1
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Rebolledo LP, Ke W, Cedrone E, Wang J, Majithia K, Johnson MB, Dokholyan NV, Dobrovolskaia MA, Afonin KA. Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure-Activity Relationship and Mechanistic Insights. ACS Appl Mater Interfaces 2024; 16:8430-8441. [PMID: 38344840 PMCID: PMC10895590 DOI: 10.1021/acsami.3c17779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Fibrous nanomaterials containing silica, titanium oxide, and carbon nanotubes are notoriously known for their undesirable inflammatory responses and associated toxicities that have been extensively studied in the environmental and occupational toxicology fields. Biopersistance and inflammation of "hard" nanofibers prevent their broader biomedical applications. To utilize the structural benefits of fibrous nanomaterials for functionalization with moieties of therapeutic significance while preventing undesirable immune responses, researchers employ natural biopolymers─RNA and DNA─to design "soft" and biodegradable nanomaterials with controlled immunorecognition. Nucleic acid nanofibers have been shown to be safe and efficacious in applications that do not require their delivery into the cells such as the regulation of blood coagulation. Previous studies demonstrated that unlike traditional therapeutic nucleic acids (e.g., CpG DNA oligonucleotides) nucleic acid nanoparticles (NANPs), when used without a carrier, are not internalized by the immune cells and, as such, do not induce undesirable cytokine responses. In contrast, intracellular delivery of NANPs results in cytokine responses that are dependent on the physicochemical properties of these nanomaterials. However, the structure-activity relationship of innate immune responses to intracellularly delivered fibrous NANPs is poorly understood. Herein, we employ the intracellular delivery of model RNA/DNA nanofibers functionalized with G-quadruplex-based DNA aptamers to investigate how their structural properties influence cytokine responses. We demonstrate that nanofibers' scaffolds delivered to the immune cells using lipofectamine induce interferon response via the cGAS-STING signaling pathway activation and that DNA aptamers incorporation shields the fibers from recognition by cGAS and results in a lower interferon response. This structure-activity relationship study expands the current knowledge base to inform future practical applications of intracellularly delivered NANPs as vaccine adjuvants and immunotherapies.
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Affiliation(s)
- Laura P Rebolledo
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21701, United States
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Krishna Majithia
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Biochemistry & Molecular Biology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, Maryland 21701, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina 28223, United States
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2
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Arnaboldi S. Wireless electrochemical actuation of soft materials towards chiral stimuli. Chem Commun (Camb) 2023; 59:2072-2080. [PMID: 36748650 PMCID: PMC9933456 DOI: 10.1039/d2cc06630k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Different areas of modern chemistry, require wireless systems able to transfer chirality from the molecular to the macroscopic event. The ability to recognize the enantiomers of a chiral analyte is highly desired, since in the majority of cases such molecules present different physico-chemical properties that could lead, eventually, to dangerous or harmful interactions with the environment or the human body. From an electrochemical point of view, enantiomers have the same electrochemical behavior except when they interact in a chiral environment. In this Feature Article, different approaches for the electrochemical recognition of chiral information based on the actuation of conducting polymers are described. Such a dynamic behavior of π-conjugated materials is based on an electrochemically induced shrinking/swelling transition of the polymeric matrix. Since all the systems, described so far in the literature, are achiral and require a direct connection to a power supply, new strategies will be presented in the manuscript, concerning the implementation of chirality in electrochemical actuators and their use in a wireless manner through bipolar electrochemistry. Herein, the synergy between the wireless unconventional actuation and the outstanding enantiorecognition of inherent chiral oligomers is presented as an easy and straightforward read out of chiral information in solution. This approach presents different advantages in comparison to classic electrochemical systems such as its wireless nature and the possible real-time data acquisition.
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Affiliation(s)
- Serena Arnaboldi
- Università degli Studi di Milano, Dipartimento di Chimica, Via Golgi 19, 20133, Milano, Italy.
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3
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Salinas G, Bonetti G, Cirilli R, Benincori T, Kuhn A, Arnaboldi S. Wireless light-emitting device for the determination of chirality in real samples. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140494] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Arnaboldi S, Salinas G, Bonetti G, Cirilli R, Benincori T, Kuhn A. Bipolar Electrochemical Measurement of Enantiomeric Excess with Inherently Chiral Polymer Actuators. ACS Meas Sci Au 2021; 1:110-116. [PMID: 34939074 PMCID: PMC8679086 DOI: 10.1021/acsmeasuresciau.1c00011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 05/11/2023]
Abstract
Straightforward enantioselective analytical methods are very important for drug safety, considering that in certain cases one of the two enantiomers of a chiral molecule might be harmful for humans. In this work, we propose a simple system for the direct and easy read-out of the enantiomeric excess of 3,4-dihydroxyphenylalanine (DOPA) as a model analyte. A conducting oligomer, i.e. oligo-(3,3'-dibenzothiophene), bearing inherently chiral features, is electrogenerated on a polypyrrole film. The resulting freestanding hybrid material is used as a wireless enantioselective actuator in a bipolar electrochemical cell. Combining in a single setup two individual actuators with opposite chiral features allows a direct visual read-out of enantiomeric excess, as the bending amplitude of each of the two actuators is directly correlated with the concentration of the corresponding stereoisomer of the analyte. Optimization of the experimental parameters results in efficient bending, giving access to the percentage values of the enantiomeric excess in mixtures containing different ratios of the antipodes, thus opening the way to potential applications for chiral in situ analysis.
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Affiliation(s)
- Serena Arnaboldi
- Université
de Bordeaux, CNRS UMR 5255, Bordeaux INP,
ENSCBP, 16 avenue Pey
Berland, 33607 Pessac, France
- Dipartimento
di Chimica, Universita degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Gerardo Salinas
- Université
de Bordeaux, CNRS UMR 5255, Bordeaux INP,
ENSCBP, 16 avenue Pey
Berland, 33607 Pessac, France
| | - Giorgia Bonetti
- Dipartimento
di Scienza e Alta Tecnologia, Universita
degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Roberto Cirilli
- Centro
Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Tiziana Benincori
- Dipartimento
di Scienza e Alta Tecnologia, Universita
degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Alexander Kuhn
- Université
de Bordeaux, CNRS UMR 5255, Bordeaux INP,
ENSCBP, 16 avenue Pey
Berland, 33607 Pessac, France
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5
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Salinas G, Arnaboldi S, Bonetti G, Cirilli R, Benincori T, Kuhn A. Hybrid light-emitting devices for the straightforward readout of chiral information. Chirality 2021; 33:875-882. [PMID: 34617330 DOI: 10.1002/chir.23370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/11/2022]
Abstract
Bipolar electrochemistry has gained increasing attention in recent years as an attractive transduction concept in analytical chemistry in general and, more specifically, in the frame of chiral recognition. Herein, we use this concept of wireless electrochemistry, based on the combination of the enantioselective oxidation of a chiral probe with the emission of light from a light-emitting diode (LED), as an alternative for an easy and straightforward readout of the presence of chiral molecules in solution. A hybrid polymer-microelectronic device was designed, using an inherently chiral oligomer, that is, oligo-(3,3'-dibenzothiophene) and a polypyrrole strip as the anode and cathode of a miniaturized LED. The wireless induced redox reactions trigger light emission when the probe with the right chirality is present in solution, whereas no light emission is observed for the opposite enantiomer. The average light intensity shows a linear correlation with the analyte concentration, and the concept opens the possibility to quantify the enantiomeric excess in mixtures of the molecular antipodes.
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Affiliation(s)
- Gerardo Salinas
- Univ. Bordeaux, ISM CNRS UMR 5255, Bordeaux INP, Pessac, France
| | - Serena Arnaboldi
- Univ. Bordeaux, ISM CNRS UMR 5255, Bordeaux INP, Pessac, France.,Dip. Di Chimica, Univ. degli Studi di Milano, Milan, Italy
| | - Giorgia Bonetti
- Dip. di Scienza e Alta Tecnologia, Univ. degli Studi dell'Insubria, Como, Italy
| | - Roberto Cirilli
- Istituto Superiore di Sanità, Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Rome, Italy
| | - Tiziana Benincori
- Dip. di Scienza e Alta Tecnologia, Univ. degli Studi dell'Insubria, Como, Italy
| | - Alexander Kuhn
- Univ. Bordeaux, ISM CNRS UMR 5255, Bordeaux INP, Pessac, France
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6
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Chandler M, Minevich B, Roark B, Viard M, Johnson MB, Rizvi MH, Deaton TA, Kozlov S, Panigaj M, Tracy JB, Yingling YG, Gang O, Afonin KA. Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities. ACS Appl Mater Interfaces 2021; 13:39030-39041. [PMID: 34402305 PMCID: PMC8654604 DOI: 10.1021/acsami.1c09230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Precise control over the assembly of biocompatible three-dimensional (3D) nanostructures would allow for programmed interactions within the cellular environment. Nucleic acids can be used as programmable crosslinkers to direct the assembly of quantum dots (QDs) and tuned to demonstrate different interparticle binding strategies. Morphologies of self-assembled QDs are evaluated via gel electrophoresis, transmission electron microscopy, small-angle X-ray scattering, and dissipative particle dynamics simulations, with all results being in good agreement. The controlled assembly of 3D QD organizations is demonstrated in cells via the colocalized emission of multiple assembled QDs, and their immunorecognition is assessed via enzyme-linked immunosorbent assays. RNA interference inducers are also embedded into the interparticle binding strategy to be released in human cells only upon QD assembly, which is demonstrated by specific gene silencing. The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brandon Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Laboratory of Integrative Cancer Immunology, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, United States
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mehedi H Rizvi
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas A Deaton
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Seraphim Kozlov
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice 04154, Slovak Republic
| | - Joseph B Tracy
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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7
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Zhovmer AS, Chandler M, Manning A, Afonin KA, Tabdanov ED. Programmable DNA-augmented hydrogels for controlled activation of human lymphocytes. Nanomedicine 2021; 37:102442. [PMID: 34284132 DOI: 10.1016/j.nano.2021.102442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022]
Abstract
Contractile forces within the planar interface between T cell and antigen-presenting surface mechanically stimulate T cell receptors (TCR) in the mature immune synapses. However, the origin of mechanical stimulation during the initial, i.e., presynaptic, microvilli-based TCR activation in the course of immune surveillance remains unknown and new tools to help address this problem are needed. In this work, we develop nucleic acid nanoassembly (NAN)-based technology for functionalization of hydrogels using isothermal toehold-mediated reassociation of RNA/DNA heteroduplexes. Resulting platform allows for regulation with NAN linkers of 3D force momentum along the TCR mechanical axis, whereas hydrogels contribute to modulation of 2D shear modulus. By utilizing different lengths of NAN linkers conjugated to polyacrylamide gels of different shear moduli, we demonstrate an efficient capture of human T lymphocytes and tunable activation of TCR, as confirmed by T-cell spreading and pY foci.
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Affiliation(s)
- Alexander S Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Alexis Manning
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Erdem D Tabdanov
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.
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8
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Johnson MB, Chandler M, Afonin KA. Nucleic acid nanoparticles (NANPs) as molecular tools to direct desirable and avoid undesirable immunological effects. Adv Drug Deliv Rev 2021; 173:427-438. [PMID: 33857556 PMCID: PMC8178219 DOI: 10.1016/j.addr.2021.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022]
Abstract
Nucleic acid nanoparticles (NANPs) represent a highly versatile molecular platform for the targeted delivery of various therapeutics. However, despite their promise, further clinical translation of this innovative technology can be hindered by immunological off-target effects. All human cells are equipped with an arsenal of receptors that recognize molecular patterns specific to foreign nucleic acids and understanding the rules that guide this recognition offer the key rationale for the development of therapeutic NANPs with tunable immune stimulation. Numerous recent studies have provided increasing evidence that in addition to NANPs' physicochemical properties and therapeutic effects, their interactions with cells of the immune system can be regulated through multiple independently programmable architectural parameters. The results further suggest that defined immunomodulation by NANPs can either support their immunoquiescent delivery or be used for conditional stimulation of beneficial immunological responses.
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Affiliation(s)
- M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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9
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Juneja R, Vadarevu H, Halman J, Tarannum M, Rackley L, Dobbs J, Marquez J, Chandler M, Afonin K, Vivero-Escoto JL. Combination of Nucleic Acid and Mesoporous Silica Nanoparticles: Optimization and Therapeutic Performance In Vitro. ACS Appl Mater Interfaces 2020; 12:38873-38886. [PMID: 32805923 PMCID: PMC7748385 DOI: 10.1021/acsami.0c07106] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Programmable nucleic acid nanoparticles (NANPs) with precisely controlled functional compositions can regulate the conditional activation of various biological pathways and responses in human cells. However, the intracellular delivery of NANPs alone is hindered by their susceptibility to nuclease activity and inefficient crossing of biological membranes. In this work, we optimized the internalization and therapeutic performance of several representative NANPs delivered with mesoporous silica nanoparticles (MSNPs) tailored for efficient electrostatic association with NANPs. We compared the immunostimulatory properties of different NA-MS-NP complexes formed with globular, planar, and fibrous NANPs and demonstrated the maximum immunostimulation for globular NANPs. As a proof of concept, we assessed the specific gene silencing by NA-MS-NP complexes functionalized with siRNA targeting green fluorescent protein expressed in triple-negative human breast cancer cells. We showed that the fibrous NANPs have the highest silencing efficiency when compared to globular or planar counterparts. Finally, we confirmed the multimodal ability of MSNPs to co-deliver a chemotherapy drug, doxorubicin, and NANPs targeting apoptosis regulator gene BCL2 in triple-negative breast cancer and melanoma cell lines. Overall, the combination of NANPs and MSNPs may become a new promising approach to efficiently treat cancer and other diseases via the simultaneous targeting of various pathways.
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Affiliation(s)
- Ridhima Juneja
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Hemapriyadarshini Vadarevu
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Justin Halman
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mubin Tarannum
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Lauren Rackley
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jacob Dobbs
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jose Marquez
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Morgan Chandler
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill Afonin
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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10
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Arnaboldi S, Gupta B, Benincori T, Bonetti G, Cirilli R, Kuhn A. Absolute Chiral Recognition with Hybrid Wireless Electrochemical Actuators. Anal Chem 2020; 92:10042-10047. [DOI: 10.1021/acs.analchem.0c01817] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Serena Arnaboldi
- Univ. Bordeaux, CNRS UMR 5255, Bordeaux INP, ENSCBP, 16 avenue Pey Berland, 33607 Pessac, France
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Bhavana Gupta
- Univ. Bordeaux, CNRS UMR 5255, Bordeaux INP, ENSCBP, 16 avenue Pey Berland, 33607 Pessac, France
- Engineering Research Center for Nanomaterials, Henan University, Kaifeng 475004, China
| | - Tiziana Benincori
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Giorgia Bonetti
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Roberto Cirilli
- Centro Nazionale per il Controllo e la Valutazione dei Farmaci, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy
| | - Alexander Kuhn
- Univ. Bordeaux, CNRS UMR 5255, Bordeaux INP, ENSCBP, 16 avenue Pey Berland, 33607 Pessac, France
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11
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Chandler M, Panigaj M, Rolband LA, Afonin KA. Challenges to optimizing RNA nanostructures for large scale production and controlled therapeutic properties. Nanomedicine (Lond) 2020; 15:1331-1340. [PMID: 32452262 PMCID: PMC7304434 DOI: 10.2217/nnm-2020-0034] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/16/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleic acids have been utilized to construct an expansive collection of nanoarchitectures varying in design, physicochemical properties, cellular processing and biomedical applications. However, the broader therapeutic adaptation of nucleic acid nanoassemblies in general, and RNA-based nanoparticles in particular, have faced several challenges in moving towards (pre)clinical settings. For one, the large-batch synthesis of nucleic acids is still under development, with multi-stranded and chemically modified assemblies requiring greater production capacity while maintaining consistent medical-grade outputs. Furthermore, the unknown immunostimulation by these nanomaterials poses additional challenges, necessary to be overcome for optimizing future development of clinically approved RNA nanoparticles.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Martin Panigaj
- Institute of Biology & Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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12
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Liu J, Craciun I, Belluati A, Wu D, Sieber S, Einfalt T, Witzigmann D, Chami M, Huwyler J, Palivan CG. DNA-directed arrangement of soft synthetic compartments and their behavior in vitro and in vivo. Nanoscale 2020; 12:9786-9799. [PMID: 32328600 DOI: 10.1039/d0nr00361a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA has been widely used as a key tether to promote self-organization of super-assemblies with emergent properties. However, control of this process is still challenging for compartment assemblies and to date the resulting assemblies have unstable membranes precluding in vitro and in vivo testing. Here we present our approach to overcome these limitations, by manipulating molecular factors such as compartment membrane composition and DNA surface density, thereby controlling the size and stability of the resulting DNA-linked compartment clusters. The soft, flexible character of the polymer membrane and low number of ssDNA remaining exposed after cluster formation determine the interaction of these clusters with the cell surface. These clusters exhibit in vivo stability and lack of toxicity in a zebrafish model. To display the breadth of therapeutic applications attainable with our system, we encapsulated the medically established enzyme laccase within the inner compartment and demonstrated its activity within the clustered compartments. Most importantly, these clusters can interact selectively with different cell lines, opening a new strategy to modify and expand cellular functions by attaching such pre-organized soft DNA-mediated compartment clusters on cell surfaces for cell engineering or therapeutic applications.
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Affiliation(s)
- Juan Liu
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Ioana Craciun
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Andrea Belluati
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Dalin Wu
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
| | - Sandro Sieber
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Tomaz Einfalt
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Dominik Witzigmann
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Mohamed Chami
- BioEM lab, Biozentrum, University of Basel, Mattenstrasse 26, Basel-4058, Switzerland
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, Basel-4056, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, Basel-4058, Switzerland.
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Oliver RC, Rolband LA, Hutchinson-Lundy AM, Afonin KA, Krueger JK. Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment. Nanomaterials (Basel) 2019; 9:E681. [PMID: 31052508 PMCID: PMC6566709 DOI: 10.3390/nano9050681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 12/23/2022]
Abstract
Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.
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Affiliation(s)
- Ryan C Oliver
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Lewis A Rolband
- UNC Charlotte Chemistry Department, Charlotte, NC 28223, USA.
| | | | - Kirill A Afonin
- UNC Charlotte Chemistry Department, Charlotte, NC 28223, USA.
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Ali AA, Kang M, Kharbash R, Kim Y. Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomed Eng 2019; 1:6. [PMID: 32903305 DOI: 10.1186/s42490-019-0008-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response. Results In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.
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Chandler M, Lyalina T, Halman J, Rackley L, Lee L, Dang D, Ke W, Sajja S, Woods S, Acharya S, Baumgarten E, Christopher J, Elshalia E, Hrebien G, Kublank K, Saleh S, Stallings B, Tafere M, Striplin C, Afonin KA. Broccoli Fluorets: Split Aptamers as a User-Friendly Fluorescent Toolkit for Dynamic RNA Nanotechnology. Molecules 2018; 23:E3178. [PMID: 30513826 PMCID: PMC6321606 DOI: 10.3390/molecules23123178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023] Open
Abstract
RNA aptamers selected to bind fluorophores and activate their fluorescence offer a simple and modular way to visualize native RNAs in cells. Split aptamers which are inactive until the halves are brought within close proximity can become useful for visualizing the dynamic actions of RNA assemblies and their interactions in real time with low background noise and eliminated necessity for covalently attached dyes. Here, we design and test several sets of F30 Broccoli aptamer splits, that we call fluorets, to compare their relative fluorescence and physicochemical stabilities. We show that the splits can be simply assembled either through one-pot thermal annealing or co-transcriptionally, thus allowing for direct tracking of transcription reactions via the fluorescent response. We suggest a set of rules that enable for the construction of responsive biomaterials that readily change their fluorescent behavior when various stimuli such as the presence of divalent ions, exposure to various nucleases, or changes in temperature are applied. We also show that the strand displacement approach can be used to program the controllable fluorescent responses in isothermal conditions. Overall, this work lays a foundation for the future development of dynamic systems for molecular computing which can be used to monitor real-time processes in cells and construct biocompatible logic gates.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Tatiana Lyalina
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, 191002 St. Petersburg, Russia.
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Lauren Rackley
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Lauren Lee
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Dylan Dang
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Sameer Sajja
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Steven Woods
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Shrija Acharya
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Elijah Baumgarten
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Jonathan Christopher
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Emman Elshalia
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Gabriel Hrebien
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kinzey Kublank
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Saja Saleh
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Bailey Stallings
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Michael Tafere
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Caryn Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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Affiliation(s)
- Zheng Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jon R. Askim
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Kenneth S. Suslick
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Affiliation(s)
- Shuaidi Zhang
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Ren Geryak
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Jeffrey Geldmeier
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Sunghan Kim
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
| | - Vladimir V. Tsukruk
- School of Materials Science
and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245, United States
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