1
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Singh N, Singh A, Dhanka M, Bhatia D. DNA functionalized programmable hybrid biomaterials for targeted multiplexed applications. J Mater Chem B 2024. [PMID: 38973587 DOI: 10.1039/d4tb00287c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
With the advent of DNA nanotechnology, DNA-based biomaterials have emerged as a unique class of materials at the center of various biological advances. Owing to DNA's high modification capacity via programmable Watson-Crick base-pairing, DNA structures of desired design with increased complexity have been developed. However, the limited scalability, along with poor mechanical properties, high synthesis costs, and poor stability, reduced the adaptability of DNA-based materials to complex biological applications. DNA-based hybrid biomaterials were designed to overcome these limitations by conjugating DNA with functional materials. Today, DNA-based hybrid materials have attracted significant attention in biological engineering with broad application prospects in biomedicine, clinical diagnosis, and nanodevices. Here, we summarize the recent advances in DNA-based hybrid materials with an in-depth understanding of general molecular design principles, functionalities, and applications. Finally, the challenges and prospects associated with DNA-based hybrid materials are discussed at the end of this review.
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Affiliation(s)
- Nihal Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Ankur Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Mukesh Dhanka
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Dhiraj Bhatia
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
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2
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Yadav K, Gnanakani SPE, Sahu KK, Veni Chikkula CK, Vaddi PS, Srilakshmi S, Yadav R, Sucheta, Dubey A, Minz S, Pradhan M. Nano revolution of DNA nanostructures redefining cancer therapeutics-A comprehensive review. Int J Biol Macromol 2024; 274:133244. [PMID: 38901506 DOI: 10.1016/j.ijbiomac.2024.133244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
DNA nanostructures are a promising tool in cancer treatment, offering an innovative way to improve the effectiveness of therapies. These nanostructures can be made solely from DNA or combined with other materials to overcome the limitations of traditional single-drug treatments. There is growing interest in developing nanosystems capable of delivering multiple drugs simultaneously, addressing challenges such as drug resistance. Engineered DNA nanostructures are designed to precisely deliver different drugs to specific locations, enhancing therapeutic effects. By attaching targeting molecules, these nanostructures can recognize and bind to cancer cells, increasing treatment precision. This approach offers tailored solutions for targeted drug delivery, enabling the delivery of multiple drugs in a coordinated manner. This review explores the advancements and applications of DNA nanostructures in cancer treatment, with a focus on targeted drug delivery and multi-drug therapy. It discusses the benefits and current limitations of nanoscale formulations in cancer therapy, categorizing DNA nanostructures into pure forms and hybrid versions optimized for drug delivery. Furthermore, the review examines ongoing research efforts and translational possibilities, along with challenges in clinical integration. By highlighting the advancements in DNA nanostructures, this review aims to underscore their potential in improving cancer treatment outcomes.
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Affiliation(s)
- Krishna Yadav
- Rungta College of Pharmaceutical Sciences and Research, Kohka, Bhilai 490024, India
| | - S Princely E Gnanakani
- Department of Pharmaceutical Biotechnology, Parul Institute of Pharmacy, Parul University, Post Limda, Ta.Waghodia - 391760, Dist. Vadodara, Gujarat, India
| | - Kantrol Kumar Sahu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh 281406, India
| | - C Krishna Veni Chikkula
- Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, USA
| | - Poorna Sai Vaddi
- Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, USA
| | - S Srilakshmi
- Gitam School of Pharmacy, Department of Pharmaceutical Chemistry, Gitams University, Vishakhapatnam, India
| | - Renu Yadav
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana 122103, India
| | - Sucheta
- School of Medical and Allied Sciences, K. R. Mangalam University, Sohna Road, Gurugram, Haryana 122103, India
| | - Akhilesh Dubey
- Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics, Mangaluru 575018, Karnataka, India
| | - Sunita Minz
- Department of Pharmacy, Indira Gandhi National Tribal University, Amarkantak (M.P.), India
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3
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Mathis K, Gaddam S, Koneru R, Sunkavalli N, Wang C, Patel M, Kohon AI, Meckes B. Multifunctional hydrogels with spatially controlled light activation with photocaged oligonucleotides. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101922. [PMID: 38911357 PMCID: PMC11192495 DOI: 10.1016/j.xcrp.2024.101922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Recreating tissue environments with precise control over mechanical, biochemical, and cellular organization is essential for next-generation tissue models for drug discovery, development studies, and the replication of disease environments. However, controlling these properties at cell-scale lengths remains challenging. Here, we report the development of printing approaches that leverage polyethylene glycol diacrylate (PEGDA) hydrogels containing photocaged oligonucleotides to spatially program material characteristics with non-destructive, non-ultraviolet light. We further integrate this system with a perfusion chamber to allow us to alter the composition of PEGDA hydrogels while retaining common light-activatable photocaged DNAs. We demonstrate that the hydrogels can capture DNA functionalized materials, including cells coated with complementary oligonucleotides with spatial control using biocompatible wavelengths. Overall, these materials open pathways to orthogonal capture of any DNA functionalized materials while not changing the sequences of the DNA.
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Affiliation(s)
- Katelyn Mathis
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Saanvi Gaddam
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Rishi Koneru
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Nikhil Sunkavalli
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Catherine Wang
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Manan Patel
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- Texas Academy of Mathematics and Science, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Afia Ibnat Kohon
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Brian Meckes
- Department of Biomedical Engineering, University of North Texas, 3940 North Elm St., Denton, TX 76207, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
- Lead contact
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4
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Lemke P, Moench S, Jäger PS, Oelschlaeger C, Rabe KS, Domínguez CM, Niemeyer CM. Micromechanical Indentation Platform for Rapid Analysis of Viscoelastic Biomolecular Hydrogels. SMALL METHODS 2024:e2400251. [PMID: 38607949 DOI: 10.1002/smtd.202400251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The advent of biomedical applications of soft bioinspired materials has entailed an increasing demand for streamlined and expedient characterization methods meant for both research and quality control objectives. Here, a novel measurement system for the characterization of biological hydrogels with volumes as low as 75 µL was developed. The system is based on an indentation platform equipped with micrometer drive actuators that allow the determination of both the fracture points and Young's moduli of relatively stiff polymers, including agarose, as well as the measurements of viscosity for exceptionally soft and viscous hydrogels, such as DNA hydrogels. The sensitivity of the method allows differentiation between DNA hydrogels produced by rolling circle amplification based on different template sequences and synthesis protocols. In addition, the polymerization kinetics of the hydrogels can be determined by time-resolved measurements, and the apparent viscosities of even more complex DNA-based nanocomposites can be measured. The platform presented here thus offers the possibility to characterize a broad variety of soft biomaterials in a targeted, fast, and cost-effective manner, holding promises for applications in fundamental materials science and ensuring reproducibility in the handling of complex materials.
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Affiliation(s)
- Phillip Lemke
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Svenja Moench
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Paula S Jäger
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Claude Oelschlaeger
- Karlsruhe Institute of Technology (KIT), Institute for Mechanical Process Engineering and Mechanics, Gotthard-Franz-Straße 3, 76131, Karlsruhe, Germany
| | - Kersten S Rabe
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Carmen M Domínguez
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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5
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Singh A, Sharma JJ, Mohanta B, Sood A, Han SS, Sharma A. Synthetic and biopolymers-based antimicrobial hybrid hydrogels: a focused review. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2024; 35:675-716. [PMID: 37943320 DOI: 10.1080/09205063.2023.2278814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/29/2023] [Indexed: 11/10/2023]
Abstract
The constantly accelerating occurrence of microbial infections and their antibiotic resistance has spurred advancement in the field of material sciences and has guided the development of novel materials with anti-bacterial properties. To address the clinical exigencies, the material of choice should be biodegradable, biocompatible, and able to offer prolonged antibacterial effects. As an attractive option, hydrogels have been explored globally as a potent biomaterial platform that can furnish essential antibacterial attributes owing to its three-dimensional (3D) hydrophilic polymeric network, adequate biocompatibility, and cellular adhesion. The current review focuses on the utilization of different antimicrobial hydrogels based on their sources (natural and synthetic). Further, the review also highlights the strategies for the generation of hydrogels with their advantages and disadvantages and their applications in different biomedical fields. Finally, the prospects in the development of hydrogels-based antimicrobial biomaterials are discussed along with some key challenges encountered during their development and clinical translation.
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Affiliation(s)
- Anand Singh
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Janmay Jai Sharma
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Billeswar Mohanta
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Ankur Sood
- School of Chemical Engineering, Yeungnam University, Gyeongsan, South Korea
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, Gyeongsan, South Korea
| | - Anirudh Sharma
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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6
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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7
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Ong Q, Xufeng X, Stellacci F. Versatile Capillary Cells for Handling Concentrated Samples in Analytical Ultracentrifugation. Anal Chem 2024; 96:2567-2573. [PMID: 38301115 PMCID: PMC10867799 DOI: 10.1021/acs.analchem.3c05006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
In concentrated macromolecular dispersions, far-from-ideal intermolecular interactions determine the dispersion behaviors including phase transition, crystallization, and liquid-liquid phase separation. Here, we present a novel versatile capillary-cell design for analytical ultracentrifugation-sedimentation equilibrium (AUC-SE), ideal for studying samples at high concentrations. Current setups for such studies are difficult and unreliable to handle, leading to a low experimental success rate. The design presented here is easy to use, robust, and reusable for samples in both aqueous and organic solvents while requiring no special tools or chemical modification of AUC cells. The key and unique feature is the fabrication of liquid reservoirs directly on the bottom window of AUC cells, which can be easily realized by laser ablation or mechanical drilling. The channel length and optical path length are therefore tunable. The success rate for assembling this new cell is close to 100%. We demonstrate the practicality of this cell by studying: (1) the equation of state and second virial coefficients of concentrated gold nanoparticle dispersions in water and bovine serum albumin (BSA) as well as lysozyme solution in aqueous buffers, (2) the gelation phase transition of DNA and BSA solutions, and (3) liquid-liquid phase separation of concentrated BSA/polyethylene glycol (PEG) droplets.
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Affiliation(s)
- Quy Ong
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
| | - Xu Xufeng
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
| | - Francesco Stellacci
- Laboratory Of Supramolecular
Nanomaterials And Interfaces, Ecole Polytechnique
Fédérale de Lausanne (EPFL), Station 12, 1015 Lausanne, Switzerland
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8
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Maffeis V, Heuberger L, Nikoletić A, Schoenenberger C, Palivan CG. Synthetic Cells Revisited: Artificial Cells Construction Using Polymeric Building Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305837. [PMID: 37984885 PMCID: PMC10885666 DOI: 10.1002/advs.202305837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
The exponential growth of research on artificial cells and organelles underscores their potential as tools to advance the understanding of fundamental biological processes. The bottom-up construction from a variety of building blocks at the micro- and nanoscale, in combination with biomolecules is key to developing artificial cells. In this review, artificial cells are focused upon based on compartments where polymers are the main constituent of the assembly. Polymers are of particular interest due to their incredible chemical variety and the advantage of tuning the properties and functionality of their assemblies. First, the architectures of micro- and nanoscale polymer assemblies are introduced and then their usage as building blocks is elaborated upon. Different membrane-bound and membrane-less compartments and supramolecular structures and how they combine into advanced synthetic cells are presented. Then, the functional aspects are explored, addressing how artificial organelles in giant compartments mimic cellular processes. Finally, how artificial cells communicate with their surrounding and each other such as to adapt to an ever-changing environment and achieve collective behavior as a steppingstone toward artificial tissues, is taken a look at. Engineering artificial cells with highly controllable and programmable features open new avenues for the development of sophisticated multifunctional systems.
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Affiliation(s)
- Viviana Maffeis
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- NCCR‐Molecular Systems EngineeringBPR 1095, Mattenstrasse 24aBaselCH‐4058Switzerland
| | - Lukas Heuberger
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
| | - Anamarija Nikoletić
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- Swiss Nanoscience InstituteUniversity of BaselKlingelbergstrasse 82BaselCH‐4056Switzerland
| | | | - Cornelia G. Palivan
- Department of ChemistryUniversity of BaselMattenstrasse 22BaselCH‐4002Switzerland
- NCCR‐Molecular Systems EngineeringBPR 1095, Mattenstrasse 24aBaselCH‐4058Switzerland
- Swiss Nanoscience InstituteUniversity of BaselKlingelbergstrasse 82BaselCH‐4056Switzerland
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9
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Raguseo F, Wang Y, Li J, Petrić Howe M, Balendra R, Huyghebaert A, Vadukul DM, Tanase DA, Maher TE, Malouf L, Rubio-Sánchez R, Aprile FA, Elani Y, Patani R, Di Michele L, Di Antonio M. The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes. Nat Commun 2023; 14:8272. [PMID: 38092738 PMCID: PMC10719400 DOI: 10.1038/s41467-023-43872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases that exist on a clinico-pathogenetic spectrum, designated ALS/FTD. The most common genetic cause of ALS/FTD is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here, we investigate the formation of nucleic acid secondary structures in these expansion repeats, and their role in generating condensates characteristic of ALS/FTD. We observe significant aggregation of the hexanucleotide sequence (GGGGCC)n, which we associate to the formation of multimolecular G-quadruplexes (mG4s) by using a range of biophysical techniques. Exposing the condensates to G4-unfolding conditions leads to prompt disassembly, highlighting the key role of mG4-formation in the condensation process. We further validate the biological relevance of our findings by detecting an increased prevalence of G4-structures in C9orf72 mutant human motor neurons when compared to healthy motor neurons by staining with a G4-selective fluorescent probe, revealing signal in putative condensates. Our findings strongly suggest that RNA G-rich repetitive sequences can form protein-free condensates sustained by multimolecular G-quadruplexes, highlighting their potential relevance as therapeutic targets for C9orf72 mutation-related ALS/FTD.
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Affiliation(s)
- Federica Raguseo
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jessica Li
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Rubika Balendra
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anouk Huyghebaert
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Devkee M Vadukul
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Diana A Tanase
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Thomas E Maher
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Layla Malouf
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Roger Rubio-Sánchez
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Francesco A Aprile
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yuval Elani
- Imperial College London, Department of Chemical Engineering, South Kensington, London, SW7 2AZ, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | - Lorenzo Di Michele
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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10
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Das G, Nayak S, Kotness DK, Das P. A biomass-derived dual crosslinked DNA-nanoparticle hydrogel for visible light-induced photodynamic bacterial inactivation. SOFT MATTER 2023; 19:9511-9519. [PMID: 38047904 DOI: 10.1039/d3sm01400b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Sustainability in developing novel nanomaterials (NPs) from biomass sources is a challenging proposition mainly due to the difficulty of infusing or retaining desired chemical functionalities in the biomass substrate. In this study, we demonstrate the synthesis of DNA-nanoparticles (DNA-NP) from onion genomic DNA as a plant biomass source through controlled hydrothermal pyrolysis to retain functional groups in the NPs for predictable downstream chemical transformations. A dual crosslinking scheme was introduced that involves the DNA-NP to form a hydrogel. Chemical crosslinking was achieved through the formation of a Schiff base between the -CHO groups of glutaraldehyde and the amine functionality present on the DNA-NP surface as well as in the nucleobases of the dangling DNA strands of DNA-NP. Simultaneous physical entanglement was attained through hybridization-mediated self-assembly of the dangling DNA strands of the DNA-NP with untransformed onion genomic DNA. As a corollary of the dual crosslinking, the resulting hydrogel not only displayed remarkable mechanical strength but also showed self-healing properties. The ability of the DNA-NP to generate reactive oxygen species (ROS) with visible light irradiation is translated to the hydrogel, making the system potent for biofilm destruction. The high loading efficiency of the model drug ampicillin sodium (Amp) in the hydrogel was achieved which was released in four days. This hints towards the application of the hydrogel through combination antibiotic-antibacterial photodynamic treatment (APDT) as demonstrated here with both Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Gourab Das
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, Patna, Bihar, 801106, India.
| | - Suman Nayak
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, Patna, Bihar, 801106, India.
| | - Dinesh Kumar Kotness
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, Patna, Bihar, 801106, India.
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Bihta, Patna, Bihar, 801106, India.
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11
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Schneider L, Richter M, Oelschlaeger C, Rabe KS, Domínguez CM, Niemeyer CM. Accurate quantification of DNA content in DNA hydrogels prepared by rolling circle amplification. Chem Commun (Camb) 2023; 59:12184-12187. [PMID: 37750315 DOI: 10.1039/d3cc04374f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Accurate quantification of polymerized DNA in rolling circle amplification (RCA)-based hydrogels is challenging due to the high viscosity of these materials, however, it can be achieved with a photometric nucleotide depletion assay or qPCR. We show that the DNA content strongly depends on the template sequence and correlates with the mechanical properties of the hydrogels.
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Affiliation(s)
- Leonie Schneider
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Madleen Richter
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Claude Oelschlaeger
- Institute for Mechanical Process Engineering and Mechanics, Karlsruhe Institute of Technology (KIT), Gotthard-Franz-Straße 3, 76131 Karlsruhe, Germany
| | - Kersten S Rabe
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Carmen M Domínguez
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Christof M Niemeyer
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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12
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Lee M, Kang S, Kim S, Park N. Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors. BIOSENSORS 2023; 13:856. [PMID: 37754090 PMCID: PMC10526965 DOI: 10.3390/bios13090856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023]
Abstract
miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea (S.K.)
| | - Seungjae Kang
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea (S.K.)
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
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13
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Alexander S, Moghadam MG, Rothenbroker M, Y T Chou L. Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics. Adv Drug Deliv Rev 2023; 199:114898. [PMID: 37230305 DOI: 10.1016/j.addr.2023.114898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.
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Affiliation(s)
- Shana Alexander
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | | | - Meghan Rothenbroker
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Leo Y T Chou
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.
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14
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Quazi MZ, Hwang J, Song Y, Park N. Hydrogel-Based Biosensors for Effective Therapeutics. Gels 2023; 9:545. [PMID: 37504424 PMCID: PMC10378974 DOI: 10.3390/gels9070545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Nanotechnology and polymer engineering are navigating toward new developments to control and overcome complex problems. In the last few decades, polymer engineering has received researchers' attention and similarly, polymeric network-engineered structures have been vastly studied. Prior to therapeutic application, early and rapid detection analyses are critical. Therefore, developing hydrogel-based sensors to manage the acute expression of diseases and malignancies to devise therapeutic approaches demands advanced nanoengineering. However, nano-therapeutics have emerged as an alternative approach to tackling strenuous diseases. Similarly, sensing applications for multiple kinds of analytes in water-based environments and other media are gaining wide interest. It has also been observed that these functional roles can be used as alternative approaches to the detection of a wide range of biomolecules and pathogenic proteins. Moreover, hydrogels have emerged as a three-dimensional (3D) polymeric network that consists of hydrophilic natural or synthetic polymers with multidimensional dynamics. The resemblance of hydrogels to tissue structure makes them more unique to study inquisitively. Preceding studies have shown a vast spectrum of synthetic and natural polymer applications in the field of biotechnology and molecular diagnostics. This review explores recent studies on synthetic and natural polymers engineered hydrogel-based biosensors and their applications in multipurpose diagnostics and therapeutics. We review the latest studies on hydrogel-engineered biosensors, exclusively DNA-based and DNA hydrogel-fabricated biosensors.
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Affiliation(s)
- Mohzibudin Z Quazi
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Jimin Hwang
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Youngseo Song
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
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15
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Zare I, Taheri-Ledari R, Esmailzadeh F, Salehi MM, Mohammadi A, Maleki A, Mostafavi E. DNA hydrogels and nanogels for diagnostics, therapeutics, and theragnostics of various cancers. NANOSCALE 2023. [PMID: 37337663 DOI: 10.1039/d3nr00425b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
As an efficient class of hydrogel-based therapeutic drug delivery systems, deoxyribonucleic acid (DNA) hydrogels (particularly DNA nanogels) have attracted massive attention in the last five years. The main contributor to this is the programmability of these 3-dimensional (3D) scaffolds that creates fundamental effects, especially in treating cancer diseases. Like other active biological ingredients (ABIs), DNA hydrogels can be functionalized with other active agents that play a role in targeting drug delivery and modifying the half-life of the therapeutic cargoes in the body's internal environment. Considering the brilliant advantages of DNA hydrogels, in this survey, we intend to submit an informative collection of feasible methods for the design and preparation of DNA hydrogels and nanogels, and the responsivity of the immune system to these therapeutic cargoes. Moreover, the interactions of DNA hydrogels with cancer biomarkers are discussed in this account. Theragnostic DNA nanogels as an advanced species for both detection and therapeutic purposes are also briefly reviewed.
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Affiliation(s)
- Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz 7178795844, Iran
| | - Reza Taheri-Ledari
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Farhad Esmailzadeh
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Mohammad Mehdi Salehi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Adibeh Mohammadi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology, Tehran, 16846-13114, Iran
| | - Ebrahim Mostafavi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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16
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Fei Z, Gupta N, Li M, Xiao P, Hu X. Toward highly effective loading of DNA in hydrogels for high-density and long-term information storage. SCIENCE ADVANCES 2023; 9:eadg9933. [PMID: 37163589 PMCID: PMC10171811 DOI: 10.1126/sciadv.adg9933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Digital information, when converted into a DNA sequence, provides dense, stable, energy-efficient, and sustainable data storage. The most stable method for encapsulating DNA has been in an inorganic matrix of silica, iron oxide, or both, but are limited by low DNA uptake and complex recovery techniques. This study investigated a rationally designed thermally responsive functionally graded (TRFG) hydrogel as a simple and cost-effective method for storing DNA. The TRFG hydrogel shows high DNA uptake, long-term protection, and reusability due to nondestructive DNA extraction. The high loading capacity was achieved by directly absorbing DNA from the solution, which is then retained because of its interaction with a hyperbranched cationic polymer loaded into a negatively charged hydrogel matrix used as a support and because of its thermoresponsive nature, which allows DNA concentration within the hydrogel through multiple swelling/deswelling cycles. We were able to achieve a high DNA data density of 7.0 × 109 gigabytes per gram using a hydrogel-based system.
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Affiliation(s)
- Zhongjie Fei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Nupur Gupta
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore 639798, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Mengjie Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiao Hu
- School of Material Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
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17
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Naskar S, Bhatia D, Lin ST, Maiti PK. Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars. Phys Chem Chem Phys 2023; 25:7847-7858. [PMID: 36857659 DOI: 10.1039/d2cp04683k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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18
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i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. Commun Chem 2023; 6:31. [PMID: 36797370 PMCID: PMC9935537 DOI: 10.1038/s42004-023-00831-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC5 normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC5 to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.
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19
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Borum RM, Moore C, Mantri Y, Xu M, Jokerst JV. Supramolecular Loading of DNA Hydrogels with Dye-Drug Conjugates for Real-Time Photoacoustic Monitoring of Chemotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2204330. [PMID: 36403233 PMCID: PMC9811488 DOI: 10.1002/advs.202204330] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/18/2022] [Indexed: 06/16/2023]
Abstract
A longstanding problem with conventional cancer therapy is the nonspecific distribution of chemotherapeutics. Monitoring drug release in vivo via noninvasive bioimaging can thus have value, but it is difficult to distinguish loaded from released drug in live tissue. Here, this work describes an injectable supramolecular hydrogel that allows slow and trackable release of doxorubicin (Dox) via photoacoustic (PA) tomography. Dox is covalently linked with photoacoustic methylene blue (MB) to monitor Dox before, during, and after release from the hydrogel carrier. The conjugate (MB-Dox) possesses an IC50 of 161.4 × 10-9 m against human ovarian carcinoma (SKOV3) cells and loads into a DNA-clad hydrogel with 91.3% loading efficiency due to MB-Dox's inherent intramolecular affinity to DNA. The hydrogel is biodegradable by nuclease digestion, which causes gradual release of MB-Dox. This release rate is tunable based on the wt% of the hydrogel. This hydrogel maintains distinct PA contrast on the order of days when injected in vivo and demonstrates activatable PA spectral shifts during hydrogel degradation. The released and loaded payload can be imaged relative to live tissue via PA and ultrasound signal being overlaid in real-time. The hydrogel slowed the rate of the murine intraperitoneal tumor growth 72.2% more than free Dox.
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Affiliation(s)
- Raina M. Borum
- Department of NanoEngineeringUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
| | - Colman Moore
- Department of NanoEngineeringUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
| | - Yash Mantri
- Department of BioEngineeringUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
| | - Ming Xu
- Department of NanoEngineeringUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
| | - Jesse V. Jokerst
- Department of NanoEngineeringUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
- Department of RadiologyUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
- Materials Science ProgramUniversity of California, San Diego9500 Gilman DriveLa JollaCalifornia92093United States
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20
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Nayak S, Kumar P, Shankar R, Mukhopadhyay AK, Mandal D, Das P. Biomass derived self-assembled DNA-dot hydrogels for enhanced bacterial annihilation. NANOSCALE 2022; 14:16097-16109. [PMID: 36226636 DOI: 10.1039/d2nr03810b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanotization of biomass for interesting biomedical applications is still in the nascent stage with no visible market available products. While products derived from biomass DNA and protein have unquestionable biocompatibility, induction of desired properties needs careful manipulation of the biomolecules. Herein, for the first time, we report the transformation of onion derived biomass DNA into DNA-dots through its partial hydrothermal pyrolysis to induce improved mechanical and photophysical properties. The DNA-dots were further used as crosslinkers to create a hydrogel through hybridization-mediated self-assembly with untransformed genomic DNA. The DNA dot-DNA hydrogel sustainably delivers the ciprofloxacin antibiotic as well as produces on-demand reactive oxygen species (ROS) with visible light irradiation. This prompted us to explore the hydrogel as a topical formulation for combination antibiotic Antibacterial-Photodynamic Therapy (APDT) applications. Remarkable annihilation of E. coli and S. aureus, and most importantly two drug-resistant strains of E. coli, shows the success of our sustainable approach.
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Affiliation(s)
- Suman Nayak
- Department of Chemistry, Indian Institute of Technology Patna, Patna-801103, Bihar, India.
| | - Prakash Kumar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur-844102, Bihar, India
| | - Ravi Shankar
- Department of Chemistry, Indian Institute of Technology Patna, Patna-801103, Bihar, India.
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Debabrata Mandal
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Hajipur-844102, Bihar, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna-801103, Bihar, India.
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21
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Cao L, Huang Y, Parakhonskiy B, Skirtach AG. Nanoarchitectonics beyond perfect order - not quite perfect but quite useful. NANOSCALE 2022; 14:15964-16002. [PMID: 36278502 DOI: 10.1039/d2nr02537j] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Nanoarchitectonics, like architectonics, allows the design and building of structures, but at the nanoscale. Unlike those in architectonics, and even macro-, micro-, and atomic-scale architectonics, the assembled structures at the nanoscale do not always follow the projected design. In fact, they do follow the projected design but only for self-assembly processes producing structures with perfect order. Here, we look at nanoarchitectonics allowing the building of nanostructures without a perfect arrangement of building blocks. Here, fabrication of structures from molecules, polymers, nanoparticles, and nanosheets to polymer brushes, layer-by-layer assembly structures, and hydrogels through self-assembly processes is discussed, where perfect order is not necessarily the aim to be achieved. Both planar substrate and spherical template-based assemblies are discussed, showing the challenging nature of research in this field and the usefulness of such structures for numerous applications, which are also discussed here.
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Affiliation(s)
- Lin Cao
- Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Yanqi Huang
- Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Bogdan Parakhonskiy
- Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
| | - Andre G Skirtach
- Nano-Biotechnology Laboratory, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
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22
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Abstract
Recent years have seen substantial efforts aimed at constructing artificial cells from various molecular components with the aim of mimicking the processes, behaviours and architectures found in biological systems. Artificial cell development ultimately aims to produce model constructs that progress our understanding of biology, as well as forming the basis for functional bio-inspired devices that can be used in fields such as therapeutic delivery, biosensing, cell therapy and bioremediation. Typically, artificial cells rely on a bilayer membrane chassis and have fluid aqueous interiors to mimic biological cells. However, a desire to more accurately replicate the gel-like properties of intracellular and extracellular biological environments has driven increasing efforts to build cell mimics based on hydrogels. This has enabled researchers to exploit some of the unique functional properties of hydrogels that have seen them deployed in fields such as tissue engineering, biomaterials and drug delivery. In this Review, we explore how hydrogels can be leveraged in the context of artificial cell development. We also discuss how hydrogels can potentially be incorporated within the next generation of artificial cells to engineer improved biological mimics and functional microsystems.
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23
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Chen Q, Tian R, Liu G, Wen Y, Bian X, Luan D, Wang H, Lai K, Yan J. Fishing unfunctionalized SERS tags with DNA hydrogel network generated by ligation-rolling circle amplification for simple and ultrasensitive detection of kanamycin. Biosens Bioelectron 2022; 207:114187. [PMID: 35325717 DOI: 10.1016/j.bios.2022.114187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022]
Abstract
Simple assay format-based SERS methods for sensitive target substance analysis is of great significance for the development of on-site monitoring biosensors. Herein, taking the typical antibacterial kanamycin (KANA) as a subject, a simple, highly sensitive and specific SERS aptasensor was developed by manipulating DNA hydrogel network to fish plasmonic core-shell nanoparticles. A competitive binding mode of aptamer, ligation-rolling circle amplification (L-RCA), gap-containing Au@Au nanoparticles (GCNPs) with embedded Raman reporters were integrated into the sensor. In the presence of KANA, the double stranded DNA (dsDNA) structure of the aptamer was disrupted, and the released primers were used to construct two kinds of circularized padlock probes (CPPs) which were partially complementary. DNA hydrogel network was formed through the intertwining and self-assembly of two RCA-generated single stranded DNA (ssDNA) chains, during which GCNPs and magnetic beads (MBs) were entangled and incorporated. Finally, KANA quantification was successfully achieved through the quantification of the DNA hydrogel. Overall, this novel SERS aptasensor realized a simple and ultrasensitive quantification of KANA down to 2.3 fM, plus excellent selectivity, and precision even for real food samples. In view of innovative fusion across L-RCA-based DNA hydrogel and SERS technique, the proposed method has promising potential for application in on-site detection and quantification of trace food contaminants.
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Affiliation(s)
- Qian Chen
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Run Tian
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Lihu Road 1800, 214122, Wuxi, China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203, China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203, China
| | - Xiaojun Bian
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Donglei Luan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Huiyuan Wang
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Keqiang Lai
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
| | - Juan Yan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai Engineering Research Center of Aquatic-Product Process & Preservation, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
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24
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Wang Q, Qu Y, Zhang Z, Huang H, Xu Y, Shen F, Wang L, Sun L. Injectable DNA Hydrogel-Based Local Drug Delivery and Immunotherapy. Gels 2022; 8:gels8070400. [PMID: 35877485 PMCID: PMC9320917 DOI: 10.3390/gels8070400] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022] Open
Abstract
Regulated drug delivery is an important direction in the field of medicine and healthcare research. In recent years, injectable hydrogels with good biocompatibility and biodegradability have attracted extensive attention due to their promising application in controlled drug release. Among them, DNA hydrogel has shown great potentials in local drug delivery and immunotherapy. DNA hydrogel is a three-dimensional network formed by cross-linking of hydrophilic DNA strands with extremely good biocompatibility. Benefiting from the special properties of DNA, including editable sequence and specificity of hybridization reactions, the mechanical properties and functions of DNA hydrogels can be precisely designed according to specific applications. In addition, other functional materials, including peptides, proteins and synthetic organic polymers can be easily integrated with DNA hydrogels, thereby enriching the functions of the hydrogels. In this review, we first summarize the types and synthesis methods of DNA hydrogels, and then review the recent research progress of injectable DNA hydrogels in local drug delivery, especially in immunotherapy. Finally, we discuss the challenges facing DNA hydrogels and future development directions.
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Affiliation(s)
- Qi Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Yanfei Qu
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Ziyi Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Hao Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Yufei Xu
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Fengyun Shen
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 201240, China
- Correspondence: (F.S.); (L.S.)
| | - Lihua Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China;
| | - Lele Sun
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
- Correspondence: (F.S.); (L.S.)
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25
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Hivare P, Gangrade A, Swarup G, Bhavsar K, Singh A, Gupta R, Thareja P, Gupta S, Bhatia D. Peptide functionalized DNA hydrogel enhances neuroblastoma cell growth and differentiation. NANOSCALE 2022; 14:8611-8620. [PMID: 35687044 DOI: 10.1039/d1nr07187d] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Designing programmable biomaterials that could act as extracellular matrices and permit functionalization is a current need for tissue engineering advancement. DNA based hydrogels are gaining significant attention owing to their self-assembling properties, biocompatibility, chemical robustness and low batch to batch variability. The real potential of DNA hydrogels in the biomedical domain remains to be explored. In this work, a DNA hydrogel was coated on a glass surface and coupled to a synthetic IKVAV peptide by a chemical crosslinker. We observe enhanced neuronal differentiation, prolonged neurite length, dynamic movement of microtubules and cytoskeleton, and altered endocytic mechanisms in neuroblastoma-based stem cells for the peptide modified DNA hydrogel compared to the unmodified DNA hydrogel and controls. We anticipate that a peptide-modified DNA hydrogel could emerge as a promising scaffold coating material to develop nerve tissue conduits in the future for application in neuroscience and neuroregeneration.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Ankit Gangrade
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Gitanjali Swarup
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Krishna Bhavsar
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Ankur Singh
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Ratnika Gupta
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Prachi Thareja
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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26
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Cao D, Xie Y, Song J. DNA Hydrogels in the Perspective of Mechanical Properties. Macromol Rapid Commun 2022; 43:e2200281. [PMID: 35575627 DOI: 10.1002/marc.202200281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/25/2022] [Indexed: 11/10/2022]
Abstract
Tailoring the mechanical properties has always been a key to the field of hydrogels in terms of different applications. Particularly, deoxyribonucleic acid (DNA) hydrogels offer an unambiguous way to precisely tune the mechanical properties, largely on account of their programmable sequences, abundant responding toolbox, and various ligation approaches. In this review, DNA hydrogels from the perspective of mechanical properties, from synthetic standpoint to different applications are introduced. The relationship between the structure and their mechanical properties in DNA hydrogels and the methods of regulating the mechanical properties of DNA hydrogels are specifically summarized. Furthermore, several recent applications of DNA hydrogels in relation to their mechanical properties are discussed. Benefiting from the tunability and flexibility, rational design of mechanical properties in DNA hydrogels provided unheralded interest from fundamental science to extensive applications. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dengjie Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yujie Xie
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, P. R. China
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27
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Yamada M, Kawamura M, Yamada T. Preparation of bioplastic consisting of salmon milt DNA. Sci Rep 2022; 12:7423. [PMID: 35523933 PMCID: PMC9076882 DOI: 10.1038/s41598-022-11482-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/18/2022] [Indexed: 11/09/2022] Open
Abstract
The microplastic that pollutes the ocean is a serious problem around the world. The bioplastic consisting of biopolymers which is degraded in nature, is one of the strategies to solve this problem. Although the bioplastics consisting of protein, polysaccharide, polylactic acid, etc., have been reported, which consist of DNA, one of the most important materials in the genetic process, have not been reported to the best of our knowledge. In addition, a large amount of DNA-containing materials, such as salmon milts, is discarded as industrial waste around the world. Therefore, we demonstrated the preparation of a bioplastic consisting of salmon milt DNA. The DNA plastic was prepared by the immersion of a DNA pellet in a formaldehyde (HCHO) solution and heating. As a result, the water-stable DNA plastics were obtained at the HCHO concentration of 20% or more. Particularly, the DNA plastic with a 25% HCHO treatment showed water-insoluble, thermally stable, and highly mechanical properties. These are due to the formation of a three-dimensional network via the crosslinking reaction between the DNA chains. In addition, since DNA in plastic possesses the double-stranded structure, these plastics effectively accumulated the DNA intercalator, such as ethidium bromide. Furthermore, the DNA plastics indicated a biodegradable property in a nuclease-containing aqueous solution and the biodegradable stability was able to be controlled by the HCHO concentration. Therefore, salmon milt DNA has shown the potential to be a biodegradable plastic.
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Affiliation(s)
- Masanori Yamada
- Department of Chemistry, Faculty of Science, Okayama University of Science, Ridaicho, Kita-ku, Okayama, 700-0005, Japan.
| | - Midori Kawamura
- Department of Chemistry, Faculty of Science, Okayama University of Science, Ridaicho, Kita-ku, Okayama, 700-0005, Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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28
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Khoris IM, Nasrin F, Chowdhury AD, Park EY. Advancement of dengue virus NS1 protein detection by 3D-nanoassembly complex gold nanoparticles utilizing competitive sandwich aptamer on disposable electrode. Anal Chim Acta 2022; 1207:339817. [DOI: 10.1016/j.aca.2022.339817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 12/25/2022]
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29
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Giraud T, Hoschtettler P, Pickaert G, Averlant-Petit MC, Stefan L. Emerging low-molecular weight nucleopeptide-based hydrogels: state of the art, applications, challenges and perspectives. NANOSCALE 2022; 14:4908-4921. [PMID: 35319034 DOI: 10.1039/d1nr06131c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the last twenty years, low-molecular weight gelators and, in particular, peptide-based hydrogels, have drawn great attention from scientists thanks to both their inherent advantages in terms of properties and their high modularity (e.g., number and nature of the amino acids). These supramolecular hydrogels originate from specific peptide self-assembly processes that can be driven, modulated and optimized via specific chemical modifications brought to the peptide sequence. Among them, the incorporation of nucleobases, another class of biomolecules well-known for their abilities to self-assemble, has recently appeared as a new promising and burgeoning approach to finely design supramolecular hydrogels. In this minireview, we would like to highlight the interest, high potential, applications and perspectives of these innovative and emerging low-molecular weight nucleopeptide-based hydrogels.
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Affiliation(s)
- Tristan Giraud
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
| | | | | | | | - Loic Stefan
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France.
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30
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Liu S, Yang Y, Shi M, Shi H, Mao D, Mao X, Zhang Y. Smartphone-Based Pure DNAzyme Hydrogel Platform for Visible and Portable Colorimetric Detection of Cell-Free DNA. ACS Sens 2022; 7:658-665. [PMID: 35107259 DOI: 10.1021/acssensors.1c02662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cell-free DNA (cfDNA), as a tumor marker, is of great importance for the diagnosis of cancer and targeted therapy. However, the need for huge analytical instruments for cfDNA analysis has restricted its practical applications, especially in rural areas and third-world countries. Herein, a portable and visual smartphone-based DNAzyme hydrogel platform is developed for cfDNA detection. The target cfDNA triggers rolling circle amplification to produce a G-quadruplex-comprised DNA hydrogel with an horseradish peroxidase (HRP)-like catalytic function, which further catalyzes the chromogenic substrate to generate a visible output signal. Notably, the naked-eye detection of cfDNA can be realized by the macroscale visibility and catalytic ability of the DNA hydrogel. The linear range of the DNAzyme hydrogel platform for cfDNA detection is 0.1 pM-1500 nM with a detection limit of 0.042 pM. Moreover, this platform is exploited for the detection of cfDNA in spiked human serum with favorable sensitivity and recovery. Therefore, the DNAzyme hydrogel platform provides highly promising potential for testing other nucleic acid biomarkers.
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Affiliation(s)
- Shaowei Liu
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Yumeng Yang
- College of Chemistry and Chemical Engineering, Anqing Normal University, Anqing 246011, China
| | - Mengqin Shi
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Hai Shi
- The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaoxia Mao
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
| | - Yuanguang Zhang
- Key Laboratory of Aqueous Environment Protection and Pollution Control of Yangtze River in Anhui of Anhui Provincial Education Department, College of Resources and Environment, Anqing Normal University, Anqing 246011, China
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31
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Jonášová EP, Stokke BT, Prot V. Interrelation between swelling, mechanical constraints and reaction-diffusion processes in molecular responsive hydrogels. SOFT MATTER 2022; 18:1510-1524. [PMID: 35099496 DOI: 10.1039/d1sm01445e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The net swelling dynamics in molecular responsive hydrogels can be viewed as an integrated effect of discernible processes involving transport of actuating species, reaction with network components like destabilization of physical crosslinks or cleavage of network strands and concomitant network relaxation. Here, we describe a finite element modeling approach coupling these interdependent, underlying processes in hydrogels including oligonucleotide duplexes as physical crosslinks that can be destabilized by a particular molecule. These molecular responsive hydrogels based on acrylamide including either DNA or oligomorpholinos (MO), a DNA analogue, as functional elements can be made with various content of dsDNA or dsMO supported cross-links. The dsDNA or dsMO integrated in the hydrogel can be fabricated with ssDNA designed to competitively displace the connectivity of the dsDNA supported crosslinks, and similar for the MO hydrogels. The overall processes can be framed in a diffusion-reaction scheme. This process is dependent on the concentration of the diffusing species, their diffusion coefficients and their location. Thus, the reaction taking place in particular molecular responsive hydrogels is coupled with the deformations due to swelling and mechanical constraints undergone by the gel. Numerical examples show the importance of coupling reaction-diffusion with mechanical deformations for such gels. Finally, our model is compared to swelling experiments of hemi-spheroidal molecular responsive hydrogels bound to an optical fiber. Parameters of the reaction-diffusion model were obtained by fitting the model to reported experimental data where molecular stimuli designed with different molecular parameters for the competitive displacement reaction were employed in the swelling experiments.
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Affiliation(s)
- Eleonóra Parelius Jonášová
- Biophysics and Medical Technology, Department of Physics, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Bjørn Torger Stokke
- Biophysics and Medical Technology, Department of Physics, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Victorien Prot
- Biomechanics, Department of Structural Engineering, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
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32
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Smart Nucleic Acid Hydrogels with High Stimuli-Responsiveness in Biomedical Fields. Int J Mol Sci 2022; 23:ijms23031068. [PMID: 35162990 PMCID: PMC8835224 DOI: 10.3390/ijms23031068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 02/01/2023] Open
Abstract
Due to their hydrophilic, biocompatible and adjustability properties, hydrogels have received a lot of attention. The introduction of nucleic acids has made hydrogels highly stimuli-responsiveness and they have become a new generation of intelligent biomaterials. In this review, the development and utilization of smart nucleic acid hydrogels (NAHs) with a high stimulation responsiveness were elaborated systematically. We discussed NAHs with a high stimuli-responsiveness, including pure NAHs and hybrid NAHs. In particular, four stimulation factors of NAHs were described in details, including pH, ions, small molecular substances, and temperature. The research progress of nucleic acid hydrogels in biomedical applications in recent years is comprehensively discussed. Finally, the opportunities and challenges facing the future development of nucleic acid hydrogels are also discussed.
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33
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Target DNA- and pH-responsive DNA hydrogel-based capillary assay for the optical detection of short SARS-CoV-2 cDNA. Mikrochim Acta 2021; 189:34. [PMID: 34940928 PMCID: PMC8695668 DOI: 10.1007/s00604-021-05138-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/07/2021] [Indexed: 11/26/2022]
Abstract
DNA is recognized as a powerful biomarker for clinical diagnostics because its specific sequences are closely related to the cause and development of diseases. However, achieving rapid, low-cost, and sensitive detection of short-length target DNA still remains a considerable challenge. Herein, we successfully combine the catalytic hairpin assembly (CHA) technique with capillary action to develop a new and cost-effective method, a target DNA- and pH-responsive DNA hydrogel–based capillary assay, for the naked eye detection of 24 nt short single-stranded target DNA. Upon contact of target DNA, three individual hairpin DNAs hybridize with each other to sufficiently amplify Y-shaped DNA nanostructures (Y-DNA) until they are completely consumed via CHA cycling reactions. Each arm of the resultant Y-DNA contains sticky ends with i-motif DNA structure-forming sequences that can be self-assembled in an acidic environment (pH 5.0) to form target DNA- and pH-responsive DNA hydrogels by means of i-motif DNA-driven crosslinking. When inserting a capillary tube in the resultant solution, the liquid level inside clearly reduces due to the decrease in capillary force induced by the gels. In this way, the developed assay demonstrates sensitive and quantitative detection, with a detection limit of approximately 10 pM of 24 nt short complementary DNA (cDNA) targeting SARS-CoV-2 RNA genes at room temperature within 1 h. The assay is further shown to successfully detect target cDNA in serum, and it is also applied to detect several types of target sequences. Requiring no analytic equipment, precise temperature control, or enzymatic reactions, the developed DNA hydrogel–based capillary assay has potential as a promising naked eye detection platform for target DNA in resource-limited clinical settings.
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34
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Walia S, Morya V, Gangrade A, Naskar S, Guduru Teja A, Dalvi S, Maiti PK, Ghoroi C, Bhatia D. Designer DNA Hydrogels Stimulate 3D Cell Invasion by Enhanced Receptor Expression and Membrane Endocytosis. ACS Biomater Sci Eng 2021; 7:5933-5942. [PMID: 34856099 DOI: 10.1021/acsbiomaterials.1c01085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA has emerged as one of the smartest biopolymers to bridge the gap between chemical science and biology to design scaffolds like hydrogels by physical entanglement or chemical bonding with remarkable properties. We present here a completely new application of DNA-based hydrogels in terms of their capacity to stimulate membrane endocytosis, leading to enhanced cell spreading and invasion for cells in ex vivo 3D spheroids models. Multiscale simulation studies along with DLS data showed that the hydrogel formation was enhanced at lower temperature and it converts to liquid with increase in temperature. DNA hydrogels induced cell spreading as observed by the increase in cellular area by almost two-fold followed by an increase in the receptor expression, the endocytosis, and the 3D invasion potential of migrating cells. Our first results lay the foundation for upcoming diverse applications of hydrogels to probe and program various cellular and physiological processes that can have lasting applications in stem cell programming and regenerative therapeutics.
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Affiliation(s)
- Shanka Walia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Vinod Morya
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Ankit Gangrade
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Aditya Guduru Teja
- Chemical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Sameer Dalvi
- Chemical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Chinmay Ghoroi
- Chemical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
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35
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Gangrade A, Stephanopoulos N, Bhatia D. Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering. NANOSCALE 2021; 13:16834-16846. [PMID: 34622910 DOI: 10.1039/d1nr04475c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA-based nanotechnology has evolved into an autonomous, highly innovative, and dynamic field of research at the nexus of supramolecular chemistry, nanotechnology, materials science, and biotechnology. DNA-based materials, including origami nanodevices, have started to emerge as an ideal scaffold for use in cellular programming, tissue engineering, and drug delivery applications. We cover herein the applications for DNA as a scaffold for interfacing with, and guiding, the activity of biological systems like cells and tissues. Although DNA is a highly programmable molecular building block, it suffers from a lack of functional capacity for guiding and modulating cells. Coupling DNA to biologically active molecules can bestow bioactivity to these nanodevices. The main goal of such nanodevices is to synthesize systems that can bind to cells and mimic the extracellular environment, and serve as a highly promising toolbox for multiple applications in cellular programming and tissue engineering. DNA-based programmable devices offer a highly promising approach for programming collections of cells, tissue engineering, and regenerative medicine applications.
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Affiliation(s)
- Ankit Gangrade
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, India
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36
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Araujo-Rocha M, Piro B, Noël V, Barbault F. Computational Studies of a DNA-Based Aptasensor: toward Theory-Driven Transduction Improvement. J Phys Chem B 2021; 125:9499-9506. [PMID: 34403245 DOI: 10.1021/acs.jpcb.1c05341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aptamers are a class of bioreceptors intensively used in current analytical tools dedicated to molecular diagnostics due to their ability to perform large structural reorganization upon target binding. However, there is a lack of methodologies allowing us to rationalize their structure in order to improve the transduction efficiency in aptamer sensors. We choose here, as a model system, a three-strand DNA structure as the probe, composed of two DNA strands anchored on a gold surface and partially hybridized with an aptamer sequence sensitive to ampicillin (AMP). The DNA structure has been designed to show strong structural change upon AMP binding to its aptamer. Using a set of computational techniques including molecular dynamics simulations, we deeply investigated the structure change upon analyte binding, taking into account the grafting on the surface. Original analyses of ion distributions along the trajectories unveil a distinct pattern between both states which can be related to changes in capacitance of the interface between these states. To our knowledge, this work demonstrates the ability of computational investigations for the first time to drive, in silico, the design of aptasensors.
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Affiliation(s)
| | - Benoît Piro
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
| | - Vincent Noël
- Université de Paris, ITODYS, CNRS, F-75006 Paris, France
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37
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Walia S, Chandrasekaran AR, Chakraborty B, Bhatia D. Aptamer-Programmed DNA Nanodevices for Advanced, Targeted Cancer Theranostics. ACS APPLIED BIO MATERIALS 2021; 4:5392-5404. [PMID: 35006722 DOI: 10.1021/acsabm.1c00413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA has been demonstrated to be a versatile material for construction at the nanoscale. DNA nanodevices are highly programmable and allow functionalization with multiple entities such as imaging modalities (fluorophores), targeting entities (aptamers), drug conjugation (chemical linkers), and triggered release (photoresponsive molecules). These features enhance the use of DNA nanodevices in biological applications, catalyzing the rapid growth of this domain of research. In this review, we focus on recent progress in the development and use of aptamer-functionalized DNA nanodevices as theranostic agents, their characterization, applications as delivery platforms, and advantages. We provide a brief background on the development of aptamers and DNA nanodevices in biomedical applications, and we present specific applications of these entities in cancer diagnosis and therapeutics. We conclude with a perspective on the challenges and possible solutions for the clinical translation of aptamer-functionalized DNA nanodevices in the domain of cancer therapeutics.
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Affiliation(s)
- Shanka Walia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | | | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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38
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Singh U, Morya V, Datta B, Ghoroi C, Bhatia D. Stimuli Responsive, Programmable DNA Nanodevices for Biomedical Applications. Front Chem 2021; 9:704234. [PMID: 34277571 PMCID: PMC8278982 DOI: 10.3389/fchem.2021.704234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Of the multiple areas of applications of DNA nanotechnology, stimuli-responsive nanodevices have emerged as an elite branch of research owing to the advantages of molecular programmability of DNA structures and stimuli-responsiveness of motifs and DNA itself. These classes of devices present multiples areas to explore for basic and applied science using dynamic DNA nanotechnology. Herein, we take the stake in the recent progress of this fast-growing sub-area of DNA nanotechnology. We discuss different stimuli, motifs, scaffolds, and mechanisms of stimuli-responsive behaviours of DNA nanodevices with appropriate examples. Similarly, we present a multitude of biological applications that have been explored using DNA nanodevices, such as biosensing, in vivo pH-mapping, drug delivery, and therapy. We conclude by discussing the challenges and opportunities as well as future prospects of this emerging research area within DNA nanotechnology.
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Affiliation(s)
- Udisha Singh
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Vinod Morya
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Bhaskar Datta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Chinmay Ghoroi
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, India
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Abune L, Davis B, Wang Y. Aptamer-functionalized hydrogels: An emerging class of biomaterials for protein delivery, cell capture, regenerative medicine, and molecular biosensing. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 13:e1731. [PMID: 34132055 DOI: 10.1002/wnan.1731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/27/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Molecular recognition is essential to the development of biomaterials. Aptamers are a unique class of synthetic ligands interacting with not only their target molecules with high affinities and specificities but also their complementary sequences with high fidelity. Thus, aptamers have recently attracted significant attention in the development of an emerging class of biomaterials, that is, aptamer-functionalized hydrogels. In this review, we introduce the methods of incorporating aptamers into hydrogels as pendant motifs or crosslinkers. We further introduce the functions of these hydrogels in recognizing proteins, cells, and analytes through four applications including protein delivery, cell capture, regenerative medicine, and molecular biosensing. Notably, as aptamer-functionalized hydrogels have the characteristics of both aptamers and hydrogels, their potential applications are broad and beyond the scope of this review. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Implantable Materials and Surgical Technologies > Nanomaterials and Implants Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Lidya Abune
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brandon Davis
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
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Jian X, Feng X, Luo Y, Li F, Tan J, Yin Y, Liu Y. Development, Preparation, and Biomedical Applications of DNA-Based Hydrogels. Front Bioeng Biotechnol 2021; 9:661409. [PMID: 34150729 PMCID: PMC8206814 DOI: 10.3389/fbioe.2021.661409] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/20/2021] [Indexed: 12/31/2022] Open
Abstract
Hydrogels have outstanding research and application prospects in the biomedical field. Among them, the design and preparation of biomedical hydrogels with deoxyribonucleic acid (DNA) as building blocks have attracted increasing research interest. DNA-based hydrogel not only has the skeleton function of hydrogel, but also retains its biological functions, including its excellent selection specificity, structural designability, precise molecular recognition ability, outstanding biocompatibility, and so on. It has shown important application prospects in the biomedical field, such as drug delivery, biosensing, and tissue engineering. In recent years, researchers have made full use of the characteristics of DNA molecules and constructed various pure DNA-based hydrogels with excellent properties through various crosslinking methods. Moreover, via introducing functional molecules or elements, or combining with other functional materials, a variety of multifunctional DNA-based hybrid hydrogels have also been constructed, which expand the breadth and depth of their applications. Here, we described the recent development trend in the area of DNA-based hydrogels and highlighted various preparation methods of DNA-based hydrogels. Representative biomedical applications are also exemplified to show the high performance of DNA-based hydrogels. Meanwhile, the existing problems and prospects are also summarized. This review provided references for the further development of DNA-based hydrogels.
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Affiliation(s)
| | | | | | | | | | | | - Yang Liu
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, University of South China, Hengyang, China
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