1
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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 DOI: 10.1038/s41467-024-48722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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2
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Lachance-Brais C, Yao C, Reyes-Valenzuela A, Asohan J, Guettler E, Sleiman HF. Exceptional Nuclease Resistance of DNA and RNA with the Addition of Small-Molecule Nucleobase Mimics. J Am Chem Soc 2024; 146:5811-5822. [PMID: 38387071 DOI: 10.1021/jacs.3c07023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Nucleases present a formidable barrier to the application of nucleic acids in biology, significantly reducing the lifetime of nucleic acid-based drugs. Here, we develop a novel methodology to protect DNA and RNA from nucleases by reconfiguring their supramolecular structure through the addition of a nucleobase mimic, cyanuric acid. In the presence of cyanuric acid, polyadenine strands assemble into triple helical fibers known as the polyA/CA motif. We report that this motif is exceptionally resistant to nucleases, with the constituent strands surviving for up to 1 month in the presence of serum. The conferred stability extends to adjacent non-polyA sequences, albeit with diminishing returns relative to their polyA sections due to hypothesized steric clashes. We introduce a strategy to regenerate stability through the introduction of free polyA strands or positively charged amino side chains, enhancing the stability of sequences of varied lengths. The proposed protection mechanism involves enzyme failure to recognize the unnatural polyA/CA motif, coupled with the motif's propensity to form long, bundling supramolecular fibers. The methodology provides a fundamentally new mechanism to protect nucleic acids from degradation using a supramolecular approach and increases lifetime in serum to days, weeks, or months.
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Affiliation(s)
| | - Chihyu Yao
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | | | - Jathavan Asohan
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | - Elizabeth Guettler
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
| | - Hanadi F Sleiman
- McGill University, 801 Sherbrooke St. W., Montreal, Quebec H3A0B8, Canada
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Fakih HH, Tang Q, Summers A, Shin M, Buchwald JE, Gagnon R, Hariharan VN, Echeverria D, Cooper DA, Watts JK, Khvorova A, Sleiman HF. Dendritic amphiphilic siRNA: Selective albumin binding, in vivo efficacy, and low toxicity. Mol Ther Nucleic Acids 2023; 34:102080. [PMID: 38089931 PMCID: PMC10711485 DOI: 10.1016/j.omtn.2023.102080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/14/2023] [Indexed: 01/12/2024]
Abstract
Although an increasing number of small interfering RNA (siRNA) therapies are reaching the market, the challenge of efficient extra-hepatic delivery continues to limit their full therapeutic potential. Drug delivery vehicles and hydrophobic conjugates are being used to overcome the delivery bottleneck. Previously, we reported a novel dendritic conjugate that can be appended efficiently to oligonucleotides, allowing them to bind albumin with nanomolar affinity. Here, we explore the ability of this novel albumin-binding conjugate to improve the delivery of siRNA in vivo. We demonstrate that the conjugate binds albumin exclusively in circulation and extravasates to various organs, enabling effective gene silencing. Notably, we show that the conjugate achieves a balance between hydrophobicity and safety, as it significantly reduces the side effects associated with siRNA interactions with blood components, which are commonly observed in some hydrophobically conjugated siRNAs. In addition, it reduces siRNA monocyte uptake, which may lead to cytokine/inflammatory responses. This work showcases the potential of using this dendritic conjugate as a selective albumin binding handle for the effective and safe delivery of nucleic acid therapeutics. We envision that these properties may pave the way for new opportunities to overcome delivery hurdles of oligonucleotides in future applications.
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Affiliation(s)
- Hassan H. Fakih
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Qi Tang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Ashley Summers
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Minwook Shin
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- College of Pharmacy, Sookmyung Women’s University, Yongsan-gu, Seoul, Korea
| | - Julianna E. Buchwald
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rosemary Gagnon
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Vignesh N. Hariharan
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - David A. Cooper
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jonathan K. Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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7
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Luo X, Saliba D, Yang T, Gentile S, Mori K, Islas P, Das T, Bagheri N, Porchetta A, Guarne A, Cosa G, Sleiman HF. Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309869. [PMID: 37610293 DOI: 10.1002/anie.202309869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross-sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h-motif structure incorporating double-crossover (DX) tile-like DNA edges to achieve structural rigidity and provide efficient self-assembly of h-motif-based DNA nanotube (H-NT) units, thus producing programmable, micrometer-long nanotubes. We demonstrate control of the H-NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H-NTs can assemble at near-physiological salt conditions and will serve as an easily synthesized, DNA-economical modular template for biosensors, plasmonics, or other functional materials and as cost-efficient drug-delivery vehicles for biomedical applications.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Tianxiao Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal QC, Canada
| | - Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Keita Mori
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Patricia Islas
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Trishalina Das
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | | | - Alba Guarne
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal QC, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
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8
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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: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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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. Adv Sci (Weinh) 2023; 10:e2205713. [PMID: 36752390 PMCID: PMC10131789 DOI: 10.1002/advs.202205713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Saliba D, Luo X, Rizzuto FJ, Sleiman HF. Programming rigidity into size-defined wireframe DNA nanotubes. Nanoscale 2023; 15:5403-5413. [PMID: 36826342 DOI: 10.1039/d2nr06185f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada.
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11
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Brown TM, Fakih HH, Saliba D, Asohan J, Sleiman HF. Stabilization of Functional DNA Structures with Mild Photochemical Methods. J Am Chem Soc 2023; 145:2142-2151. [PMID: 36651186 DOI: 10.1021/jacs.2c08808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A significant barrier to biological applications of DNA structures is their instability to nucleases. UV-mediated thymine dimerization can crosslink and stabilize DNA nanostructures, but its effect on DNA strand hybridization fidelity and function is unclear. In this work, we first compare a number of methods for DNA irradiation with different wavelengths of light and different photosensitizers. We demonstrate that all approaches can achieve nuclease protection; however, the levels of DNA off-target crosslinking and damage vary. We then describe mild irradiation conditions intended to safeguard DNA against nuclease degradation. We demonstrate up to 25× increase in serum stability while minimizing off-target damage and maintaining functions such as hybridization efficiency, gene silencing, aptamer binding, and DNA nanostructure formation. Our methodology requires no complex instruments beyond a UV light source and no synthetic modification of the DNA itself, allowing for applications in numerous areas of nucleic acid therapy and nanotechnology.
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Affiliation(s)
- Tyler M Brown
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Jathavan Asohan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal , Québec City H3A 0B8, Canada
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12
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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: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Saliba D, Trinh T, Lachance-Brais C, Prinzen AL, Rizzuto FJ, de Rochambeau D, Sleiman HF. Asymmetric patterning drives the folding of a tripodal DNA nanotweezer. Chem Sci 2021; 13:74-80. [PMID: 35059153 PMCID: PMC8694393 DOI: 10.1039/d1sc04793k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 11/21/2022] Open
Abstract
DNA tweezers have emerged as powerful devices for a wide range of biochemical and sensing applications; however, most DNA tweezers consist of single units activated by DNA recognition, limiting their range of motion and ability to respond to complex stimuli. Herein, we present an extended, tripodal DNA nanotweezer with a small molecule junction. Simultaneous, asymmetric elongation of our molecular core is achieved using polymerase chain reaction (PCR) to produce length- and sequence-specific DNA arms with repeating DNA regions. When rigidified, our DNA tweezer can be addressed with streptavidin-binding ligands. Full control over the number, separation, and location of these ligands enables site-specific streptavidin recognition; all three arms of the DNA nanotweezer wrap around multiple streptavidin units simultaneously. Our approach combines the simplicity of DNA tile arrays with the size regime normally provided by DNA origami, offering an integrated platform for the use of branched DNA scaffolds as structural building blocks, protein sensors, and dynamic, stimuli-responsive materials.
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Affiliation(s)
- Daniel Saliba
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | | | - Alexander L Prinzen
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Felix J Rizzuto
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Donatien de Rochambeau
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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14
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Lachance-Brais C, Hennecker CD, Alenaizan A, Luo X, Toader V, Taing M, Sherrill CD, Mittermaier AK, Sleiman HF. Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics. J Am Chem Soc 2021; 143:19824-19833. [PMID: 34783562 DOI: 10.1021/jacs.1c08972] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.
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Affiliation(s)
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Violeta Toader
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Monica Taing
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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15
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Dore MD, Trinh T, Zorman M, de Rochambeau D, Platnich CM, Xu P, Luo X, Remington JM, Toader V, Cosa G, Li J, Sleiman HF. Thermosetting supramolecular polymerization of compartmentalized DNA fibers with stereo sequence and length control. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Abstract
DNA nanotechnology has produced a wide range of self-assembled structures, offering unmatched possibilities in terms of structural design. Because of their programmable assembly and precise control of size, shape, and function, DNA particles can be used for numerous biological applications, including imaging, sensing, and drug delivery. While the biocompatibility, programmability, and ease of synthesis of nucleic acids have rapidly made them attractive building blocks, many challenges remain to be addressed before using them in biological conditions. Enzymatic hydrolysis, low cellular uptake, immune cell recognition and degradation, and unclear biodistribution profiles are yet to be solved. Rigorous methodologies are needed to study, understand, and control the fate of self-assembled DNA structures in physiological conditions. In this review, we describe the current challenges faced by the field as well as recent successes, highlighting the potential to solve biology problems or develop smart drug delivery tools. We then propose an outlook to drive the translation of DNA constructs toward preclinical design. We particularly believe that a detailed understanding of the fate of DNA nanostructures within living organisms, achieved through thorough characterization, is the next required step to reach clinical maturity.
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Affiliation(s)
- Aurélie Lacroix
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
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17
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Abstract
Single molecules can now be visualised with unprecedented precision. As the resolution of single-molecule experiments improves, so too does the breadth, quantity and quality of information that can be extracted using these methodologies. In the field of DNA nanotechnology, we use programmable interactions between nucleic acids to generate complex, multidimensional structures. We can use single-molecule techniques - ranging from electron and fluorescence microscopies to electrical and force spectroscopies - to report on the structure, morphology, robustness, sample heterogeneity and other properties of these DNA nanoconstructs. In this Tutorial Review, we will detail how complementarity between static and dynamic single-molecule techniques can provide a unified image of DNA nanoarchitectures. The single-molecule methods that we discuss provide unprecedented insight into chemical and structural behaviour, yielding not just an average outcome but reporting on the distribution of values, ultimately showing how bulk properties arise from the collective behaviour of individual structures. As the fields of both DNA nanotechnology and single-molecule characterisation intertwine, a feedback loop is generated between disciplines, providing new opportunities for the development and operation of DNA-based materials as sensors, delivery vehicles, machinery and structural scaffolds.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W, Montreal, Quebec H3A 0B8, Canada.
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18
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Fakih HH, Katolik A, Malek-Adamian E, Fakhoury JJ, Kaviani S, Damha MJ, Sleiman HF. Design and enhanced gene silencing activity of spherical 2'-fluoroarabinose nucleic acids (FANA-SNAs). Chem Sci 2021; 12:2993-3003. [PMID: 34164068 PMCID: PMC8179377 DOI: 10.1039/d0sc06645a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Drug delivery vectors for nucleic acid therapeutics (NATs) face significant barriers for translation into the clinic. Spherical nucleic acids (SNAs) – nanoparticles with an exterior shell made up of DNA strands and a hydrophobic interior – have recently shown great potential as vehicles to improve the biodistribution and efficacy of NATs. To date, SNA design has not taken advantage of the powerful chemical modifications available to NATs. Here, we modify SNAs with 2′-deoxy-2′-fluoro-d-arabinonucleic acid (FANA-SNA), and show increased stability, enhanced gene silencing potency and unaided uptake (gymnosis) as compared to free FANA. By varying the spacer region between the nucleic acid strand and the attached hydrophobic polymer, we show that a cleavable DNA based spacer is essential for maximum activity. This design feature will be important when implementing functionalized nucleic acids into nanostructures for gene silencing. The modularity of the FANA-SNA was demonstrated by silencing two different targets. Transfection-free delivery was superior for the modified SNA compared to the free FANA oligonucleotide. Optimizing FANA modified spherical nucleic acids (FANA-SNAs) for highly efficient delivery of nucleic acid therapeutics.![]()
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Affiliation(s)
- Hassan H Fakih
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Adam Katolik
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | | | - Johans J Fakhoury
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Sepideh Kaviani
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Masad J Damha
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University Montreal Quebec H3A 0B8 Canada
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19
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Li Q, Zhao J, Liu L, Jonchhe S, Rizzuto FJ, Mandal S, He H, Wei S, Sleiman HF, Mao H, Mao C. A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials. Nat Mater 2020; 19:1012-1018. [PMID: 32661383 PMCID: PMC7732259 DOI: 10.1038/s41563-020-0728-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
The diversity of DNA duplex structures is limited by a binary pair of hydrogen-bonded motifs. Here we show that poly(thymine) self-associates into antiparallel, right-handed duplexes in the presence of melamine, a small molecule that presents a triplicate set of the hydrogen-bonding face of adenine. X-ray crystallography shows that in the complex two poly(thymine) strands wrap around a helical column of melamine, which hydrogen bonds to thymine residues on two of its three faces. The mechanical strength of the thymine-melamine-thymine triplet surpasses that of adenine-thymine base pairs, which enables a sensitive detection of melamine at 3 pM. The poly(thymine)-melamine duplex is orthogonal to native DNA base pairing and can undergo strand displacement without the need for overhangs. Its incorporation into two-dimensional grids and hybrid DNA-small-molecule polymers highlights the poly(thymine)-melamine duplex as an additional tool for DNA nanotechnology.
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Affiliation(s)
- Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Longfei Liu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | - Felix J Rizzuto
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | - Huawei He
- Biological Science Research Center, Southwest University, Chongqing, China
| | - Sansen Wei
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, Québec, Canada.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA.
- Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, OH, USA.
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
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20
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Prinzen AL, Saliba D, Hennecker C, Trinh T, Mittermaier A, Sleiman HF. Amplified Self‐Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA‐Minimal Architectures. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander L. Prinzen
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Daniel Saliba
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Christopher Hennecker
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Anthony Mittermaier
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
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21
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22
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Prinzen AL, Saliba D, Hennecker C, Trinh T, Mittermaier A, Sleiman HF. Amplified Self‐Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA‐Minimal Architectures. Angew Chem Int Ed Engl 2020; 59:12900-12908. [PMID: 32277788 DOI: 10.1002/anie.202001123] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/24/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Alexander L. Prinzen
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Daniel Saliba
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Christopher Hennecker
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Anthony Mittermaier
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
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23
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Luo X, Lachance-Brais C, Bantle A, Sleiman HF. The assemble, grow and lift-off (AGLO) strategy to construct complex gold nanostructures with pre-designed morphologies. Chem Sci 2020; 11:4911-4921. [PMID: 34122947 PMCID: PMC8159246 DOI: 10.1039/d0sc00553c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The construction of metallic nanostructures with customizable morphologies and complex shapes has been an essential pursuit in nanoscience. DNA nanotechnology has enabled the fabrication of increasingly complex DNA nanostructures with unprecedented specificity, programmability and sub-nanometer precision, which makes it an ideal approach to rationally organize metallic nanostructures. Here we report an Assemble, Grow and Lift-Off (AGLO) strategy to construct robust standalone gold nanostructures with pre-designed customizable shapes in solution, using only a simple 2D DNA origami sheet as a versatile transient template. Gold nanoparticle (AuNP) seeds were firstly assembled onto the pre-designed binding sites of the DNA origami template and then additional gold was slowly deposited onto the AuNP seeds. The growing seed surfaces eventually merge with adjacent seeds to generate one continuous gold nanostructure in a pre-designed shape, which can then be lifted off the origami template. Diverse customized patterns of templated AuNP seeds were successfully transformed into corresponding gold nanostructures with the target structure transformation percentage over 80%. Moreover, the AGLO strategy can be incorporated with a magnetic bead separation platform to enable the easy recycling of the excess AuNP seeds and DNA components.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Christophe Lachance-Brais
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Amy Bantle
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
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24
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Lacroix A, Fakih HH, Sleiman HF. Detailed cellular assessment of albumin-bound oligonucleotides: Increased stability and lower non-specific cell uptake. J Control Release 2020; 324:34-46. [PMID: 32330572 DOI: 10.1016/j.jconrel.2020.04.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/11/2020] [Indexed: 01/04/2023]
Abstract
Conjugation of lipid moieties to nucleic-acid therapeutics increases their interaction with cellular membranes, enhances their uptake and influences in vivo distribution. Once injected in biological fluids, such modifications trigger the binding of various serum proteins, which in turn play a major role in determining the fate of oligonucleotides. Yet, the role played by each of these proteins, more than 300 in serum, remains to be elucidated. Albumin, the most abundant circulating protein is an attractive candidate to study, as it was previously used to enhance the therapeutic effect of various drugs. Herein, we present a thorough fluorescent-based methodology to study the effect of strong and specific albumin-binding on the fate and cellular uptake of DNA oligonucleotides. We synthesized a library of molecules that exhibit non-covalent binding to albumin, with affinities ranging from high (nanomolar) to none. Our results revealed that strong albumin binding can be used as a strategy to reduce degradation of oligonucleotides in physiological conditions caused by enzymes (nucleases), to reduce uptake and degradation by immune cells (macrophages) and to prevent non-specific uptake by cells. We believe that introducing protein-binding domains in oligonucleotides can be used as a strategy to control the fate of oligonucleotides in physiological environments. While our study focuses on albumin, we believe that such systematic studies, which elucidate the role of serum proteins systematically, will ultimately provide a toolbox to engineer the next-generation of therapeutic oligonucleotides, overcoming many of the barriers encountered by these therapeutics, such as stability, immunogenicity and off-target effects.
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Affiliation(s)
- Aurélie Lacroix
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada
| | - Hassan H Fakih
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada.
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25
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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26
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020; 59:4091-4098. [DOI: 10.1002/anie.201913956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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27
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020; 59:3573-3577. [PMID: 31867832 DOI: 10.1002/anie.201915675] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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28
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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29
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Bujold KE, Fakih HH, Sleiman HF. Design Strategy to Access siRNA-Encapsulating DNA "Nanosuitcases" That Can Conditionally Release Their Cargo. Methods Mol Biol 2019; 1974:69-81. [PMID: 31098996 DOI: 10.1007/978-1-4939-9220-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
DNA nanotechnology enables the design and assembly of DNA nanostructures with unprecedented control over their size and shape. Additionally, the programmable base-pairing alphabet of DNA allows the incorporation of responsive units within these DNA nanostructures. Here, we describe a general design strategy to construct responsive DNA prisms that can encapsulate and selectively release an encapsulated siRNA upon recognition of an oligonucleotide trigger. This prismatic DNA scaffold design is adaptable and can encapsulate oligonucleotides of any length and type. Moreover, the prism can be made to respond to an oligonucleotide trigger of interest like a messenger RNA (mRNA) or a microRNA (miRNA), thus enabling dual or synergistic therapeutic strategies. We present an overview of the design strategy used to access these DNA nanostructures, followed by the steps involved in DNA sequence generation, assembly, and validation of this construct.
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Affiliation(s)
| | - Hassan H Fakih
- Department of Chemistry, McGill University, Montréal, QC, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, QC, Canada.
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30
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Platnich CM, Hariri AA, Sleiman HF, Cosa G. Advancing Wireframe DNA Nanostructures Using Single-Molecule Fluorescence Microscopy Techniques. Acc Chem Res 2019; 52:3199-3210. [PMID: 31675207 DOI: 10.1021/acs.accounts.9b00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA nanotechnology relies on the molecular recognition properties of DNA to produce complex architectures through self-assembly. The resulting DNA nanostructures allow scientists to organize functional materials at the nanoscale and have therefore found applications in many domains of materials science over the past several years. These scaffolds have been used to position proteins, nanoparticles, carbon nanotubes, and other nanomaterials with high spatial resolution. In addition to their remarkable performance as frameworks for other species, DNA constructs also possess interesting dynamic properties, which have led to their use in logic circuits, drug delivery vehicles, and molecular walkers. Although DNA nanostructures have become increasingly complex, the development of tools to study them has lagged. Currently, gel electrophoresis, dynamic light scattering, and ensemble fluorescence measurements are widely used to characterize DNA-based assemblies. Unfortunately, ensemble averaging in these methods obscures malformed structures and may mask properties associated with structure, length, and shape in polydisperse samples. While atomic force microscopy allows for the determination of morphology at the single-molecule level, this technique cannot typically be used to assess the dynamic properties of these constructs. To analyze the function of DNA-based devices such as molecular motors and reconfigurable nanostructures in real time, new single-molecule techniques are required. This Account details the work from our laboratories toward developing single-molecule fluorescence (SMF) methodologies for the structural and dynamic characterization of wireframe DNA nanostructures, one at a time. The methods described herein provide us with two separate yet related sets of information: First, we can statically examine the nanostructures one by one to assess their robustness, structural fidelity, and morphology. This is primarily done using two-color stepwise photobleaching, wherein we can examine the subunit stoichiometry of our assemblies before and after various perturbations to the structures. For example, we can introduce length mismatches to cause the nanotube to bend or perform strand displacement reactions to generate single-stranded, flexible analogues of our materials. Second, due to the unmatched spatiotemporal resolution of SMF techniques, we can study the dynamic character of these assemblies by implementing structural changes to the nanotube and monitoring them in real time. With this structural and dynamic information in hand, our groups have additionally developed new tools for the improved construction of DNA nanotubes, inspired by solid-phase DNA synthesis. By assembling the nanotubes in a stepwise manner, highly monodisperse nanostructures of any desired length can be made without a template strand. In this way, unique building blocks can also be added sequence-specifically, allowing for the production of user-defined scaffolds to organize nanoscale materials in three dimensions. This method, in combination with our imaging and analysis protocols, may be extended to assemble and inspect other supramolecular constructs in a controlled manner. Overall, by combining synthesis, characterization, and analysis, these single-molecule techniques hold the potential to advance the study of DNA nanostructures and dynamic DNA-based devices.
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Affiliation(s)
- Casey M. Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Amani A. Hariri
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Danis AS, Metera KL, Payne NA, Sleiman HF, Mauzeroll J. Bottom‐Up Characterization and Self‐Assembly of Electrogenerated Chemiluminescence Active Ruthenium Nanospheres. ChemElectroChem 2019. [DOI: 10.1002/celc.201900702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andrew S. Danis
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal H3 A 0B8, QC Canada
| | - Kimberly L. Metera
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal, QC H3 A 0B8 Canada
| | - Nicholas A. Payne
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal H3 A 0B8, QC Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal, QC H3 A 0B8 Canada
| | - Janine Mauzeroll
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montreal H3 A 0B8, QC Canada
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Lacroix A, Vengut-Climent E, de Rochambeau D, Sleiman HF. Uptake and Fate of Fluorescently Labeled DNA Nanostructures in Cellular Environments: A Cautionary Tale. ACS Cent Sci 2019; 5:882-891. [PMID: 31139724 PMCID: PMC6535766 DOI: 10.1021/acscentsci.9b00174] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Indexed: 05/10/2023]
Abstract
Fluorescent dye labeling of DNA oligonucleotides and nanostructures is one of the most used techniques to track their fate and cellular localization inside cells. Here, we report that intracellular fluorescence, and even FRET signals, cannot be correlated with the cellular uptake of intact DNA structures. Live cell imaging revealed high colocalization of cyanine-labeled DNA oligos and nanostructures with phosphorylated small-molecule cyanine dyes, one of the degradation products from these DNA compounds. Nuclease degradation of the strands outside and inside the cell results in a misleading intracellular fluorescent signal. The signal is saturated by the fluorescence of the degradation product (phosphorylated dye). To test our hypothesis, we synthesized a range of DNA structures, including Cy3- and Cy5-labeled DNA cubes and DNA tetrahedra, and oligonucleotides with different stabilities toward nucleases. All give fluorescence signals within the mitochondria after cellular uptake and strongly colocalize with a free phosphorylated dye control. Kinetics experiments revealed that uptake of stable DNA structures is delayed. We also studied several parameters influencing fluorescent data: stability of the DNA strand, fixation methods that can wash away the signal, position of the dye on the DNA strand, and design of FRET experiments. DNA nanostructures hold tremendous potential for biomedical applications and biotechnology because of their biocompatibility, programmability, and easy synthesis. However, few examples of successful DNA machines in vivo have been reported. We believe this contribution can be used as a guide to design better cellular uptake experiments when using fluorescent dyes, in order to further propel the biological development, and application of DNA nanostructures.
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Fakih HH, Fakhoury JJ, Bousmail D, Sleiman HF. Minimalist Design of a Stimuli-Responsive Spherical Nucleic Acid for Conditional Delivery of Oligonucleotide Therapeutics. ACS Appl Mater Interfaces 2019; 11:13912-13920. [PMID: 30720262 DOI: 10.1021/acsami.8b18790] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we report a component-minimal spherical nucleic acid (SNA) from monodisperse DNA-polymer conjugates that can load and release nucleic acid therapeutics in a stimuli-responsive manner. We show that this vehicle assembles from only four strands, and conditional release of its antisense therapeutic cargo can be induced upon recognition of specific oligonucleotide triggers via strand displacement. The latter (triggers) may be a microRNA that offers additional synergistic therapy, in addition to the previously shown ability of the SNA to load hydrophobic drugs. The SNA is easy to prepare, has dynamic character, releases its cargo only upon the presence of both triggers, and can survive biological conditions while protecting its cargo. The gene silencing potency of the cargo was tested in live cells and shown to be suppressed when loaded in the SNA, and its activity was restored only upon release with the two triggers. This vehicle has the essential characteristics of versatility, ease of synthesis, low cost, highly responsive behavior, and ability to support combination therapies, making it a promising candidate for cell-selective drug delivery and clinical transition.
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Affiliation(s)
- Hassan H Fakih
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Johans J Fakhoury
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Danny Bousmail
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Hanadi F Sleiman
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
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34
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Trinh T, Saliba D, Liao C, de Rochambeau D, Prinzen AL, Li J, Sleiman HF. “Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence. Angew Chem Int Ed Engl 2019; 58:3042-3047. [PMID: 30290048 DOI: 10.1002/anie.201809251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Tuan Trinh
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Chenyi Liao
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Donatien de Rochambeau
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Alexander Lee Prinzen
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Jianing Li
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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Platnich CM, Hariri AA, Rahbani JF, Gordon JB, Sleiman HF, Cosa G. Kinetics of Strand Displacement and Hybridization on Wireframe DNA Nanostructures: Dissecting the Roles of Size, Morphology, and Rigidity. ACS Nano 2018; 12:12836-12846. [PMID: 30485067 DOI: 10.1021/acsnano.8b08016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Dynamic wireframe DNA structures have gained significant attention in recent years, with research aimed toward using these architectures for sensing and encapsulation applications. For these assemblies to reach their full potential, however, knowledge of the rates of strand displacement and hybridization on these constructs is required. Herein, we report the use of single-molecule fluorescence methodologies to observe the reversible switching between double- and single-stranded forms of triangular wireframe DNA nanotubes. Specifically, by using fluorescently labeled DNA strands, we were able to monitor changes in intensity over time as we introduced different sequences. This allowed us to extract detailed kinetic information on the strand displacement and hybridization processes. Due to the polymeric nanotube structure, the ability to individually address each of the three sides, and the inherent polydispersity of our samples as a result of the step polymerization by which they are formed, a library of compounds could be studied independently yet simultaneously. Kinetic models relying on mono-exponential decays, multi-exponential decays, or sigmoidal behavior were adjusted to the different constructs to retrieve erasing and refilling kinetics. Correlations were made between the kinetic behavior observed, the site accessibility, the nanotube length, and the structural robustness of wireframe DNA nanostructures, including fully single-stranded analogs. Overall, our results reveal how the length, morphology, and rigidity of the DNA framework modulate the kinetics of strand displacement and hybridization as well as the overall addressability and structural stability of the structures under study.
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Affiliation(s)
- Casey M Platnich
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Amani A Hariri
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Janane F Rahbani
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Jesse B Gordon
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Hanadi F Sleiman
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
| | - Gonzalo Cosa
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada
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Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF. Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions. J Am Chem Soc 2018; 141:1100-1108. [DOI: 10.1021/jacs.8b11898] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Dillon McCarthy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Xin Luo
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
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37
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Trinh T, Saliba D, Liao C, de Rochambeau D, Prinzen AL, Li J, Sleiman HF. “Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tuan Trinh
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Chenyi Liao
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Donatien de Rochambeau
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Alexander Lee Prinzen
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Jianing Li
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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de Rochambeau D, Sun Y, Barlog M, Bazzi HS, Sleiman HF. Modular Strategy To Expand the Chemical Diversity of DNA and Sequence-Controlled Polymers. J Org Chem 2018; 83:9774-9786. [DOI: 10.1021/acs.joc.8b01184] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donatien de Rochambeau
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec H3A 0B8, Canada
| | - Yuanye Sun
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec H3A 0B8, Canada
| | - Maciej Barlog
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Hassan S. Bazzi
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec H3A 0B8, Canada
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39
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Harkness V RW, Avakyan N, Sleiman HF, Mittermaier AK. Mapping the energy landscapes of supramolecular assembly by thermal hysteresis. Nat Commun 2018; 9:3152. [PMID: 30089867 PMCID: PMC6082911 DOI: 10.1038/s41467-018-05502-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/02/2018] [Indexed: 01/28/2023] Open
Abstract
Understanding how biological macromolecules assemble into higher-order structures is critical to explaining their function in living organisms and engineered biomaterials. Transient, partly-structured intermediates are essential in many assembly processes and pathway selection, but are challenging to characterize. Here we present a simple thermal hysteresis method based on rapid, non-equilibrium melting and annealing measurements that maps the rate of supramolecular assembly as a function of temperature and concentration. A straightforward analysis of these surfaces provides detailed information on the natures of assembly pathways, offering temperature resolution beyond that accessible with conventional techniques. Validating the approach using a tetrameric guanine quadruplex, we obtain strikingly good agreement with previous kinetics measurements and reveal temperature-dependent changes to the assembly pathway. In an application to the recently discovered co-assembly of polydeoxyadenosine (poly(A)) and cyanuric acid, we show that fiber elongation is initiated when an unstable complex containing three poly(A) monomers acquires a fourth strand. Complex assembly pathways often involve transient, partly-formed intermediates that are challenging to characterize. Here, the authors present a simple and rapid spectroscopic thermal hysteresis method for mapping the energy landscapes of supramolecular assembly.
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Affiliation(s)
- Robert W Harkness V
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Nicole Avakyan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada.
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40
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Rahbani JF, Hsu JCC, Chidchob P, Sleiman HF. Single-stranded templates as railroad tracks for hierarchical assembly of DNA origami. Nanoscale 2018; 10:13994-13999. [PMID: 29995052 DOI: 10.1039/c8nr03185a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA origami is one of the most effective tools for bottom-up construction of novel objects and devices at the nanometer-scale. However, many applications require larger structures than can be obtained with the conventional single-stranded scaffold, typically 7249 nucleotides. Here, we address this limitation by developing custom-made single-stranded scaffolds that bind pre-assembled origami tiles and induce their one-dimensional organization in high yields. Our synthetic method allows the conversion of multiple repetitive and unique sequences into correctly assembled, large backbones, and to finely tune the position and frequency of each building block. Granted with these regions, three and five origami tiles were successfully arranged in 1-D with the aid of one or two scaffolds, forming a nano-"railroad track". This new method increases length scale in DNA origami without increasing cost and complexity, and is anticipated to increase the yield of other approaches aiming to assemble large origami structures.
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Affiliation(s)
- Janane F Rahbani
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - John C C Hsu
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
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41
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Affiliation(s)
- Danny Bousmail
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A0B8, Canada
| | - Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A0B8, Canada
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Abstract
DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use. Recent work on incorporating blunt-end stacking and hydrophobic interactions as orthogonal instruction rules in DNA assembly, and several emerging applications of DNA nanomaterials will also be highlighted.
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Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada.
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Rahbani JF, Vengut‐Climent E, Chidchob P, Gidi Y, Trinh T, Cosa G, Sleiman HF. DNA Nanotubes with Hydrophobic Environments: Toward New Platforms for Guest Encapsulation and Cellular Delivery. Adv Healthc Mater 2018; 7:e1701049. [PMID: 29356412 DOI: 10.1002/adhm.201701049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/17/2017] [Indexed: 01/13/2023]
Abstract
Natural systems combine different supramolecular interactions in a hierarchical manner to build structures. In contrast, DNA nanotechnology relies almost exclusively on DNA base pairing for structure generation. Introducing other supramolecular interactions can expand the structural and functional range of DNA assemblies, but this requires an understanding of the interplay between these interactions. Here, an economic strategy to build DNA nanotubes functionalized with lipid-like polymers is reported. When these polymers are linked to the nanotube using a spacer, they fold inside to create a hydrophobic environment within the nanotube; the nanotube can encapsulate small molecules and conditionally release them when specific DNA strands are added, as monitored by single-molecule fluorescence microscopy. When the polymers are directly linked to the nanostructure without spacers, they interact intermolecularly to form a network of DNA bundles. This morphological switch can be directly observed using a strand displacement strategy. The two association modes result in different cellular uptake behavior. Nanotubes with internal hydrophobic association show dye-mediated mitochondrial colocalization inside cells; while the bundles disassemble into smaller polymer-coated structures that reduce the extent of nonspecific cellular uptake. This approach uncovers parameters to direct the hierarchical assembly of DNA nanostructures, and produces promising materials for targeted drug delivery.
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Affiliation(s)
- Janane F. Rahbani
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Empar Vengut‐Climent
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Pongphak Chidchob
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Yasser Gidi
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Gonzalo Cosa
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
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Luo X, Chidchob P, Rahbani JF, Sleiman HF. Encapsulation of Gold Nanoparticles into DNA Minimal Cages for 3D-Anisotropic Functionalization and Assembly. Small 2018; 14:1702660. [PMID: 29205958 DOI: 10.1002/smll.201702660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Gold nanoparticles (AuNPs) endowed with anisotropic DNA valency are an important class of materials, as they can assemble into complex structures with a minimal number of DNA strands. However, methods to encode 3D DNA strand patterns on AuNPs with a controlled number of unique DNA strands in a predesigned spatial arrangement remain elusive. In this work, a simple one-step method to yield such DNA-decorated AuNPs is demonstrated, through encapsulating AuNPs into DNA minimal nanocages. The AuNP@DNA cage encapsulation complex inherits the 3D anisotropic molecular information from the DNA nanocage with enhanced structural stability. The DNA nanocage can be further functionalized and used as a building block for the self-assembly of complex architectures, such as dimers and trimers, programmed assemblies with sequential growth DNA backbones and DNA origami.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
| | - Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
| | - Janane F Rahbani
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC, H3A 0B8, Canada
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Dore MD, Fakhoury JJ, Lacroix A, Sleiman HF. Templated synthesis of spherical RNA nanoparticles with gene silencing activity. Chem Commun (Camb) 2018; 54:11296-11299. [DOI: 10.1039/c8cc06994h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bioactive RNA nanoparticles with gene silencing activity have been synthesized in high yield using a complementary spherical DNA nanoparticle.
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Hariri AA, Hamblin GD, Hardwick JS, Godin R, Desjardins JF, Wiseman PW, Sleiman HF, Cosa G. Stoichiometry and Dispersity of DNA Nanostructures Using Photobleaching Pair-Correlation Analysis. Bioconjug Chem 2017; 28:2340-2349. [DOI: 10.1021/acs.bioconjchem.7b00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | | | - Jean-Francois Desjardins
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
| | - Paul W. Wiseman
- Department
of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 0B8, Canada
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Affiliation(s)
- Nicole Avakyan
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
| | - Justin W. Conway
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
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Bousmail D, Amrein L, Fakhoury JJ, Fakih HH, Hsu JCC, Panasci L, Sleiman HF. Precision spherical nucleic acids for delivery of anticancer drugs. Chem Sci 2017; 8:6218-6229. [PMID: 28989655 PMCID: PMC5628336 DOI: 10.1039/c7sc01619k] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022] Open
Abstract
Highly monodisperse sequence-defined spherical nucleic acids (HE12–SNAs) for delivery of small-molecule anticancer drugs.
We report a spherical nucleic acid (SNA) system for the delivery of BKM120, an anticancer drug for treatment of chronic lymphocytic leukemia (CLL). While promising for cancer treatment, this drug crosses the blood–brain barrier causing significant side-effects in patients. The DNA nanoparticle encapsulates BKM120 in high efficiency, and is unparalleled in its monodispersity, ease of synthesis and stability in different biological media and in serum. These DNA nanostructures demonstrate efficient uptake in human cervical cancer (HeLa) cells, and increased internalization of cargo. In vitro studies show that BKM120-loaded nanoparticles promote apoptosis in primary patient CLL lymphocytes, and act as sensitizers of other antitumor drugs, without causing non-specific inflammation. Evaluation of this drug delivery system in vivo shows long circulation times up to 24 hours, full body distribution, accumulation at tumor sites and minimal leakage through the blood–brain barrier. Our results demonstrate the great potential of these delivery vehicles as a general platform for chemotherapeutic drug delivery.
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Affiliation(s)
- Danny Bousmail
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - Lilian Amrein
- Department of Oncology , Jewish General Hospital , 3755 Cote Sainte-Catherine Rd. , Montreal , Canada .
| | - Johans J Fakhoury
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - Hassan H Fakih
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - John C C Hsu
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
| | - Lawrence Panasci
- Department of Oncology , Jewish General Hospital , 3755 Cote Sainte-Catherine Rd. , Montreal , Canada .
| | - Hanadi F Sleiman
- Department of Chemistry , Centre for Self-Assembled Chemical Structures (CSACS) , McGill University , 801 Sherbrooke St. W. , Montreal , Canada .
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Lacroix A, Edwardson TGW, Hancock MA, Dore MD, Sleiman HF. Development of DNA Nanostructures for High-Affinity Binding to Human Serum Albumin. J Am Chem Soc 2017; 139:7355-7362. [DOI: 10.1021/jacs.7b02917] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aurélie Lacroix
- Department
of Chemistry and Centre for Self-Assembled Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Thomas G. W. Edwardson
- Department
of Chemistry and Centre for Self-Assembled Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Mark A. Hancock
- SPR-MS
Facility, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
| | - Michael D. Dore
- Department
of Chemistry and Centre for Self-Assembled Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department
of Chemistry and Centre for Self-Assembled Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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