Hunan 411105, China
| | - Zhiyong Zhang
- Hunan Institute of Advanced Sensing and Information Technology, Hunan Provincial Key Laboratory of Smart Carbon Materials and Advanced Sensing, Xiangtan University, Hunan 411105, China
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing 100871, China
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5
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Wang G, Han S, Lu Y. From Structure to Application: The Evolutionary Trajectory of Spherical Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310026. [PMID: 38860348 DOI: 10.1002/smll.202310026] [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: 11/03/2023] [Revised: 05/09/2024] [Indexed: 06/12/2024]
Abstract
Since the proposal of the concept of spherical nucleic acids (SNAs) in 1996, numerous studies have focused on this topic and have achieved great advances. As a new delivery system for nucleic acids, SNAs have advantages over conventional deoxyribonucleic acid (DNA) nanostructures, including independence from transfection reagents, tolerance to nucleases, and lower immune reactions. The flexible structure of SNAs proves that various inorganic or organic materials can be used as the core, and different types of nucleic acids can be conjugated to realize diverse functions and achieve surprising and exciting outcomes. The special DNA nanostructures have been employed for immunomodulation, gene regulation, drug delivery, biosensing, and bioimaging. Despite the lack of rational design strategies, potential cytotoxicity, and structural defects of this technology, various successful examples demonstrate the bright and convincing future of SNAs in fields such as new materials, clinical practice, and pharmacy.
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Affiliation(s)
- Guijia Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
| | - Sanyang Han
- Institute of Biopharmaceutical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
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6
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Dore MD, Laurent Q, Lachance-Brais C, Das T, Luo X, Sleiman HF. DNA Hierarchical Superstructures from Micellar Units: Stiff Hydrogels and Anisotropic Nanofibers. Chemistry 2024; 30:e202401453. [PMID: 38951115 DOI: 10.1002/chem.202401453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
Supramolecular materials have been assembled using a wide range of interactions, including the hydrophobic effect, DNA base-pairing, and hydrogen bonding. Specifically, DNA amphiphiles with a hydrophobic building block self-assemble into diverse morphologies depending on the length and composition of both blocks. Herein, we take advantage of the orthogonality of different supramolecular interactions - the hydrophobic effect, Watson-Crick-Franklin base pairing and RNA kissing loops - to create hierarchical self-assemblies with controlled morphologies on both the nanometer and the micrometer scales. Assembly through base-pairing leads to the formation of hybrid, multi-phasic hydrogels with high stiffness and self-healing properties. Assembly via hydrophobic core interactions gives anisotropic, discrete assemblies, where DNA fibers with one sequence are terminated with DNA spheres bearing different sequences. This work opens new avenues for the bottom-up construction of DNA-based materials, with promising applications in drug delivery, tissue engineering, and the creation of complex DNA structures from a minimum array of components.
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Affiliation(s)
- Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, H3A 0B8, Montréal, QC, Canada
| | - Quentin Laurent
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, H3A 0B8, Montréal, QC, Canada
| | | | - Trishalina Das
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, H3A 0B8, Montréal, QC, Canada
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, H3A 0B8, Montréal, QC, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, H3A 0B8, Montréal, QC, Canada
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7
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Valatabar N, Oroojalian F, Kazemzadeh M, Mokhtarzadeh AA, Safaralizadeh R, Sahebkar A. Recent advances in gene delivery nanoplatforms based on spherical nucleic acids. J Nanobiotechnology 2024; 22:386. [PMID: 38951806 PMCID: PMC11218236 DOI: 10.1186/s12951-024-02648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
Gene therapy is a therapeutic option for mitigating diseases that do not respond well to pharmacological therapy. This type of therapy allows for correcting altered and defective genes by transferring nucleic acids to target cells. Notably, achieving a desirable outcome is possible by successfully delivering genetic materials into the cell. In-vivo gene transfer strategies use two major classes of vectors, namely viral and nonviral. Both of these systems have distinct pros and cons, and the choice of a delivery system depends on therapeutic objectives and other considerations. Safe and efficient gene transfer is the main feature of any delivery system. Spherical nucleic acids (SNAs) are nanotechnology-based gene delivery systems (i.e., non-viral vectors). They are three-dimensional structures consisting of a hollow or solid spherical core nanoparticle that is functionalized with a dense and highly organized layer of oligonucleotides. The unique structural features of SNAs confer them a high potency in internalization into various types of tissue and cells, a high stability against nucleases, and efficay in penetrating through various biological barriers (such as the skin, blood-brain barrier, and blood-tumor barrier). SNAs also show negligible toxicity and trigger minimal immune response reactions. During the last two decades, all these favorable physicochemical and biological attributes have made them attractive vehicles for drug and nucleic acid delivery. This article discusses the unique structural properties, types of SNAs, and also optimization mechanisms of SNAs. We also focus on recent advances in the synthesis of gene delivery nanoplatforms based on the SNAs.
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Affiliation(s)
| | - Fatemeh Oroojalian
- Department of Medical Nanotechnology, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mina Kazemzadeh
- Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | | | - Reza Safaralizadeh
- Department of Animal Biology Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Dore MD, Rafique MG, Yang TP, Zorman M, Platnich CM, Xu P, Trinh T, Rizzuto FJ, Cosa G, Li J, Guarné A, Sleiman HF. Heat-activated growth of metastable and length-defined DNA fibers expands traditional polymer assembly. Nat Commun 2024; 15:4384. [PMID: 38782917 PMCID: PMC11116425 DOI: 10.1038/s41467-024-48722-2] [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: 11/03/2022] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Biopolymers such as nucleic acids and proteins exhibit dynamic backbone folding, wherein site-specific intramolecular interactions determine overall structure. Proteins then hierarchically assemble into supramolecular polymers such as microtubules, that are robust yet dynamic, constantly growing or shortening to adjust to cellular needs. The combination of dynamic, energy-driven folding and growth with structural stiffness and length control is difficult to achieve in synthetic polymer self-assembly. Here we show that highly charged, monodisperse DNA-oligomers assemble via seeded growth into length-controlled supramolecular fibers during heating; when the temperature is lowered, these metastable fibers slowly disassemble. Furthermore, the specific molecular structures of oligomers that promote fiber formation contradict the typical theory of block copolymer self-assembly. Efficient curling and packing of the oligomers - or 'curlamers' - determine morphology, rather than hydrophobic to hydrophilic ratio. Addition of a small molecule stabilises the DNA fibers, enabling temporal control of polymer lifetime and underscoring their potential use in nucleic-acid delivery, stimuli-responsive biomaterials, and soft robotics.
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Affiliation(s)
- Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | | | - Tianxiao Peter Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Marlo Zorman
- Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Pengfei Xu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47906, USA
| | - Alba Guarné
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
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9
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Yang B, Cui T, Guo L, Dong L, Wu J, Xing Y, Xu Y, Chen J, Wang Y, Cui Z, Dong Y. Advanced Smart Biomaterials for Regenerative Medicine and Drug Delivery Based on Phosphoramidite Chemistry: From Oligonucleotides to Precision Polymers. Biomacromolecules 2024; 25:2701-2714. [PMID: 38608139 DOI: 10.1021/acs.biomac.4c00259] [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: 04/14/2024]
Abstract
Over decades of development, while phosphoramidite chemistry has been known as the leading method in commercial synthesis of oligonucleotides, it has also revolutionized the fabrication of sequence-defined polymers (SDPs), offering novel functional materials in polymer science and clinical medicine. This review has introduced the evolution of phosphoramidite chemistry, emphasizing its development from the synthesis of oligonucleotides to the creation of universal SDPs, which have unlocked the potential for designing programmable smart biomaterials with applications in diverse areas including data storage, regenerative medicine and drug delivery. The key methodologies, functions, biomedical applications, and future challenges in SDPs, have also been summarized in this review, underscoring the significance of breakthroughs in precisely synthesized materials.
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Affiliation(s)
- Bo Yang
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Ting Cui
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Liang Guo
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Lianqiang Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wu
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongzheng Xing
- National Engineering Research Center for Colloidal Materials, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Yun Xu
- Center for Medical Device Evaluation, China Food and Drug Administration (CFDA), Beijing 100084, China
| | - Jian Chen
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Yufei Wang
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Zhonghui Cui
- Sinopec (Beijing) Research Institute of Chemical Industry CO., Ltd., Beijing 100013, P. R. China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Park J, Evangelopoulos M, Vasher MK, Kudruk S, Ramani N, Mayer V, Solivan AC, Lee A, Mirkin CA. Enhancing Endosomal Escape and Gene Regulation Activity for Spherical Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306902. [PMID: 37932003 PMCID: PMC10947971 DOI: 10.1002/smll.202306902] [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: 08/11/2023] [Revised: 10/19/2023] [Indexed: 11/08/2023]
Abstract
The therapeutic potential of small interfering RNAs (siRNAs) is limited by their poor stability and low cellular uptake. When formulated as spherical nucleic acids (SNAs), siRNAs are resistant to nuclease degradation and enter cells without transfection agents with enhanced activity compared to their linear counterparts; however, the gene silencing activity of SNAs is limited by endosomal entrapment, a problem that impacts many siRNA-based nanoparticle constructs. To increase cytosolic delivery, SNAs are formulated using calcium chloride (CaCl2 ) instead of the conventionally used sodium chloride (NaCl). The divalent calcium (Ca2+ ) ions remain associated with the multivalent SNA and have a higher affinity for SNAs compared to their linear counterparts. Importantly, confocal microscopy studies show a 22% decrease in the accumulation of CaCl2 -salted SNAs within the late endosomes compared to NaCl-salted SNAs, indicating increased cytosolic delivery. Consistent with this finding, CaCl2 -salted SNAs comprised of siRNA and antisense DNA all exhibit enhanced gene silencing activity (up to 20-fold), compared to NaCl-salted SNAs regardless of sequence or cell line (U87-MG and SK-OV-3) studied. Moreover, CaCl2 -salted SNA-based forced intercalation probes show improved cytosolic mRNA detection.
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Affiliation(s)
- Jungsoo Park
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
| | - Michael Evangelopoulos
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, 60208, United States
| | - Matthew K. Vasher
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, 60208, United States
| | - Sergej Kudruk
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
| | - Namrata Ramani
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Material Sciences and Engineering, Northwestern University, Evanston, Illinois, 60208, United States
| | - Vinzenz Mayer
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
| | - Alexander C. Solivan
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
| | - Andrew Lee
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, 60208
| | - Chad A. Mirkin
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois, 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Material Sciences and Engineering, Northwestern University, Evanston, Illinois, 60208, United States
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, 60208
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11
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Asohan J, Fakih HH, Das T, Sleiman HF. Control of the Assembly and Disassembly of Spherical Nucleic Acids Is Critical for Enhanced Gene Silencing. ACS NANO 2024; 18:3996-4007. [PMID: 38265027 DOI: 10.1021/acsnano.3c05940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Spherical nucleic acids─nanospheres with nucleic acids on their corona─have emerged as a promising class of nanocarriers, aiming to address the shortcomings of traditional nucleic therapeutics, namely, their poor stability, biodistribution, and cellular entry. By conjugating hydrophobic monomers to a growing nucleic acid strand in a sequence-defined manner, our group has developed self-assembled spherical nucleic acids (SaSNAs), for unaided, enhanced gene silencing. By virtue of their self-assembled nature, SaSNAs can disassemble under certain conditions in contrast to covalent or gold nanoparticle SNAs. Gene silencing involves multiple steps including cellular uptake, endosomal escape, and therapeutic cargo release. Whether assembly vs disassembly is advantageous to any of these steps has not been previously studied. In this work, we modify the DNA and hydrophobic portions of SaSNAs and examine their effects on stability, cellular uptake, and gene silencing. When the linkages between the hydrophobic units are changed from phosphate to phosphorothioate, we find that the SaSNAs disassemble better in endosomal conditions and exhibit more efficacious silencing, despite having cellular uptake similar to that of their phosphate counterparts. Thus, disassembly in the endolysosomal compartments is advantageous, facilitating the release of the nucleic acid cargo and the interactions between the hydrophobic units and endosomal lipids. We also find that SaSNAs partially disassemble in serum to bind albumin; the disassembled, albumin-bound strands are less efficient at cellular uptake and gene silencing than their assembled counterparts, which can engage scavenger receptors for internalization. When the DNA portion is cross-linked by G-quadruplex formation, disassembly decreases and cellular uptake significantly increases. However, this does not translate to greater gene silencing, again illustrating the need for disassembly of the SaSNAs when they are in the endosome. This work showcases the advantages of the dual nature of SaSNAs for gene silencing, requiring extracellular assembly and disassembly inside the cell compartments.
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Affiliation(s)
- Jathavan Asohan
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
| | - Trishalina Das
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St West, Montreal, Québec Canada, H3A 0B8
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12
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Zhao F, Frandsen M, Capodaglio S, Sleiman HF. DNA-Mediated Peptide Assembly into Protein Mimics. J Am Chem Soc 2024; 146:1946-1956. [PMID: 38226787 DOI: 10.1021/jacs.3c08984] [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: 01/17/2024]
Abstract
The design of new protein structures is challenging due to their vast sequence space and the complexity of protein folding. Here, we report a new modular DNA-templated strategy to construct protein mimics. We achieve the spatial control of multiple peptide units by conjugation with DNA and hybridization to a branched DNA trimer template followed by covalent stapling of the preorganized peptides into a single unit. A library of protein mimics with different lengths, sequences, and heptad registers has been efficiently constructed. DNA-templated protein mimics show an α-helix or coiled-coil motif formation even when they are constructed from weakly interacting peptide units. Their attached DNA handles can be used to exert dynamic control over the protein mimics' secondary and tertiary structures. This modular strategy will facilitate the development of DNA-encoded protein libraries for the rapid discovery of new therapeutics, enzymes, and antibody mimics.
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Affiliation(s)
- Fangzhou Zhao
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Martin Frandsen
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, Aarhus 8000, Denmark
| | - Sabrina Capodaglio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma I-43124, Italy
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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13
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Faiad S, Laurent Q, Prinzen AL, Asohan J, Saliba D, Toader V, Sleiman HF. Impact of the Core Chemistry of Self-Assembled Spherical Nucleic Acids on their In Vitro Fate. Angew Chem Int Ed Engl 2023; 62:e202315768. [PMID: 37905978 DOI: 10.1002/anie.202315768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Nucleic acid therapeutics (NATs), such as mRNA, small interfering RNA or antisense oligonucleotides are extremely efficient tools to modulate gene expression and tackle otherwise undruggable diseases. Spherical nucleic acids (SNAs) can efficiently deliver small NATs to cells while protecting their payload from nucleases, and have improved biodistribution and muted immune activation. Self-assembled SNAs have emerged as nanostructures made from a single DNA-polymer conjugate with similar favorable properties as well as small molecule encapsulation. However, because they maintain their structure by non-covalent interactions, they might suffer from disassembly in biologically relevant conditions, especially with regard to their interaction with serum proteins. Here, we report a systematic study of the factors that govern the fate of self-assembled SNAs. Varying the core chemistry and using stimuli-responsive disulfide crosslinking, we show that extracellular stability upon binding with serum proteins is important for recognition by membrane receptors, triggering cellular uptake. At the same time, intracellular dissociation is required for efficient therapeutic release. Disulfide-crosslinked SNAs combine these two properties and result in efficient and non-toxic unaided gene silencing therapeutics. We anticipate these investigations will help the translation of promising self-assembled structures towards in vivo gene silencing applications.
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Affiliation(s)
- Sinan Faiad
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
| | - Quentin Laurent
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
| | - Alexander L Prinzen
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
| | - Jathavan Asohan
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
| | - Violeta Toader
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St West, H3A 0B8, Montreal, Québec, Canada
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14
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Mangla P, Vicentini Q, Biscans A. Therapeutic Oligonucleotides: An Outlook on Chemical Strategies to Improve Endosomal Trafficking. Cells 2023; 12:2253. [PMID: 37759475 PMCID: PMC10527716 DOI: 10.3390/cells12182253] [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: 06/21/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The potential of oligonucleotide therapeutics is undeniable as more than 15 drugs have been approved to treat various diseases in the liver, central nervous system (CNS), and muscles. However, achieving effective delivery of oligonucleotide therapeutics to specific tissues still remains a major challenge, limiting their widespread use. Chemical modifications play a crucial role to overcome biological barriers to enable efficient oligonucleotide delivery to the tissues/cells of interest. They provide oligonucleotide metabolic stability and confer favourable pharmacokinetic/pharmacodynamic properties. This review focuses on the various chemical approaches implicated in mitigating the delivery problem of oligonucleotides and their limitations. It highlights the importance of linkers in designing oligonucleotide conjugates and discusses their potential role in escaping the endosomal barrier, a bottleneck in the development of oligonucleotide therapeutics.
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Affiliation(s)
- Priyanka Mangla
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
| | - Quentin Vicentini
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
- Department of Laboratory Medicine, Clinical Research Centre, Karolinska Institute, 141 57 Stockholm, Sweden
| | - Annabelle Biscans
- Oligonucleotide Discovery, Discovery Sciences Research and Development, AstraZeneca, 431 38 Gothenburg, Sweden; (P.M.); (Q.V.)
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15
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Kaviani S, Fakih HH, Asohan J, Katolik A, Damha MJ, Sleiman HF. Sequence-Controlled Spherical Nucleic Acids: Gene Silencing, Encapsulation, and Cellular Uptake. Nucleic Acid Ther 2023; 33:265-276. [PMID: 37196168 DOI: 10.1089/nat.2022.0062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Antisense oligonucleotides (ASOs) can predictably alter RNA processing and control protein expression; however, challenges in the delivery of these therapeutics to specific tissues, poor cellular uptake, and endosomal escape have impeded progress in translating these agents into the clinic. Spherical nucleic acids (SNAs) are nanoparticles with a DNA external shell and a hydrophobic core that arise from the self-assembly of ASO strands conjugated to hydrophobic polymers. SNAs have recently shown significant promise as vehicles for improving the efficacy of ASO cellular uptake and gene silencing. However, to date, no studies have investigated the effect of the hydrophobic polymer sequence on the biological properties of SNAs. In this study, we created a library of ASO conjugates by covalently attaching polymers with linear or branched [dodecanediol phosphate] units and systematically varying polymer sequence and composition. We show that these parameters can significantly impact encapsulation efficiency, gene silencing activity, SNA stability, and cellular uptake, thus outlining optimized polymer architectures for gene silencing.
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Affiliation(s)
- Sepideh Kaviani
- Department of Chemistry, McGill University, Montreal, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, Montreal, Canada
| | - Jathavan Asohan
- Department of Chemistry, McGill University, Montreal, Canada
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, Canada
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Canada
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16
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Lachance‐Brais C, Rammal M, Asohan J, Katolik A, Luo X, Saliba D, Jonderian A, Damha MJ, Harrington MJ, Sleiman HF. Small Molecule-Templated DNA Hydrogel with Record Stiffness Integrates and Releases DNA Nanostructures and Gene Silencing Nucleic Acids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205713. [PMID: 36752390 PMCID: PMC10131789 DOI: 10.1002/advs.202205713] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/18/2022] [Indexed: 05/31/2023]
Abstract
Deoxyribonucleic acid (DNA) hydrogels are a unique class of programmable, biocompatible materials able to respond to complex stimuli, making them valuable in drug delivery, analyte detection, cell growth, and shape-memory materials. However, unmodified DNA hydrogels in the literature are very soft, rarely reaching a storage modulus of 103 Pa, and they lack functionality, limiting their applications. Here, a DNA/small-molecule motif to create stiff hydrogels from unmodified DNA, reaching 105 Pa in storage modulus is used. The motif consists of an interaction between polyadenine and cyanuric acid-which has 3-thymine like faces-into multimicrometer supramolecular fibers. The mechanical properties of these hydrogels are readily tuned, they are self-healing and thixotropic. They integrate a high density of small, nontoxic molecules, and are functionalized simply by varying the molecule sidechain. They respond to three independent stimuli, including a small molecule stimulus. These stimuli are used to integrate and release DNA wireframe and DNA origami nanostructures within the hydrogel. The hydrogel is applied as an injectable delivery vector, releasing an antisense oligonucleotide in cells, and increasing its gene silencing efficacy. This work provides tunable, stimuli-responsive, exceptionally stiff all-DNA hydrogels from simple sequences, extending these materials' capabilities.
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Affiliation(s)
| | - Mostafa Rammal
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Jathavan Asohan
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Adam Katolik
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Xin Luo
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Antranik Jonderian
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | - Masad J. Damha
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
| | | | - Hanadi F. Sleiman
- Department of ChemistryMcGill University801 Sherbrooke St WMontrealH3A 0B8Canada
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17
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Zhang C, Zhao X, Li D, Ji F, Dong A, Chen X, Zhang J, Wang X, Zhao Y, Chen X. Advances in 5-aminoketovaleric acid(5-ALA) nanoparticle delivery system based on cancer photodynamic therapy. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Rizzuto FJ, Dore MD, Rafique MG, Luo X, Sleiman HF. DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers. J Am Chem Soc 2022; 144:12272-12279. [PMID: 35762655 DOI: 10.1021/jacs.2c03506] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The self-assembly of block copolymers is often rationalized by structure and microphase separation; pathways that diverge from this parameter space may provide new mechanisms of polymer assembly. Here, we show that the sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. While increasing the length of DNA led to predictable changes in self-assembly, changing only the sequence of DNA produced three distinct structures: spherical micelles (spherical nucleic acids, SNAs) from flexible poly(thymine) DNA, fibers from semirigid mixed-sequence DNA, and networked superstructures from rigid poly(adenine) DNA. The secondary structure of poly(adenine) DNA strands drives a temperature-dependent polymerization and assembly mechanism: copolymers stored in an SNA reservoir form fibers after thermal activation, which then aggregate upon cooling to form interwoven networks. DNA is often used as a programming code that aids in nanostructure addressability and function. Here, we show that the inherent physical and chemical properties of single-stranded DNA sequences also make them an ideal material to direct self-assembled morphologies and select for new methods of supramolecular polymerization.
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Affiliation(s)
- Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
| | - Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
| | | | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC H3A 08B, Canada
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19
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Fan S, Liu X, Yu S, Wang J, Li C, Cheng S, Hong M. Aptamer-functionalized fluorine-containing DNAsomes for targeted drug delivery to cancer cells. NEW J CHEM 2022. [DOI: 10.1039/d2nj00967f] [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
A drug-loaded aptamer functionalized fluorine-containing DNAsome was reported here, which can deliver doxorubicin into cancer cells in a targeted manner through receptor mediated endocytosis and induce the apoptosis of cancer cells.
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Affiliation(s)
- Shuhua Fan
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Xiaoyan Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Shuxian Yu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Juan Wang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Chuan Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Shuang Cheng
- School of Agriculture, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Min Hong
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
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20
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Chen L, Li G, Wang X, Li J, Zhang Y. Spherical Nucleic Acids for Near-Infrared Light-Responsive Self-Delivery of Small-Interfering RNA and Antisense Oligonucleotide. ACS NANO 2021; 15:11929-11939. [PMID: 34170121 DOI: 10.1021/acsnano.1c03072] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Herein, we developed a photolabile spherical nucleic acid (PSNA) for carrier-free and near-infrared (NIR) photocontrolled self-delivery of small-interfering RNA (siRNA) and antisense oligonucleotide (ASO). PSNA comprised a hydrophilic siRNA shell with a hydrophobic core containing a peptide nucleic acid-based ASO (pASO) and NIR photosensitizer (PS). The incorporation of a singlet oxygen (1O2)-cleavable linker between the siRNA and pASO allowed on-demand disassembly of PSNA in tumor cells once 1O2 was produced by the inner PS upon NIR light irradiation. The generated 1O2 could also concurrently promote lysosomal escape of the released siRNA and pASO to reach cytosolic targets. Both in vitro and in vivo results demonstrated that, under NIR light irradiation, PSNA could suppress hypoxia inducible factor-1α (HIF-1α) and B-cell lymphoma 2 (Bcl-2) for gene therapy (GT), which further combined photodynamic therapy (PDT) favored by the released PS to inhibit tumor cell growth. Given its carrier-free, NIR-sensitive, designable, and biocompatible merits, PSNA represents a promising self-delivery nanoplatform for cancer therapy.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Gaigai Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xingxing Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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21
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El-Khoury R, Damha MJ. 2'-Fluoro-arabinonucleic Acid (FANA): A Versatile Tool for Probing Biomolecular Interactions. Acc Chem Res 2021; 54:2287-2297. [PMID: 33861067 DOI: 10.1021/acs.accounts.1c00125] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This Account highlights the structural features that render 2'-deoxy-2'-fluoro-arabinonucleic acid (FANA) an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions relevant to chemical biology.The high binding affinity of FANA to DNA and RNA has had implications in therapeutics. FANA can hybridize to complementary RNA, resulting in a predominant A-form helix stabilized by a network of 2'F-H8(purine) pseudohydrogen bonding interactions. We have shown that FANA/RNA hybrids are substrates of RNase H and Ago2, both implicated in the mechanism of action of antisense oligonucleotides (ASOs) and siRNA, respectvely. This knowledge has helped us study the conformational preferences of ASOs and siRNA as well as crRNA in CRISPR-associated Cas9, thereby revealing structural features crucial to biochemical activity.Additionally, FANA is of particular use in stabilizing noncanonical DNA structures. For instance, we have taken advantage of the anti N-glycosidic bond conformation of FANA monomers to induce a parallel topology in telomeric G-quadruplexes. Subsequent single-molecule FRET studies elucidated the mechanism by which these parallel G-quadruplexes are recognized and extended by telomerase. Similarly, we have utilized FANA to stabilize elusive telomeric i-motifs in the presence of concomitant parallel G-quadruplexes and under physiological conditions, thereby reinforcing their potential relevance to telomere biology. In another study, we adapted microarray technology and used FANA substitutions to enhance the binding affinity of the G-quadruplex thrombin-binding aptamer to its thrombin target.Finally, we discovered that DNA polymerases can synthesize FANA strands from DNA templates. On the basis of this property, other groups demonstrated that FANA, like DNA, can store hereditary information. They did so by engineering polymerases to efficiently transfer genetic information from DNA to FANA and retrieve it back into DNA. Subsequent studies showed that FANA could be evolved to acquire ribozyme-like endonuclease or ligase activity and to form high-affinity aptamers.Overall, the implications of these studies are remarkable because they promise a deeper understanding of human biochemistry for innovative therapeutic avenues. This Account summarizes past achievements and provides an outlook for inspiring the increased use of FANA in biological applications and fostering interdisciplinary collaborations.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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