1
|
Chakraborty A, Diwan A, Tatake J. Prospect of nanomaterials as antimicrobial and antiviral regimen. AIMS Microbiol 2023; 9:444-466. [PMID: 37649798 PMCID: PMC10462459 DOI: 10.3934/microbiol.2023024] [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: 01/05/2023] [Revised: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 09/01/2023] Open
Abstract
In recent years studies of nanomaterials have been explored in the field of microbiology due to the increasing evidence of antibiotic resistance. Nanomaterials could be inorganic or organic, and they may be synthesized from natural products from plant or animal origin. The therapeutic applications of nano-materials are wide, from diagnosis of disease to targeted delivery of drugs. Broad-spectrum antiviral and antimicrobial activities of nanoparticles are also well evident. The ratio of nanoparticles surface area to their volume is high and that allows them to be an advantageous vehicle of drugs in many respects. Effective uses of various materials for the synthesis of nanoparticles impart much specificity in them to meet the requirements of specific therapeutic strategies. The potential therapeutic use of nanoparticles and their mechanisms of action against infections from bacteria, fungi and viruses were the focus of this review. Further, their potential advantages, drawbacks, limitations and side effects are also included here. Researchers are characterizing the exposure pathways of nano-medicines that may cause serious toxicity to the subjects or the environment. Indeed, societal ethical issues in using nano-medicines pose a serious question to scientists beyond anything.
Collapse
|
2
|
Mouli MSSV, Agrawal HG, Kumar M, Mishra AK. Luminescent and morphological behavior of the aromatic dipeptide pair having singular structural variability. LUMINESCENCE 2022. [PMID: 35560861 DOI: 10.1002/bio.4275] [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: 03/01/2022] [Revised: 04/15/2022] [Accepted: 05/07/2022] [Indexed: 11/07/2022]
Abstract
In the present manuscript, the luminescence and the self-assembly behavior of the two aromatic dipeptides having singular structure variable are investigated. The terminally protected dipeptides tryptophan-tyrosine (WYp ) and tryptophan-phenylalanine (WFp ) were synthesized using standard solution phase procedure. Significant solvatochromic effect was observed for both the dipeptidyl entities; while the influence was more pronounced in case of the WYp entity when compared to WFp . Interesting morphological variation was observed for WFp and WYp , wherein discrete and interconnected nanospheres were observed for the respective dipeptides. The results obtained signifies the influence of the singular structural variation on modulating the overall functional behavior of the short peptides motifs.
Collapse
Affiliation(s)
- M S S Vinod Mouli
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Harsha Gopal Agrawal
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Mohit Kumar
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Ashutosh Kumar Mishra
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Liu F, Liu X, Huang Q, Arai T. Recent Progress of Magnetically Actuated DNA Micro/Nanorobots. CYBORG AND BIONIC SYSTEMS 2022; 2022:9758460. [PMID: 36285315 PMCID: PMC9494703 DOI: 10.34133/2022/9758460] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/22/2021] [Indexed: 01/12/2023] Open
Abstract
In the past few decades, the field of DNA origami-based micro/nanotechnology has developed dramatically and spawned attention increasingly, as its high integrality, rigid structure, and excellent resistance ability to enzyme digestion. Many two-dimensional and three-dimensional DNA nanostructures coordinated with optical, chemical, or magnetic triggers have been designed and assembled, extensively used as versatile templates for molecular robots, nanosensors, and intracellular drug delivery. The magnetic field has been widely regarded as an ideal driving and operating system for micro/nanomaterials, as it does not require high-intensity lasers like light control, nor does it need to change the chemical composition similar to chemical activation. Herein, we review the recent achievements in the induction and actuation of DNA origami-based nanodevices that respond to magnetic fields. These magnetic actuation-based DNA nanodevices were regularly combined with magnetic beads or gold nanoparticles and applied to generate single-stranded scaffolds, assemble various DNA nanostructures, and purify specific DNA nanostructures. Moreover, they also produced artificial magnetism or moved regularly driven by external magnetic fields to explain deeper scientific issues.
Collapse
Affiliation(s)
- Fengyu Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoming Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiang Huang
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Tatsuo Arai
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Tokyo 182-8585, Japan
| |
Collapse
|
5
|
Valero J, Škugor M. Mechanisms, Methods of Tracking and Applications of DNA Walkers: A Review. Chemphyschem 2020; 21:1971-1988. [DOI: 10.1002/cphc.202000235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/04/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Julián Valero
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Marko Škugor
- LIMES Chemical Biology Unit Universität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Germany
| |
Collapse
|
6
|
Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies. Molecules 2020; 25:molecules25153386. [PMID: 32722650 PMCID: PMC7435391 DOI: 10.3390/molecules25153386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.
Collapse
|
7
|
Interaction of particles with mucosae and cell membranes. Colloids Surf B Biointerfaces 2020; 186:110657. [DOI: 10.1016/j.colsurfb.2019.110657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/15/2023]
|
8
|
Graczyk A, Pawlowska R, Jedrzejczyk D, Chworos A. Gold Nanoparticles in Conjunction with Nucleic Acids as a Modern Molecular System for Cellular Delivery. Molecules 2020; 25:E204. [PMID: 31947834 PMCID: PMC6982881 DOI: 10.3390/molecules25010204] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
Development of nanotechnology has become prominent in many fields, such as medicine, electronics, production of materials, and modern drugs. Nanomaterials and nanoparticles have gained recognition owing to the unique biochemical and physical properties. Considering cellular application, it is speculated that nanoparticles can transfer through cell membranes following different routes exclusively owing to their size (up to 100 nm) and surface functionalities. Nanoparticles have capacity to enter cells by themselves but also to carry other molecules through the lipid bilayer. This quality has been utilized in cellular delivery of substances like small chemical drugs or nucleic acids. Different nanoparticles including lipids, silica, and metal nanoparticles have been exploited in conjugation with nucleic acids. However, the noble metal nanoparticles create an alternative, out of which gold nanoparticles (AuNP) are the most common. The hybrids of DNA or RNA and metal nanoparticles can be employed for functional assemblies for variety of applications in medicine, diagnostics or nano-electronics by means of biomarkers, specific imaging probes, or gene expression regulatory function. In this review, we focus on the conjugates of gold nanoparticles and nucleic acids in the view of their potential application for cellular delivery and biomedicine. This review covers the current advances in the nanotechnology of DNA and RNA-AuNP conjugates and their potential applications. We emphasize the crucial role of metal nanoparticles in the nanotechnology of nucleic acids and explore the role of such conjugates in the biological systems. Finally, mechanisms guiding the process of cellular intake, essential for delivery of modern therapeutics, will be discussed.
Collapse
Affiliation(s)
| | | | | | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (A.G.); (R.P.); (D.J.)
| |
Collapse
|
9
|
Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes. Structure 2017; 26:40-50.e2. [PMID: 29225080 PMCID: PMC5758106 DOI: 10.1016/j.str.2017.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/12/2017] [Accepted: 11/12/2017] [Indexed: 02/01/2023]
Abstract
Synthesis and scission of phosphodiester bonds in DNA and RNA regulate vital processes within the cell. Enzymes that catalyze these reactions operate mostly via the recognized two-metal-ion mechanism. Our analysis reveals that basic amino acids and monovalent cations occupy structurally conserved positions nearby the active site of many two-metal-ion enzymes for which high-resolution (<3 Å) structures are known, including DNA and RNA polymerases, nucleases such as Cas9, and splicing ribozymes. Integrating multiple-sequence and structural alignments with molecular dynamics simulations, electrostatic potential maps, and mutational data, we found that these elements always interact with the substrates, suggesting that they may play an active role for catalysis, in addition to their electrostatic contribution. We discuss possible mechanistic implications of this expanded two-metal-ion architecture, including inferences on medium-resolution cryoelectron microscopy structures. Ultimately, our analysis may inspire future experiments and strategies for enzyme engineering or drug design to modulate nucleic acid processing. Basic residues in the active site of two-metal-ion enzymes are structurally conserved These residues are also conserved in evolution Mutagenesis suggests these residues may exert an effect on DNA- and RNA processing Our work offers insights into CRISPR/Cas9, spliceosome, and DNA/RNA polymerases
Collapse
|
10
|
Michálik J, Touzet H, Ponty Y. Efficient approximations of RNA kinetics landscape using non-redundant sampling. Bioinformatics 2017; 33:i283-i292. [PMID: 28882001 PMCID: PMC5870705 DOI: 10.1093/bioinformatics/btx269] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Kinetics is key to understand many phenomena involving RNAs, such as co-transcriptional folding and riboswitches. Exact out-of-equilibrium studies induce extreme computational demands, leading state-of-the-art methods to rely on approximated kinetics landscapes, obtained using sampling strategies that strive to generate the key landmarks of the landscape topology. However, such methods are impeded by a large level of redundancy within sampled sets. Such a redundancy is uninformative, and obfuscates important intermediate states, leading to an incomplete vision of RNA dynamics. RESULTS We introduce RNANR, a new set of algorithms for the exploration of RNA kinetics landscapes at the secondary structure level. RNANR considers locally optimal structures, a reduced set of RNA conformations, in order to focus its sampling on basins in the kinetic landscape. Along with an exhaustive enumeration, RNANR implements a novel non-redundant stochastic sampling, and offers a rich array of structural parameters. Our tests on both real and random RNAs reveal that RNANR allows to generate more unique structures in a given time than its competitors, and allows a deeper exploration of kinetics landscapes. AVAILABILITY AND IMPLEMENTATION RNANR is freely available at https://project.inria.fr/rnalands/rnanr . CONTACT yann.ponty@lix.polytechnique.fr.
Collapse
Affiliation(s)
- Juraj Michálik
- AMIB project, Inria Saclay, Palaiseau, France
- LIX CNRS UMR 7161, Ecole Polytechnique, Palaiseau, France
| | - Hélène Touzet
- CNRS, CRIStAL (UMR 9189, University of Lille), Villeneuve d’Ascq, France
- Bonsai project, Inria Lille-Nord Europe, Villeneuve d’Ascq, France
| | - Yann Ponty
- AMIB project, Inria Saclay, Palaiseau, France
- LIX CNRS UMR 7161, Ecole Polytechnique, Palaiseau, France
| |
Collapse
|
11
|
Nair BG, Zhou Y, Hagiwara K, Ueki M, Isoshima T, Abe H, Ito Y. Enhancement of synergistic gene silencing by RNA interference using branched “3-in-1” trimer siRNA. J Mater Chem B 2017; 5:4044-4051. [DOI: 10.1039/c7tb00846e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanostructured RNA carrying three different siRNAs was assembled to silence three target genes (Axin, APC, and GSK-3β) in the Wnt/β-catenin signaling pathway. This nanostructured ‘3-in-1’ siRNA showed high activity at a low concentration due to the long-term resistance, and enhancing the effect of RNA interference.
Collapse
Affiliation(s)
| | - Yue Zhou
- Nano Medical Engineering Laboratory
- RIKEN
- Wako
- Japan
| | - Kyoji Hagiwara
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
- Wako
- Japan
| | - Masashi Ueki
- Nano Medical Engineering Laboratory
- RIKEN
- Wako
- Japan
| | | | - Hiroshi Abe
- Nano Medical Engineering Laboratory
- RIKEN
- Wako
- Japan
- Emergent Bioengineering Materials Research Team
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory
- RIKEN
- Wako
- Japan
- Emergent Bioengineering Materials Research Team
| |
Collapse
|
12
|
Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
Collapse
Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
| |
Collapse
|
13
|
Ponsiglione AM, Russo M, Netti PA, Torino E. Impact of biopolymer matrices on relaxometric properties of contrast agents. Interface Focus 2016; 6:20160061. [PMID: 27920897 PMCID: PMC5071819 DOI: 10.1098/rsfs.2016.0061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Properties of water molecules at the interface between contrast agents (CAs) for magnetic resonance imaging and macromolecules could have a valuable impact on the effectiveness of metal chelates. Recent studies, indeed, demonstrated that polymer architectures could influence CAs' relaxivity by modifying the correlation times of the metal chelate. However, an understanding of the physico-chemical properties of polymer/CA systems is necessary to improve the efficiency of clinically used CAs, still exhibiting low relaxivity. In this context, we investigate the impact of hyaluronic acid (HA) hydrogels on the relaxometric properties of Gd-DTPA, a clinically used CA, to understand better the determining role of the water, which is crucial for both the relaxation enhancement and the polymer conformation. To this aim, water self-diffusion coefficients, thermodynamic interactions and relaxometric properties of HA/Gd-DTPA solutions are studied through time-domain NMR relaxometry and isothermal titration calorimetry. We observed that the presence of Gd-DTPA could alter the polymer conformation and the behaviour of water molecules at the HA/Gd-DTPA interface, thus modulating the relaxivity of the system. In conclusion, the tunability of hydrogel structures could be exploited to improve magnetic properties of metal chelates, inspiring the development of new CAs as well as metallopolymer complexes with applications as sensors and memory devices.
Collapse
Affiliation(s)
- Alfonso Maria Ponsiglione
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
- Center for Advanced Biomaterials for Healthcare IIT@CRIB, Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Maria Russo
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
- Center for Advanced Biomaterials for Healthcare IIT@CRIB, Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Paolo Antonio Netti
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
- Interdisciplinary Research Center on Biomaterials, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
- Center for Advanced Biomaterials for Healthcare IIT@CRIB, Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Enza Torino
- Interdisciplinary Research Center on Biomaterials, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
- Center for Advanced Biomaterials for Healthcare IIT@CRIB, Istituto Italiano di Tecnologia, Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| |
Collapse
|
14
|
Franch O, Iacovelli F, Falconi M, Juul S, Ottaviani A, Benvenuti C, Biocca S, Ho YP, Knudsen BR, Desideri A. DNA hairpins promote temperature controlled cargo encapsulation in a truncated octahedral nanocage structure family. NANOSCALE 2016; 8:13333-13341. [PMID: 27341703 DOI: 10.1039/c6nr01806h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the present study we investigate the mechanism behind temperature controlled cargo uptake using a truncated octahedral DNA cage scaffold functionalized with one, two, three or four hairpin forming DNA strands inserted in one corner of the structure. This investigation was inspired by our previous demonstration of temperature controlled reversible encapsulation of the cargo enzyme, horseradish peroxidase, in the cage with four hairpin forming strands. However, in this previous study the mechanism of cargo uptake was not directly addressed (Juul, et al., Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage, ACS Nano, 2013, 7, 9724-9734). In the present study we use a combination of molecular dynamics simulations and in vitro analyses to unravel the mechanism of cargo uptake in hairpin containing DNA cages. We find that two hairpin forming strands are necessary and sufficient to facilitate efficient cargo uptake, which argues against a full opening-closing of one corner of the structure being responsible for encapsulation. Molecular dynamics simulations were carried out to evaluate the atomistic motions responsible for encapsulation and showed that the two hairpin forming strands facilitated extension of at least one of the face surfaces of the cage scaffold, allowing entrance of the cargo protein into the cavity of the structure. Hence, the presented data demonstrate that cargo uptake does not involve a full opening of the structure. Rather, the uptake mechanism represents a feature of increased flexibility integrated in this nanocage structure upon the addition of at least two hairpin-forming strands.
Collapse
Affiliation(s)
- Oskar Franch
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Pedersen RO, Kong J, Achim C, LaBean TH. Comparative Incorporation of PNA into DNA Nanostructures. Molecules 2015; 20:17645-58. [PMID: 26404232 PMCID: PMC6331967 DOI: 10.3390/molecules200917645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022] Open
Abstract
DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.
Collapse
Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0354, USA.
| | - Jing Kong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695-7907, USA.
| |
Collapse
|
16
|
Goltry S, Hallstrom N, Clark T, Kuang W, Lee J, Jorcyk C, Knowlton WB, Yurke B, Hughes WL, Graugnard E. DNA topology influences molecular machine lifetime in human serum. NANOSCALE 2015; 7:10382-90. [PMID: 25959862 PMCID: PMC4457601 DOI: 10.1039/c5nr02283e] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/27/2015] [Indexed: 05/28/2023]
Abstract
DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology-programmable molecular shape-plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation.
Collapse
Affiliation(s)
- Sara Goltry
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| | - Natalya Hallstrom
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| | - Tyler Clark
- Department of Physics , Boise State University , Boise , Idaho 83725 , USA
- Department of Mathematics , Boise State University , Boise , Idaho 83725 , USA
| | - Wan Kuang
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , USA
| | - Jeunghoon Lee
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
- Department of Chemistry & Biochemistry , Boise State University , Boise , Idaho 83725 , USA
| | - Cheryl Jorcyk
- Department of Biological Sciences , Boise State University , Boise , Idaho 83725 , USA
| | - William B. Knowlton
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , USA
| | - Bernard Yurke
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , USA
| | - William L. Hughes
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| | - Elton Graugnard
- Department of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , USA . ; Fax: +1-208-426-4466 ; Tel: +1-208-426-4026
| |
Collapse
|
17
|
Ohno H, Inoue T. Designed Regular Tetragon-Shaped RNA-Protein Complexes with Ribosomal Protein L1 for Bionanotechnology and Synthetic Biology. ACS NANO 2015; 9:4950-4956. [PMID: 25933202 DOI: 10.1021/nn5069622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA nanotechnology has been established by employing the molecular architecture of RNA structural motifs. Here, we report two designed RNA-protein complexes (RNPs) composed of ribosomal protein L1 (RPL1) and its RNA-binding motif that are square-shaped nano-objects. The formation and the shape of the objects were confirmed by gel electrophoresis analysis and atomic force microscopy, respectively. Any protein can be attached to the RNA via a fusion protein with RPL1, indicating that it can be used as a scaffold for loading a variety of functional proteins or for building higher-order structures. In summary, the RNP object will serve as a useful tool in the fields of bionanotechnology and synthetic biology. Moreover, the RNP interaction enhances the RNA stability against nucleases, rendering these complexes stable in cells.
Collapse
Affiliation(s)
- Hirohisa Ohno
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tan Inoue
- Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
18
|
Agostinelli E, Vianello F, Magliulo G, Thomas T, Thomas TJ. Nanoparticle strategies for cancer therapeutics: Nucleic acids, polyamines, bovine serum amine oxidase and iron oxide nanoparticles (Review). Int J Oncol 2015; 46:5-16. [PMID: 25333509 DOI: 10.3892/ijo.2014.2706] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 09/01/2014] [Indexed: 11/06/2022] Open
Abstract
Nanotechnology for cancer gene therapy is an emerging field. Nucleic acids, polyamine analogues and cytotoxic products of polyamine oxidation, generated in situ by an enzyme-catalyzed reaction, can be developed for nanotechnology-based cancer therapeutics with reduced systemic toxicity and improved therapeutic efficacy. Nucleic acid-based gene therapy approaches depend on the compaction of DNA/RNA to nanoparticles and polyamine analogues are excellent agents for the condensation of nucleic acids to nanoparticles. Polyamines and amine oxidases are found in higher levels in tumours compared to that of normal tissues. Therefore, the metabolism of polyamines spermidine and spermine, and their diamine precursor, putrescine, can be targets for antineoplastic therapy since these naturally occurring alkylamines are essential for normal mammalian cell growth. Intracellular polyamine concentrations are maintained at a cell type-specific set point through the coordinated and highly regulated interplay between biosynthesis, transport, and catabolism. In particular, polyamine catabolism involves copper-containing amine oxidases. Several studies showed an important role of these enzymes in developmental and disease-related processes in animals through the control of polyamine homeostasis in response to normal cellular signals, drug treatment, and environmental and/or cellular stress. The production of toxic aldehydes and reactive oxygen species (ROS), H2O2 in particular, by these oxidases suggests a mechanism by which amine oxidases can be exploited as antineoplastic drug targets. The combination of bovine serum amine oxidase (BSAO) and polyamines prevents tumour growth, particularly well if the enzyme has been conjugated with a biocompatible hydrogel polymer. The findings described herein suggest that enzymatically formed cytotoxic agents activate stress signal transduction pathways, leading to apoptotic cell death. Consequently, superparamagnetic nanoparticles or other advanced nanosystem based on directed nucleic acid assemblies, polyamine-induced DNA condensation, and bovine serum amine oxidase may be proposed for futuristic anticancer therapy utilizing nucleic acids, polyamines and BSAO. BSAO based nanoparticles can be employed for the generation of cytotoxic polyamine metabolites.
Collapse
Affiliation(s)
- Enzo Agostinelli
- Istituto Pasteur-Fondazione Cenci Bolognetti Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and CNR, Institute of Biology and Molecular Pathology, 00185 Rome, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, 35020 Legnaro, Italy and Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University in Olomouc, Olomouc 77146, Czech Republic
| | - Giuseppe Magliulo
- Department Organi di Senso, Sapienza University of Rome, 00185 Rome, Italy
| | - Thresia Thomas
- Formerly Department of Environmental and Occupational Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, Piscataway, NJ 08854, USA
| | - T J Thomas
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| |
Collapse
|
19
|
Salila Vijayalal Mohan HK, An J, Zhang Y, Wong CH, Zheng L. Effect of channel length on the electrical response of carbon nanotube field-effect transistors to deoxyribonucleic acid hybridization. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:2081-2091. [PMID: 25551036 PMCID: PMC4273243 DOI: 10.3762/bjnano.5.217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/25/2014] [Indexed: 05/29/2023]
Abstract
A single-walled carbon nanotube (SWCNT) in a field-effect transistor (FET) configuration provides an ideal electronic path for label-free detection of nucleic acid hybridization. The simultaneous influence of more than one response mechanism in hybridization detection causes a variation in electrical parameters such as conductance, transconductance, threshold voltage and hysteresis gap. The channel length (L) dependence of each of these parameters necessitates the need to include them when interpreting the effect of L on the response to hybridization. Using the definitions of intrinsic effective mobility (µe) and device field-effect mobility (µf), two new parameters were defined to interpret the effect of L on the FET response to hybridization. Our results indicate that FETs with ≈300 µm long SWCNT exhibited the most appreciable response to hybridization, which complied with the variation trend in response to the newly defined parameters.
Collapse
Affiliation(s)
| | - Jianing An
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Yani Zhang
- Temasek Laboratories, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
- Science and Technology on Thermostructural Composite Materials Laboratory, Northwestern Polytechnical University, 710072, Xi'an, PR China
| | - Chee How Wong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
| | - Lianxi Zheng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
- Department of Mechanical Engineering, Khalifa University of Science, Technology & Research (KUSTAR), P.O. Box 127788, Abu Dhabi, United Arab Emirates
| |
Collapse
|
20
|
Hernández-Ainsa S, Keyser UF. DNA origami nanopores: developments, challenges and perspectives. NANOSCALE 2014; 6:14121-32. [PMID: 25325422 DOI: 10.1039/c4nr04094e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA nanotechnology has enabled the construction of DNA origami nanopores; synthetic nanopores that present improved capabilities for the area of single molecule detection. Their extraordinary versatility makes them a new and powerful tool in nanobiotechnology for a wide range of important applications beyond molecular sensing. In this review, we briefly present the recent developments in this emerging field of research. We discuss the current challenges and possible solutions that would enhance the sensing capabilities of DNA origami nanopores. Finally, we anticipate novel avenues for future research and highlight a range of exciting ideas and applications that could be explored in the near future.
Collapse
|
21
|
Mandal T, Kumar MVS, Maiti PK. DNA Assisted Self-Assembly of PAMAM Dendrimers. J Phys Chem B 2014; 118:11805-15. [DOI: 10.1021/jp504175f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Taraknath Mandal
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Mattaparthi Venkata Satish Kumar
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560 012, India
- Department
of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam 784 028, India
| | - Prabal K. Maiti
- Center
for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| |
Collapse
|
22
|
Torelli E, Marini M, Palmano S, Piantanida L, Polano C, Scarpellini A, Lazzarino M, Firrao G. A DNA origami nanorobot controlled by nucleic acid hybridization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2918-2926. [PMID: 24648163 DOI: 10.1002/smll.201400245] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/26/2014] [Indexed: 06/03/2023]
Abstract
A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators.
Collapse
Affiliation(s)
- Emanuela Torelli
- Department of Agricultural and Environmental Sciences, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Charoenphol P, Bermudez H. Design and application of multifunctional DNA nanocarriers for therapeutic delivery. Acta Biomater 2014; 10:1683-91. [PMID: 23896566 DOI: 10.1016/j.actbio.2013.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/17/2013] [Accepted: 07/17/2013] [Indexed: 12/31/2022]
Abstract
The unique programmability of nucleic acids offers versatility and flexibility in the creation of self-assembled DNA nanostructures. To date, many three-dimensional DNA architectures of varying sizes and shapes have been precisely formed. Their biocompatibility, biodegradability and high intrinsic stability in physiological environments emphasize their emerging use as carriers for drug and gene delivery. Furthermore, DNA nanocarriers have been shown to enter cells efficiently and without the aid of transfection reagents. A key strength of DNA nanocarriers over other delivery systems is their modularity and their ability to control the spatial distribution of cargoes and ligands. Optimizing DNA nanocarrier properties to dictate their localization, uptake and intracellular trafficking is also possible. This review presents design considerations for DNA nanocarriers and examples of their use in the context of therapeutic delivery applications. The assembly of DNA nanocarriers and approaches for loading and releasing cargo are described. The stability and safety of DNA nanocarriers are also discussed, with particular attention to the in vivo physiological environment. Mechanisms of cellular uptake and intracellular trafficking are examined, and the paper concludes with strategies to enhance the delivery efficiency of DNA nanocarriers.
Collapse
Affiliation(s)
- P Charoenphol
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| | - H Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA.
| |
Collapse
|
24
|
Shi X, Lu W, Wang Z, Pan L, Cui G, Xu J, LaBean TH. Programmable DNA tile self-assembly using a hierarchical sub-tile strategy. NANOTECHNOLOGY 2014; 25:075602. [PMID: 24451169 DOI: 10.1088/0957-4484/25/7/075602] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA 'sub-tile' strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.
Collapse
Affiliation(s)
- Xiaolong Shi
- School of Automation, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | | | | | | | | | | | | |
Collapse
|
25
|
Hakker L, Marchi AN, Harris KA, LaBean TH, Agris PF. Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles. J Biomol Struct Dyn 2014; 32:319-29. [DOI: 10.1080/07391102.2012.763184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
26
|
Naserian-Nik AM, Tahani M, Karttunen M. Molecular dynamics study of DNA oligomers under angled pulling. RSC Adv 2014. [DOI: 10.1039/c3ra45604h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
27
|
Juul S, Iacovelli F, Falconi M, Kragh SL, Christensen B, Frøhlich R, Franch O, Kristoffersen EL, Stougaard M, Leong KW, Ho YP, Sørensen ES, Birkedal V, Desideri A, Knudsen BR. Temperature-controlled encapsulation and release of an active enzyme in the cavity of a self-assembled DNA nanocage. ACS NANO 2013; 7:9724-9734. [PMID: 24168393 DOI: 10.1021/nn4030543] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We demonstrate temperature-controlled encapsulation and release of the enzyme horseradish peroxidase using a preassembled and covalently closed three-dimensional DNA cage structure as a controllable encapsulation device. The utilized cage structure was covalently closed and composed of 12 double-stranded B-DNA helices that constituted the edges of the structure. The double stranded helices were interrupted by short single-stranded thymidine linkers constituting the cage corners except for one, which was composed by four 32 nucleotide long stretches of DNA with a sequence that allowed them to fold into hairpin structures. As demonstrated by gel-electrophoretic and fluorophore-quenching experiments this design imposed a temperature-controlled conformational transition capability to the structure, which allowed entrance or release of an enzyme cargo at 37 °C while ensuring retainment of the cargo in the central cavity of the cage at 4 °C. The entrapped enzyme was catalytically active inside the DNA cage and was able to convert substrate molecules penetrating the apertures in the DNA lattice that surrounded the central cavity of the cage.
Collapse
Affiliation(s)
- Sissel Juul
- Department of Biomedical Engineering, Duke University , Durham, North Carolina 27708, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Mendes AC, Baran ET, Reis RL, Azevedo HS. Self-assembly in nature: using the principles of nature to create complex nanobiomaterials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:582-612. [DOI: 10.1002/wnan.1238] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 06/03/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Ana C. Mendes
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine; Guimarães Portugal
- ICVS/3B's-PT Government Associate Laboratory; Braga/Guimarães Portugal
| | - Erkan T. Baran
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine; Guimarães Portugal
- ICVS/3B's-PT Government Associate Laboratory; Braga/Guimarães Portugal
| | - Rui L. Reis
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine; Guimarães Portugal
- ICVS/3B's-PT Government Associate Laboratory; Braga/Guimarães Portugal
| | - Helena S. Azevedo
- 3B's Research Group-Biomaterials, Biodegradables and Biomimetics; University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine; Guimarães Portugal
- ICVS/3B's-PT Government Associate Laboratory; Braga/Guimarães Portugal
| |
Collapse
|
29
|
Yamada M, Kanamori Y, Yamada T. Immobilization of double-stranded DNA onto glass beads by psolaren. Int J Biol Macromol 2013; 60:39-44. [PMID: 23707751 DOI: 10.1016/j.ijbiomac.2013.05.006] [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: 01/26/2013] [Revised: 05/13/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
Abstract
We demonstrated the immobilization of double-stranded DNA onto the glass beads by psoralen, one of the DNA-intercalators in nature. As a result, DNA-immobilized glass beads (DNA-P-beads) were prepared by the intercalation of psoralen, which was immobilized onto the glass surface, onto the double-stranded DNA. These DNA-P-beads formed covalent bondings between psoralen and the nucleic acid base by 365 nm UV irradiation. The amount of immobilized-DNA was 0.24 mg per gram of glass beads. These DNA-P-beads were stable in water, and the DNA on the bead surface maintained its double-stranded structure. These DNA-P-beads selectively removed the planar-structure containing harmful compounds, such as dioxin and polychlorinated biphenyl (PCB) derivatives, from an aqueous multi-component solution. Additionally, a DNA-P-bead column effectively removed harmful compounds. Furthermore, the DNA-P-bead column could be reused by the addition of common organic solvents, such as ethanol.
Collapse
Affiliation(s)
- Masanori Yamada
- Department of Chemistry, Faculty of Science, Okayama University of Science, Ridaicho, Kita-Ku, Okayama 700-0005, Japan.
| | | | | |
Collapse
|
30
|
Abstract
Though the pharmaceutical industry's infatuation with the therapeutic potential of RNA interference (RNAi) technology has finally come down from its initial lofty levels,[1] hope is by no means lost for the once-burgeoning enterprise, as recent clinical trials are beginning to show efficacy in areas ranging from amyloidosis to hypercholesterolemia to muscular dystrophy. With such resurgence comes a more informed perspective on the needs of such therapeutics: a renewed focus on true RNA drug development, and a desire for enhanced site-specific delivery.[2] In this review, we will discuss the latter with regard to hepatic targeting by synthetic vectors, covering the implications of organ and cellular physiology on conjugate structure, particle morphology, and active targeting. In presenting efficacy in a variety of disease models, we emphasize as well the extraordinary degree to which synthetic formulation improves upon and coordinates efforts with oligonucleotide development. Such advances in the understanding of and the technology behind RNAi have the potential to finally stabilize the long-term prospects RNA therapeutic development.
Collapse
|
31
|
Marchi AN, Saaem I, Tian J, LaBean TH. One-pot assembly of a hetero-dimeric DNA origami from chip-derived staples and double-stranded scaffold. ACS NANO 2013; 7:903-910. [PMID: 23281627 DOI: 10.1021/nn302322j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Although structural DNA nanotechnology, and especially scaffolded DNA origami, hold great promise for bottom-up fabrication of novel nanoscale materials and devices, concerns about scalability have tempered widespread enthusiasm. Here we report a single-pot reaction where both strands of double-stranded M13-bacteriophage DNA are simultaneously folded into two distinct shapes that then heterodimerize with high yield. The fully addressable, two-dimensional heterodimer DNA origami, with twice the surface area of standard M13 origami, formed in high yield (81% of the well-formed monomers undergo dimerization). We also report the concurrent production of entire sets of staple strands by a unique, nicking strand-displacement amplification (nSDA) involving reusable surface-bound template strands that were synthesized in situ using a custom piezoelectric inkjet system. The combination of chip-based staple strand production, double-sized origami, and high-yield one-pot assembly markedly increases the useful scale of DNA origami.
Collapse
Affiliation(s)
- Alexandria N Marchi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | | | | | | |
Collapse
|
32
|
Saaem I, LaBean TH. Overview of DNA origami for molecular self-assembly. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:150-62. [DOI: 10.1002/wnan.1204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
33
|
Advanced materials and processing for drug delivery: the past and the future. Adv Drug Deliv Rev 2013; 65:104-20. [PMID: 23088863 DOI: 10.1016/j.addr.2012.10.003] [Citation(s) in RCA: 591] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/09/2012] [Accepted: 10/16/2012] [Indexed: 11/21/2022]
Abstract
Design and synthesis of efficient drug delivery systems are of vital importance for medicine and healthcare. Materials innovation and nanotechnology have synergistically fueled the advancement of drug delivery. Innovation in material chemistry allows the generation of biodegradable, biocompatible, environment-responsive, and targeted delivery systems. Nanotechnology enables control over size, shape and multi-functionality of particulate drug delivery systems. In this review, we focus on the materials innovation and processing of drug delivery systems and how these advances have shaped the past and may influence the future of drug delivery.
Collapse
|
34
|
Ramanathan M, Kilbey, II SM, Ji Q, Hill JP, Ariga K. Materials self-assembly and fabrication in confined spaces. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm16629a] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
35
|
Affiliation(s)
- Kuo-Kang Liu
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Vincent Chan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| |
Collapse
|