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Yi SA, Pongkulapa T, Nevins S, Goldston LL, Chen M, Lee KB. Developing MiR-133a Zipper Nanoparticles for Targeted Enhancement of Thermogenic Adipocyte Generation. Adv Healthc Mater 2024:e2400654. [PMID: 38795000 DOI: 10.1002/adhm.202400654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/17/2024] [Indexed: 05/27/2024]
Abstract
Existing delivery methods for RNAi therapeutics encounter challenges, including stability, specificity, and off-target effects, which restrict their clinical effectiveness. In this study, a novel miR-133a zipper nanoparticle (NP) system that integrates miRNA zipper technology with rolling circle transcription (RCT) to achieve targeted delivery and specific regulation of miR-133a in adipocytes, is presented. This innovative approach can greatly enhance the delivery and release of miR-133a zippers, increasing the expression of thermogenic genes and mitochondrial biogenesis. he miR-133a zipper NP is utilized for the delivery of miRNA zipper-blocking miR-133a, an endogenous inhibitor of Prdm16 expression, to enhance the thermogenic activity of adipocytes by modulating their transcriptional program. Inhibition of miR-133a through the miR-133a zipper NP leads to more significant upregulation of thermogenic gene expression (Prdm16 and Ucp1) than with the free miR-133a zipper strand. Furthermore, miR-133a zipper NPs increase the number of mitochondria and induce heat production, reducing the size of 3D adipose spheroids. In short, this study emphasizes the role of RNA NPs in improving RNAi stability and specificity and paves the way for broader applications in gene therapy. Moreover, this research represents a significant advancement in RNAi-based treatments, pointing toward a promising direction for future therapeutic strategies.
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Affiliation(s)
- Sang Ah Yi
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Sarah Nevins
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Li Ling Goldston
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Meizi Chen
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 123 Bevier Road, Piscataway, NJ, 08854, USA
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2
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Jeong J, An SY, Hu X, Zhao Y, Yin R, Szczepaniak G, Murata H, Das SR, Matyjaszewski K. Biomass RNA for the Controlled Synthesis of Degradable Networks by Radical Polymerization. ACS NANO 2023; 17:21912-21922. [PMID: 37851525 PMCID: PMC10655241 DOI: 10.1021/acsnano.3c08244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
Nucleic acids extracted from biomass have emerged as sustainable and environmentally friendly building blocks for the fabrication of multifunctional materials. Until recently, the fabrication of biomass nucleic acid-based structures has been facilitated through simple crosslinking of biomass nucleic acids, which limits the possibility of material properties engineering. This study presents an approach to convert biomass RNA into an acrylic crosslinker through acyl imidazole chemistry. The number of acrylic moieties on RNA was engineered by varying the acylation conditions. The resulting RNA crosslinker can undergo radical copolymerization with various acrylic monomers, thereby offering a versatile route for creating materials with tunable properties (e.g., stiffness and hydrophobic characteristics). Further, reversible-deactivation radical polymerization methods, such as atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT), were also explored as additional approaches to engineer the hydrogel properties. The study also demonstrated the metallization of the biomass RNA-based material, thereby offering potential applications in enhancing electrical conductivity. Overall, this research expands the opportunities in biomass-based biomaterial fabrication, which allows tailored properties for diverse applications.
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Affiliation(s)
- Jaepil Jeong
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - So Young An
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaolei Hu
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yuqi Zhao
- Department
of Materials Science & Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rongguan Yin
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Grzegorz Szczepaniak
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- University
of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland
| | - Hironobu Murata
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Subha R. Das
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Center
for Nucleic Acids Science & Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Krzysztof Matyjaszewski
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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3
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Ma X, Zhang Y, Huang K, Zhu L, Xu W. Multifunctional rolling circle transcription-based nanomaterials for advanced drug delivery. Biomaterials 2023; 301:122241. [PMID: 37451000 DOI: 10.1016/j.biomaterials.2023.122241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
As the up-and-comer in the development of RNA nanotechnology, RNA nanomaterials based on functionalized rolling circle transcription (RCT) have become promising carriers for drug production and delivery. This is due to RCT technology can self-produce polyvalent tandem nucleic acid prodrugs for intervention in intracellular gene expression and protein production. RNA component strands participating in de novo assembly enable RCT-based nanomaterials to exhibit good mechanical properties, biostability, and biocompatibility as delivery carriers. The biostability makes it to suitable for thermodynamically/kinetically favorable assembly, enzyme resistance and efficient expression in vivo. Controllable RCT system combined with polymers enables customizable and adjustable size, shape, structure, and stoichiometry of RNA building materials, which provide groundwork for the delivery of advanced drugs. Here, we review the assembly strategies and the dynamic regulation of RCT-based nanomaterials, summarize its functional properties referring to the bottom-up design philosophy, and describe its advancements in tumor gene therapy, synergistic chemotherapy, and immunotherapy. Last, we elaborate on the unique and practical value of RCT-based nanomaterials, namely "self-production and self-sale", and their potential challenges in nanotechnology, material science and biomedicine.
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Affiliation(s)
- Xuan Ma
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China
| | - Kunlun Huang
- College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Nutrition Engineering, China Agricultural University, Beijing, 100083, China.
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4
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Tripathy DB, Gupta A. Nanomembranes-Affiliated Water Remediation: Chronology, Properties, Classification, Challenges and Future Prospects. MEMBRANES 2023; 13:713. [PMID: 37623773 PMCID: PMC10456521 DOI: 10.3390/membranes13080713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023]
Abstract
Water contamination has become a global crisis, affecting millions of people worldwide and causing diseases and illnesses, including cholera, typhoid, and hepatitis A. Conventional water remediation methods have several challenges, including their inability to remove emerging contaminants and their high cost and environmental impact. Nanomembranes offer a promising solution to these challenges. Nanomembranes are thin, selectively permeable membranes that can remove contaminants from water based on size, charge, and other properties. They offer several advantages over conventional methods, including their ability to remove evolving pollutants, low functioning price, and reduced ecological influence. However, there are numerous limitations linked with the applications of nanomembranes in water remediation, including fouling and scaling, cost-effectiveness, and potential environmental impact. Researchers are working to reduce the cost of nanomembranes through the development of more cost-effective manufacturing methods and the use of alternative materials such as graphene. Additionally, there are concerns about the release of nanomaterials into the environment during the manufacturing and disposal of the membranes, and further research is needed to understand their potential impact. Despite these challenges, nanomembranes offer a promising solution for the global water crisis and could have a significant impact on public health and the environment. The current article delivers an overview on the exploitation of various engineered nanoscale substances, encompassing the carbonaceous nanomaterials, metallic, metal oxide and metal-organic frameworks, polymeric nano-adsorbents and nanomembranes, for water remediation. The article emphasizes the mechanisms involved in adsorption and nanomembrane filtration. Additionally, the authors aim to deliver an all-inclusive review on the chronology, technical execution, challenges, restrictions, reusability, and future prospects of these nanomaterials.
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Affiliation(s)
- Divya Bajpai Tripathy
- Division of Chemistry, School of Basic Sciences, Galgotias University, Greater Noida 201312, India;
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5
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Tockary TA, Abbasi S, Matsui-Masai M, Hayashi A, Yoshinaga N, Boonstra E, Wang Z, Fukushima S, Kataoka K, Uchida S. Comb-structured mRNA vaccine tethered with short double-stranded RNA adjuvants maximizes cellular immunity for cancer treatment. Proc Natl Acad Sci U S A 2023; 120:e2214320120. [PMID: 37428918 PMCID: PMC10629565 DOI: 10.1073/pnas.2214320120] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 06/09/2023] [Indexed: 07/12/2023] Open
Abstract
Integrating antigen-encoding mRNA (Messenger RNA) and immunostimulatory adjuvant into a single formulation is a promising approach to potentiating the efficacy of mRNA vaccines. Here, we developed a scheme based on RNA engineering to integrate adjuvancy directly into antigen-encoding mRNA strands without hampering the ability to express antigen proteins. Short double-stranded RNA (dsRNA) was designed to target retinoic acid-inducible gene-I (RIG-I), an innate immune receptor, for effective cancer vaccination and then tethered onto the mRNA strand via hybridization. Tuning the dsRNA structure and microenvironment by changing its length and sequence enabled the determination of the structure of dsRNA-tethered mRNA efficiently stimulating RIG-I. Eventually, the formulation loaded with dsRNA-tethered mRNA of the optimal structure effectively activated mouse and human dendritic cells and drove them to secrete a broad spectrum of proinflammatory cytokines without increasing the secretion of anti-inflammatory cytokines. Notably, the immunostimulating intensity was tunable by modulating the number of dsRNA along the mRNA strand, which prevents excessive immunostimulation. Versatility in the applicable formulation is a practical advantage of the dsRNA-tethered mRNA. Its formulation with three existing systems, i.e., anionic lipoplex, ionizable lipid-based lipid nanoparticles, and polyplex micelles, induced appreciable cellular immunity in the mice model. Of particular interest, dsRNA-tethered mRNA encoding ovalbumin (OVA) formulated in anionic lipoplex used in clinical trials exerted a significant therapeutic effect in the mouse lymphoma (E.G7-OVA) model. In conclusion, the system developed here provides a simple and robust platform to supply the desired intensity of immunostimulation in various formulations of mRNA cancer vaccines.
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Affiliation(s)
- Theofilus A. Tockary
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, Kawasaki-ku, Kawasaki210-0821, Japan
| | - Saed Abbasi
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, Kawasaki-ku, Kawasaki210-0821, Japan
| | - Miki Matsui-Masai
- Department of Research, NanoCarrier Co., Ltd., Kawasaki-ku, Kawasaki210-0821, Japan
| | - Akimasa Hayashi
- Department of Pathology, Kyorin University School of Medicine, Mitaka-shi, Tokyo181-8611, Japan
| | - Naoto Yoshinaga
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Saitama351-0198, Japan
| | - Eger Boonstra
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Zheng Wang
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, Kawasaki-ku, Kawasaki210-0821, Japan
| | - Shigeto Fukushima
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, Kawasaki-ku, Kawasaki210-0821, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, Kawasaki-ku, Kawasaki210-0821, Japan
| | - Satoshi Uchida
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, Kawasaki-ku, Kawasaki210-0821, Japan
- Department of Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto606-0823, Japan
- Department of Advanced Nanomedical Engineering, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo113-8510, Japan
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6
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Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023; 7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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7
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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8
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Ahn SY, Kim J, Vellampatti S, Oh S, Lim YT, Park SH, Luo D, Chung J, Um SH. Protein-Encoding Free-Standing RNA Hydrogel for Sub-Compartmentalized Translation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2110424. [PMID: 35263477 DOI: 10.1002/adma.202110424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/20/2022] [Indexed: 06/14/2023]
Abstract
RNA can self-fold into complex structures that can serve as major biological regulators in protein synthesis and in catalysis. Due to the abundance of structural primitives and functional diversity, RNA has been utilized for designing nature-defined goals despite its intrinsic chemical instability and lack of technologies. Here, a robust, free-standing RNA hydrogel is developed through a sequential process involving both ligation and rolling circle transcription to form RNA G-quadruplexes, capable of both catalytic activity and enhancing expression of several proteins in sub-compartmentalized, phase-separated translation environments. The observations suggest that this hydrogel will expand RNA research and impact practical RNA principles and applications.
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Affiliation(s)
- So Yeon Ahn
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
| | - Jeonghun Kim
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
| | | | - Sung Oh
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
| | - Yong Taik Lim
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
| | - Sung Ha Park
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- Department of Physics, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
| | - Dan Luo
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Soong Ho Um
- Progeneer Incorporation, 12, Digital-ro 31-gil, Guro-gu, Seoul, 08380, Korea
- School of Chemical Engineering, Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Korea
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9
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Kim D, Han S, Ji Y, Moon S, Nam H, Lee JB. Multimeric RNAs for efficient RNA-based therapeutics and vaccines. J Control Release 2022; 345:770-785. [PMID: 35367477 PMCID: PMC8970614 DOI: 10.1016/j.jconrel.2022.03.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 11/17/2022]
Abstract
There has been a growing interest in RNA therapeutics globally, and much progress has been made in this area, which has been further accelerated by the clinical applications of RNA-based vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Following these successful clinical trials, various technologies have been developed to improve the efficacy of RNA-based drugs. Multimerization of RNA therapeutics is one of the most attractive approaches to ensure high stability, high efficacy, and prolonged action of RNA-based drugs. In this review, we offer an overview of the representative approaches for generating repetitive functional RNAs by chemical conjugation, structural self-assembly, enzymatic elongation, and self-amplification. The therapeutic and vaccine applications of engineered multimeric RNAs in various diseases have also been summarized. By outlining the current status of multimeric RNAs, the potential of multimeric RNA as a promising treatment strategy is highlighted.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Sunghyun Moon
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Hyangsu Nam
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea.
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10
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Jeon H, Kim YM, Han S, Moon HC, Lee JB. DNA Optoelectronics: Versatile Systems for On-Demand Functional Electrochemical Applications. ACS NANO 2022; 16:241-250. [PMID: 34978802 DOI: 10.1021/acsnano.1c06087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Herein, we propose innovative deoxyribonucleic acid (DNA)-based gels and their applications in diverse optoelectronics. We prepared the optoelectronic DNA-based gels (OpDNA Gel) through molecular complexation, that is, groove binding and ionic interactions of DNA and 1,1'-diheptyl-4,4'-bipyridinium (DHV). This process is feasible even with sequence-nonspecific DNA extracted from nature (e.g., salmon testes), resulting in the expansion of the application scope of DNA-based gels. OpDNA Gel possessed good mechanical characteristics (e.g., high compressibility, thermoplasticity, and outstanding viscoelastic properties) that have not been observed in typical DNA hydrogels. Moreover, the electrochromic (EC) characteristics of DHV were not lost when combined with OpDNA Gel. By taking advantage of the facile moldability, voltage-tunable EC behavior, and biocompatibility/biodegradability of OpDNA Gel, we successfully demonstrated its applicability in a variety of functional electrochemical systems, including on-demand information coding systems, user-customized EC displays, and microorganism monitoring systems. The OpDNA Gel is a promising platform for the application of DNA-based biomaterials in electrochemical optoelectronics.
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Affiliation(s)
- Hyunsu Jeon
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Yong Min Kim
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Hong Chul Moon
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
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11
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Ji Y, Kim D, Kim H, Han S, Lee JB. Construction of a two-dimensional DNA-RNA hybridized membrane for collecting tumor-derived exosomes. Chem Commun (Camb) 2021; 58:266-269. [PMID: 34878445 DOI: 10.1039/d1cc05924f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Macroscopic nucleic acid-based structures have attracted much attention in biomedical fields. Here, we introduce a novel DNA-RNA hybridized membrane structure via enzymatic dual polymerization. The membrane exhibited enhanced rigidity and functionality. Encoded with an aptamer, the membrane showed great potential as a collecting platform of tumor-derived exosomes without additional labeling.
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Affiliation(s)
- Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea.
| | - Dajeong Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea.
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea.
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea.
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea.
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12
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Kim D, Han S, Ji Y, Youn H, Kim H, Ko O, Lee JB. RNA polymerization actuating nucleic acid membrane (RANAM)-based biosensing for universal RNA virus detection. Biosens Bioelectron 2021; 199:113880. [PMID: 34915215 PMCID: PMC8662841 DOI: 10.1016/j.bios.2021.113880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/18/2022]
Abstract
The coronavirus disease (COVID-19) pandemic has shown the importance of early disease diagnosis in preventing further infection and mortality. Despite major advances in the development of highly precise and rapid detection approaches, the time-consuming process of designing a virus-specific diagnostic kit has been a limiting factor in the early management of the pandemic. Here, we propose an RNA polymerase activity-sensing strategy utilizing an RNA polymerization actuating nucleic acid membrane (RANAM) partially metallized with gold for colorimetric RNA virus detection. Following RANAM-templated amplification of newly synthesized RNA, the presence of the RNA polymerase was determined by visualization of the inhibition of an oxidation/reduction (redox) reaction between 3,3′,5,5′-tetramethylbenzidine (TMB) and blocked Au3+. As a proof of concept, a viral RNA-dependent RNA polymerase (RdRP), which is found in various RNA virus-infected cells, was chosen as a target molecule. With this novel RANAM biosensor, as little as 10 min of RdRP incubation could significantly reduce the colorimetric signal. Further development into an easy-to-use prototype kit in viral infection diagnosis detected RdRP present at levels even as low as 100 aM. Color formation based on the presence of RdRP could be simply and clearly confirmed through smartphone-assisted color imaging of the prototype kit. This study provides a non-PCR-based RNA virus detection including its variants using RdRP-mediated polymerization.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Heejeong Youn
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Ohsung Ko
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea.
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13
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Advances in the synthesis and application of self-assembling biomaterials. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:46-62. [PMID: 34329646 DOI: 10.1016/j.pbiomolbio.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 02/08/2023]
Abstract
The present study scrutinized some of the crucial advancements in the synthesis and functionalisation of self-assembling biomaterials for application in biomedicine. The basic concept of self-organization was discussed along with the mechanisms and methods involved in its implementation with biomaterials. Further, several recent applications of this technology in the biological and medical domain, and the avenues for future research and development were presented. This study brought to focus the vast potential of basic and applied research involved, especially in the context of hybrids and composites, as well as the difference in pace of new developments for different types of biomolecular materials. As nanobiotechnology matures, the tools and techniques available for developing and controlling self-assembled biomaterials as well as studying their interaction with biological tissue, will grow exponentially. Presently, self-assembly remains a potent tool for the synthesis of functional biomaterials.
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14
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Li C, Luo S, Wang J, Shen Z, Wu ZS. Nuclease-resistant signaling nanostructures made entirely of DNA oligonucleotides. NANOSCALE 2021; 13:7034-7051. [PMID: 33889882 DOI: 10.1039/d1nr00197c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Nucleic acid probes have the advantages of excellent biocompatibility, biodegradability, versatile functionalities and remarkable programmability. However, the low biostability of nucleic acid probes under complex physiological conditions limits their in vivo application. Despite impressive progress in the development of inorganic material-mediated biostable nucleic acid nanostructures, uncertain systemic toxicity of composite nanocarriers has hindered their application in living organisms. In the field of biomedicine, as a promising alternative capable of avoiding potential cytotoxicity, biologically stable nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in recent years, offering an exciting in vivo tool for cancer diagnosis and clinical treatment. In this review, we summarize the recent advances in the development of nuclease-resistant DNA nanostructures with different geometrical shapes, such as tetrahedron, octahedron, DNA triangular prism (DTP), DNA nanotubes and DNA origami, introduce innovative assembly strategies, and discuss unique structural advantages and especially biological applications in cellular imaging and targeted drug delivery in an organism. Finally, we conclude with the challenges in the clinical development of DNA nanostructures and present an outlook of the future of this rapidly expanding field.
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Affiliation(s)
- Congcong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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15
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Han S, Park Y, Kim H, Nam H, Ko O, Lee JB. Double Controlled Release of Therapeutic RNA Modules through Injectable DNA-RNA Hybrid Hydrogel. ACS APPLIED MATERIALS & INTERFACES 2020; 12:55554-55563. [PMID: 33259200 DOI: 10.1021/acsami.0c12506] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Advances in the DNA nanotechnology have enabled the fabrication of DNA-based hydrogels with precisely controlled structures and tunable mechanical and biological properties. Compared to DNA hydrogel, preparation of RNA-based hydrogel remains challenging due to the inherent instability of naked RNA. To overcome these limitations, we fabricated a DNA-RNA hybrid hydrogel via stepwise dual enzymatic polymerization. Multimeric short hairpin RNAs (shRNAs) were hybridized with functional DNA aptamers for targeting and mechanical properties of the hydrogel. The obtained DNA-RNA hybrid hydrogel was ultrasoft, robust, and injectable hence reconfigurable into any confined structures. As a model system, the hydrogel was able to mimic microtubule structures under physiological conditions and designed to release the functional small interfering RNA (siRNA)-aptamer complex (SAC) sequentially. In addition, we encoded restriction enzyme-responsive sites in DNA-RNA hybrid hydrogel to boost the release of SAC. This novel strategy provides an excellent platform for systematic RNA delivery through double-controlled release, SAC release from hydrogel, and subsequent release of siRNA from the SAC, which has promising potential in RNA therapy.
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Affiliation(s)
- Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Yongkuk Park
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Hyangsu Nam
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Ohsung Ko
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
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16
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Ghimire C, Wang H, Li H, Vieweger M, Xu C, Guo P. RNA Nanoparticles as Rubber for Compelling Vessel Extravasation to Enhance Tumor Targeting and for Fast Renal Excretion to Reduce Toxicity. ACS NANO 2020; 14:13180-13191. [PMID: 32902260 PMCID: PMC7799665 DOI: 10.1021/acsnano.0c04863] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rubber is a fascinating material in both industry and daily life. The development of elastomeric material in nanotechnology is imperative due to its economic and technological potential. By virtue of their distinctive physicochemical properties, nucleic acids have been extensively explored in material science. The Phi29 DNA packaging motor contains a 3WJ with three angles of 97°, 125°, and 138°. Here, the rubber-like property of RNA architectures was investigated using optical tweezers and in vivo imaging technologies. The 3WJ 97° interior angle was contracted or stretched to 60°, 90°, and 108° at will to build elegant RNA triangles, squares, pentagons, cubes, tetrahedrons, dendrimers, and prisms. RNA nanoarchitecture was stretchable and shrinkable by optical tweezer with multiple extension and relaxation repeats like a rubber. Comparing to gold and iron nanoparticles with the same size, RNA nanoparticles display stronger cancer-targeting outcomes, while less accumulation in healthy organs. Generally, the upper limit of renal excretion is 5.5 nm; however, the 5, 10, and 20 nm RNA nanoparticles passed the renal filtration and resumed their original structure identified in urine. These findings solve two previous mysteries: (1) Why RNA nanoparticles have an unusually high tumor targeting efficiency since their rubber or amoeba-like deformation property enables them to squeeze out of the leaky vasculature to improve the EPR effect; and (2) why RNA nanoparticles remain non-toxic since they can be rapidly cleared from the body via renal excretion into urine with little accumulation in the body. Considering its controllable shape and size plus its rubber-like property, RNA holds great promises for industrial and biomedical applications especially in cancer therapeutics delivery.
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Affiliation(s)
| | | | | | - Mario Vieweger
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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17
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Sun Y, Chen C, Wang X, Zhang F, Lu S, Li X, Suo X, Lin Z. Self-Assembly of Metallacages into Centimeter Films with Tunable Size and Emissions. J Am Chem Soc 2020; 142:17933-17937. [DOI: 10.1021/jacs.0c09781] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yan Sun
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, P. R. China
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Chongyi Chen
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Ningbo University, Ningbo, Zhejiang 315211, P. R. China
| | - Xinqiong Wang
- Department of Pediatrics, Ruijin Hospital and Ruijin North Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, P. R. China
| | - Fengmin Zhang
- Testing Center of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225002, P. R. China
| | - Shuai Lu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
- College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, P. R. China
| | - Xiaopeng Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, P. R. China
| | - Xiaocen Suo
- Testing Center of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225002, P. R. China
| | - Zixia Lin
- Testing Center of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225002, P. R. China
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18
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Jakšić Z, Jakšić O. Biomimetic Nanomembranes: An Overview. Biomimetics (Basel) 2020; 5:E24. [PMID: 32485897 PMCID: PMC7345464 DOI: 10.3390/biomimetics5020024] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 11/30/2022] Open
Abstract
Nanomembranes are the principal building block of basically all living organisms, and without them life as we know it would not be possible. Yet in spite of their ubiquity, for a long time their artificial counterparts have mostly been overlooked in mainstream microsystem and nanosystem technologies, being a niche topic at best, instead of holding their rightful position as one of the basic structures in such systems. Synthetic biomimetic nanomembranes are essential in a vast number of seemingly disparate fields, including separation science and technology, sensing technology, environmental protection, renewable energy, process industry, life sciences and biomedicine. In this study, we review the possibilities for the synthesis of inorganic, organic and hybrid nanomembranes mimicking and in some way surpassing living structures, consider their main properties of interest, give a short overview of possible pathways for their enhancement through multifunctionalization, and summarize some of their numerous applications reported to date, with a focus on recent findings. It is our aim to stress the role of functionalized synthetic biomimetic nanomembranes within the context of modern nanoscience and nanotechnologies. We hope to highlight the importance of the topic, as well as to stress its great applicability potentials in many facets of human life.
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Affiliation(s)
- Zoran Jakšić
- Center of Microelectronic Technologies, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, 11000 Belgrade, Serbia;
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19
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20
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Shang X, Liu F, Hu Y, Guo Y, Liu J, Wu F, You J, Zhang X, Li D. Hyper-dendritic rolling circle amplification for RNA and GSH detection. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Kim D, Kim J, Lee JB. An enzymatically self-assembled DNA patch for enhanced blood coagulation. Chem Commun (Camb) 2020; 56:5917-5920. [DOI: 10.1039/d0cc00974a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The assembly of a DNA patch combining enzymatically fabricated DNA film and aptamer-based thrombin binding for enhanced blood coagulation is demonstrated.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering
- University of Seoul
- Seoul
- South Korea
| | - Jieun Kim
- Department of Chemical Engineering
- University of Seoul
- Seoul
- South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering
- University of Seoul
- Seoul
- South Korea
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22
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Li D, Yang F, Yuan R, Xiang Y. Lighting-up RNA aptamer transcription synchronization amplification for ultrasensitive and label-free imaging of microRNA in single cells. Anal Chim Acta 2019; 1102:84-90. [PMID: 32043999 DOI: 10.1016/j.aca.2019.12.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/29/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022]
Abstract
Sensitive imaging of intracellular microRNAs (miRNAs) in cells is of great significance in clinical diagnoses and disease treatments, and it remains a major challenge to achieve this goal. Herein, we report a new in situ rolling circle transcription synchronization machinery (RCTsm) of lighting-up RNA aptamer strategy for highly sensitive imaging and selective differentiation of miRNA expression levels in cells. Such a RCTsm approach utilizes a DNA promoter to recycle the target miRNAs to trigger the initiation of multiple RCT process for the yield of many lighting-up RNA aptamers. The malachite green dye further binds these aptamers to show significantly enhanced fluorescence for completely label-free detection of the target miRNAs with a high sensitivity in vitro with a low femtomolar detection limit. More importantly, sensitive detection of under-expressed miRNAs in cells and distinct differentiation of the miRNA expression variations in different cells can also be realized with this RCTsm approach in a washing-free format, making it a versatile and useful tool for imaging trace miRNAs in single cells with the great potential for early cancer diagnosis as well as biomedical research.
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Affiliation(s)
- Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Fang Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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23
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Kim H, Lee YK, Han KH, Jeon H, Jeong IH, Kim SY, Lee JB, Lee PCW. BRC-mediated RNAi targeting of USE1 inhibits tumor growth in vitro and in vivo. Biomaterials 2019; 230:119630. [PMID: 31791842 DOI: 10.1016/j.biomaterials.2019.119630] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/12/2019] [Indexed: 01/18/2023]
Abstract
USE1 has been demonstrated to play crucial roles in the development and progression of human lung cancer. However, the antitumor efficacy of RNA interference (RNAi) targeting of USE1 has not yet been evaluated as a possible clinical application. We here synthesized USE1 targeting bubbled RNA-based cargo (BRC) composed of densely packed multimeric pre-siRNAs with specific Dicer cleavage sites to enable efficient siRNA release upon entry to target cells. The physical entanglement and continuous networking of RNAs via hybridization during enzymatic replication serve as a driving force for the self-assembly of BRCs. These molecules effectively suppressed the transcription of their target genes, leading to tumor growth suppression in vitro and in vivo. Moreover, their repeated intravenous administration efficiently inhibited the growth of A549 tumor xenografts. Based on these findings of a reduced cancer cell viability following a USE1 knockdown, we further explored cell cycle arrest and apoptosis pathways. The observed tumor cell growth suppression was found to be controlled by cell cycle arrest and apoptosis signals induced by the USE1 reduction. These results suggest that USE1 BRCs may have future clinical applications as an RNAi-based cancer therapy.
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Affiliation(s)
- Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - Yeon Kyung Lee
- Department of Biomedical Sciences University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Kyung Ho Han
- Department of Biomedical Sciences University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Hyunsu Jeon
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea
| | - In-Ho Jeong
- Department of Biomedical Sciences University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Sang-Yeob Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine, Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul, South Korea.
| | - Peter C W Lee
- Department of Biomedical Sciences University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
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24
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Wang T, Hong S, Luo Y, Lv H, Zhang Y, Pei R. Self-Assembled saRNA Delivery System Based on Rolling Circle Transcription for Aptamer-Targeting Cancer Therapy. ACS APPLIED BIO MATERIALS 2019; 2:4737-4746. [DOI: 10.1021/acsabm.9b00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tengfei Wang
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanni Hong
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yu Luo
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Haiyin Lv
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Ye Zhang
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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25
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Li J, Lin L, Yu J, Zhai S, Liu G, Tian L. Fabrication and Biomedical Applications of “Polymer-Like” Nucleic Acids Enzymatically Produced by Rolling Circle Amplification. ACS APPLIED BIO MATERIALS 2019; 2:4106-4120. [DOI: 10.1021/acsabm.9b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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26
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Li H, Wang S, Ji Z, Xu C, Shlyakhtenko LS, Guo P. Construction of RNA nanotubes. NANO RESEARCH 2019; 12:1952-1958. [PMID: 32153728 PMCID: PMC7062307 DOI: 10.1007/s12274-019-2463-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Nanotubes are miniature materials with significant potential applications in nanotechnological, medical, biological and material sciences. The quest for manufacturing methods of nano-mechanical modules is in progress. For example, the application of carbon nanotubes has been extensively investigated due to the precise width control, but the precise length control remains challenging. Here we report two approaches for the one-pot self-assembly of RNA nanotubes. For the first approach, six RNA strands were used to assemble the nanotube by forming a 11 nm long hollow channel with the inner diameter of 1.7 nm and the outside diameter of 6.3 nm. For the second approach, six RNA strands were designed to hybridize with their neighboring strands by complementary base pairing and formed a nanotube with a six-helix hollow channel similar to the nanotube assembled by the first approach. The fabricated RNA nanotubes were characterized by gel electrophoresis and atomic force microscopy (AFM), confirming the formation of nanotube-shaped RNA nanostructures. Cholesterol molecules were introduced into RNA nanotubes to facilitate their incorporation into lipid bilayer. Incubation of RNA nanotube complex with the free-standing lipid bilayer membrane under applied voltage led to discrete current signatures. Addition of peptides into the sensing chamber revealed discrete steps of current blockage. Polyarginine peptides with different lengths can be detected by current signatures, suggesting that the RNA-cholesterol complex holds the promise of achieving single molecule sensing of peptides.
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Affiliation(s)
- Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Shaoying Wang
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Lyudmila S Shlyakhtenko
- UNMC Nanoimaging Core Facility, Department of Pharmaceutical Sciences, College of Pharmacy University of Nebraska Medical Center, Omaha, NE, 68182, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Department of Physiology & Cell Biology, College of Medicine; Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
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27
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Wang Y, Kim E, Lin Y, Kim N, Kit-Anan W, Gopal S, Agarwal S, Howes PD, Stevens MM. Rolling Circle Transcription-Amplified Hierarchically Structured Organic-Inorganic Hybrid RNA Flowers for Enzyme Immobilization. ACS APPLIED MATERIALS & INTERFACES 2019; 11:22932-22940. [PMID: 31252470 PMCID: PMC6613047 DOI: 10.1021/acsami.9b04663] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/03/2019] [Indexed: 05/07/2023]
Abstract
Programmable nucleic acids have emerged as powerful building blocks for the bottom-up fabrication of two- or three-dimensional nano- and microsized constructs. Here we describe the construction of organic-inorganic hybrid RNA flowers (hRNFs) via rolling circle transcription (RCT), an enzyme-catalyzed nucleic acid amplification reaction. These hRNFs are highly adaptive structures with controlled sizes, specific nucleic acid sequences, and a highly porous nature. We demonstrated that hRNFs are applicable as potential biological platforms, where the hRNF scaffold can be engineered for versatile surface functionalization and the inorganic component (magnesium ions) can serve as an enzyme cofactor. For surface functionalization, we proposed robust and straightforward approaches including in situ synthesis of functional hRNFs and postfunctionalization of hRNFs that enable facile conjugation with various biomolecules and nanomaterials (i.e., proteins, enzymes, organic dyes, inorganic nanoparticles) using selective chemistries (i.e., avidin-biotin interaction, copper-free click reaction). In particular, we showed that hRNFs can serve as soft scaffolds for β-galactosidase immobilization and greatly enhance enzymatic activity and stability. Therefore, the proposed concepts and methodologies are not only fundamentally interesting when designing RNA scaffolds or RNA bionanomaterials assembled with enzymes but also have significant implications on their future utilization in biomedical applications ranging from enzyme cascades to biosensing and drug delivery.
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Affiliation(s)
| | | | - Yiyang Lin
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nayoung Kim
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Worrapong Kit-Anan
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Sahana Gopal
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Shweta Agarwal
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Molly M. Stevens
- Department of Materials, Department of Bioengineering,
and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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28
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Jasinski DL, Binzel DW, Guo P. One-Pot Production of RNA Nanoparticles via Automated Processing and Self-Assembly. ACS NANO 2019; 13:4603-4612. [PMID: 30888787 PMCID: PMC6542271 DOI: 10.1021/acsnano.9b00649] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
From the original sequencing of the human genome, it was found that about 98.5% of the genome did not code for proteins. Subsequent studies have now revealed that a much larger portion of the genome is related to short or long noncoding RNAs that regulate cellular activities. In addition to the milestones of chemical and protein drugs, it has been proposed that RNA drugs or drugs targeting RNA will become the third milestone in drug development ( Shu , Y. ; Adv. Drug Deliv. Rev. 2014 , 66 , 74 . ). Currently, the yield and cost for RNA nanoparticle or RNA drug production requires improvement in order to advance the RNA field in both research and clinical translation by reducing the multiple tedious manufacturing steps. For example, with 98.5% incorporation efficiency of chemical synthesis of a 100 nucleotide RNA strand, RNA oligos will result with 78% contamination of aborted byproducts. Thus, RNA nanotechnology is one of the remedies, because large RNA can be assembled from small RNA fragments via bottom-up self-assembly. Here we report the one-pot production of RNA nanoparticles via automated processing and self-assembly. The continuous production of RNA by rolling circle transcription (RCT) using a circular dsDNA template is coupled with self-cleaving ribozymes encoded in the concatemeric RNA transcripts. Production was monitored in real-time. Automatic production of RNA fragments enabled their assembly either in situ or via one-pot co-transcription to obtain RNA nanoparticles of desired motifs and functionalities from bottom-up assembly of multiple RNA fragments. In combination with the RNA nanoparticle construction process, a purification method using a large-scale electrophoresis column was also developed.
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Affiliation(s)
| | | | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Department of Physiology & Cell Biology; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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29
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Jorge AF, Eritja R. Overview of DNA Self-Assembling: Progresses in Biomedical Applications. Pharmaceutics 2018; 10:E268. [PMID: 30544945 PMCID: PMC6320858 DOI: 10.3390/pharmaceutics10040268] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature's assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.
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Affiliation(s)
- Andreia F Jorge
- Coimbra Chemistry Centre (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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30
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Guo Y, Shang X, Liu F, Hu Y, Li S, Liu J, Wu F. Novel Enhancer for Luminol-AuNP Electrochemiluminescence and Decoration on RNA Membranes for Effective Cytosensing. ACS APPLIED BIO MATERIALS 2018; 1:1647-1655. [DOI: 10.1021/acsabm.8b00478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yingshu Guo
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
- Shandong Provincial Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Xinxin Shang
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
- Shandong Provincial Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | - Fei Liu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, People’s Republic of China
| | - Yinhua Hu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
- Shandong Provincial Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | - Shuang Li
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
- Shandong Provincial Key Laboratory of Life-Organic Analysis, College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
| | - Jia Liu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People’s Republic of China
| | - Fei Wu
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, China
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31
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Kim KR, Röthlisberger P, Kang SJ, Nam K, Lee S, Hollenstein M, Ahn DR. Shaping Rolling Circle Amplification Products into DNA Nanoparticles by Incorporation of Modified Nucleotides and Their Application to In Vitro and In Vivo Delivery of a Photosensitizer. Molecules 2018; 23:molecules23071833. [PMID: 30041480 PMCID: PMC6099487 DOI: 10.3390/molecules23071833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 12/31/2022] Open
Abstract
Rolling circle amplification (RCA) is a robust way to generate DNA constructs, which are promising materials for biomedical applications including drug delivery because of their high biocompatibility. To be employed as a drug delivery platform, however, the DNA materials produced by RCA need to be shaped into nanoparticles that display both high cellular uptake efficiency and nuclease resistance. Here, we showed that the DNA nanoparticles (DNPs) can be prepared with RCA and modified nucleotides that have side-chains appended on the nucleobase are capable of interacting with the DNA strands of the resulting RCA products. The incorporation of the modified nucleotides improved cellular uptake efficiency and nuclease resistance of the DNPs. We also demonstrated that these DNPs could be employed as carriers for the delivery of a photosensitizer into cancer cells to achieve photodynamic therapy upon irradiation at both the in vitro and in vivo levels.
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Affiliation(s)
- Kyoung-Ran Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
| | - Pascal Röthlisberger
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris CEDEX 15, France.
| | - Seong Jae Kang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
| | - Kihwan Nam
- Center for Bionics, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
| | - Sangyoup Lee
- Center for Bionics, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris CEDEX 15, France.
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
- Division of Biomedical Science and Technology, KIST School, Korea University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea.
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32
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Kim H, Kim D, Jeong J, Jeon H, Lee JB. Size-Controllable Enzymatic Synthesis of Short Hairpin RNA Nanoparticles by Controlling the Rate of RNA Polymerization. Polymers (Basel) 2018; 10:polym10060589. [PMID: 30966623 PMCID: PMC6403749 DOI: 10.3390/polym10060589] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022] Open
Abstract
Thanks to a wide range of biological functions of RNA, and advancements in nanotechnology, RNA nanotechnology has developed in multiple ways for RNA-based therapeutics. In particular, among RNA engineering techniques, enzymatic self-assembly of RNA structures has gained great attention for its high packing density of RNA, with a low cost and one-pot synthetic process. However, manipulation of the overall size of particles, especially a reduction in size, has not been studied in depth. Here, we reported the enzymatic self-assembly of short hairpin RNA particles for the downregulation of target genes, and a rational approach to the manipulation of the resultant particle size. This is the first report of the size-controllable enzymatic self-assembly of short hairpin RNA nanoparticles. While keeping all the benefits of an enzymatic approach, the overall size of the RNA particles was controlled on a scale of 2 μm to 100 nm, falling within the therapeutically applicable size range.
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Affiliation(s)
- Hyejin Kim
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Korea.
| | - Dajeong Kim
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Korea.
| | - Jaepil Jeong
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Korea.
| | - Hyunsu Jeon
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Korea.
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Korea.
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33
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Kageyama R, Kawamata I, Tanabe K, Suzuki Y, Nomura SIM, Murata S. Construction of T-Motif-Based DNA Nanostructures through Enzymatic Reactions. Chembiochem 2018; 19:873-876. [PMID: 29399977 DOI: 10.1002/cbic.201700682] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 11/06/2022]
Abstract
The most common way to fabricate DNA nanostructures is to mix individually synthesized DNA oligomers in one pot. However, if DNA nanostructures could be produced through enzymatic reactions, they could be applied in various environments, including in vivo. Herein, an enzymatic method developed to construct a DNA nanostructure from a simple motif called a T-motif is reported. A long, repeated structure was replicated from a circular template by rolling circle amplification and then cleaved into T-motif segments by restriction enzymes. These motifs have been successfully assembled into a ladder-like nanostructure without purification or controlled annealing. This approach is widely applicable to constructing a variety of DNA nanostructures through enzymatic reactions.
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Affiliation(s)
- Ryo Kageyama
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Ibuki Kawamata
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Kaori Tanabe
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Yuki Suzuki
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.,Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Shin-Ichiro M Nomura
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Murata
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
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34
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Kim H, Lee E, Kang YY, Song J, Mok H, Lee JB. Enzymatically Produced miR34a Nanoparticles for Enhanced Antiproliferation Activity. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hyejin Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Eunju Lee
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Yoon Young Kang
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Jihyun Song
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Hyejung Mok
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
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35
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Xu C, Haque F, Jasinski DL, Binzel DW, Shu D, Guo P. Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy. Cancer Lett 2017; 414:57-70. [PMID: 28987384 DOI: 10.1016/j.canlet.2017.09.043] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 01/22/2023]
Abstract
The past decades have witnessed the successful transition of several nanotechnology platforms into the clinical trials. However, specific delivery of therapeutics to tumors is hindered by several barriers including cancer recognition and tissue penetration, particle heterogeneity and aggregation, and unfavorable pharmacokinetic profiles such as fast clearance and organ accumulation. With the advent of RNA nanotechnology, a series of RNA nanoparticles have been successfully constructed to overcome many of the aforementioned challenges for in vivo cancer targeting with favorable biodistribution profiles. Compared to other nanodelivery platforms, the physiochemical properties of RNA nanoparticles can be tuned with relative ease for investigating the in vivo behavior of nanoparticles upon systemic injection. The size, shape, and surface chemistry, especially hydrophobic modifications, exert significant impacts on the in vivo fate of RNA nanoparticles. Rationally designed RNA nanoparticles with defined stoichiometry and high homogeneity have been demonstrated to specifically target tumor cells while avoiding accumulation in healthy vital organs after systemic injection. RNA nanoparticles were proven to deliver therapeutics such as siRNA and anti-miRNA to block tumor growth in several animal models. Although the release of anti-miRNA from the RNA nanoparticles has achieved high efficiency of tumor regression in multiple animal models, the efficiency of endosomal escape for siRNA delivery needs further improvement. This review focuses on the advances and perspectives of this promising RNA nanotechnology platform for cancer targeting and therapy.
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Affiliation(s)
- Congcong Xu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Farzin Haque
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, OH, USA
| | - Daniel L Jasinski
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Daniel W Binzel
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Dan Shu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
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36
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Kim H, Jeong J, Kim D, Kwak G, Kim SH, Lee JB. Bubbled RNA-Based Cargo for Boosting RNA Interference. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1600523. [PMID: 28852615 PMCID: PMC5566230 DOI: 10.1002/advs.201600523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Indexed: 05/23/2023]
Abstract
As ribonucleic acid (RNA) nanotechnology has advanced, it has been applied widely in RNA-based therapeutics. Among the range of approaches, enzymatically synthesized RNA structures for inducing RNA interference in cancer cells have potential for silencing genes in a target-specific manner. On the other hand, the efficiency of gene silencing needs to be improved to utilize the RNA-based system for RNAi therapeutics. This paper introduces a new approach for efficient generation of siRNA from bubbled RNA-based cargo (BRC). The presence of bubbles in between to avoid nonfunctional short dsRNAs allows the RNA-based cargoes to contain multiple Dicer-cleavage sites to release the functional siRNAs when introduced to cells. BRCs can be synthesized easily in a one-pot process and be purified by simple centrifugation. Furthermore, efficient target gene silencing by the bubbled structure is confirmed both in vitro and in vivo. Therefore, this bubbled RNA cargo system can be utilized for target-specific RNAi therapeutics with high efficiency in the generation of functional siRNAs in the target cells.
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Affiliation(s)
- Hyejin Kim
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
| | - Jaepil Jeong
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
| | - Dajeong Kim
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
| | - Gijung Kwak
- KU‐KIST Graduate School of Converging Science and TechnologyKorea University145 Anam‐roSeongbuk‐gu, Seoul02841Republic of Korea
- Center for TheragnosisBiomedical Research InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
| | - Sun Hwa Kim
- Center for TheragnosisBiomedical Research InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
| | - Jong Bum Lee
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
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37
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Nuthanakanti A, Srivatsan SG. Surface-Tuned and Metal-Ion-Responsive Supramolecular Gels Based on Nucleolipids. ACS APPLIED MATERIALS & INTERFACES 2017; 9:22864-22874. [PMID: 28614659 DOI: 10.1021/acsami.7b06037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Supramolecular synthons based on nucleic acid components, nucleobases and nucleosides, and their derivatives have been highly useful in constructing wide varieties of nanoarchitectures. While most of the design strategies have focused on developing biocompatible delivery vehicles, the potential of nucleoside hybrids in assembling smart materials with tunable and sensing properties, though challenging, is gaining significant attention. Here, we describe the development of novel functional materials with surface tunability and metal-ion responsiveness by using simple nucleolipid supramolecular synthons derived by attaching various fatty acids to the 3'-O or 3',5'-O positions of the sugar residue of thymidine nucleoside. 3',5'-O-Difatty acid-substituted thymidines formed typical organogels in pure organic solvents, whereas, 3'-O-monofatty acid-substituted thymidine nucleolipids formed water-induced gels. A detailed morphological and structural analysis using microscopy, single-crystal and powder X-ray diffraction, and NMR techniques clearly revealed the molecular interactions invoked by nucleobase, sugar, fatty acid chain, and water in setting up the path for hierarchical self-assembly and gelation of thymidine nucleolipids. Interestingly, the surface property of the xerogel film fabricated using 3'-O-monosubstituted nucleolipid gels could be switched from highly hydrophobic to hydrophilic and vice versa depending on the nature of the organic solvent-water mixture used in the gelation process. On the contrary, the gelation process of disubstituted thymidine nucleolipids was highly sensitive to the presence of Hg2+ ions as the metal ion formed a T-Hg-T base pair, thereby disrupting the H-bonding interactions that favored the gelation. Taken together, straightforward synthesis and modification-dependent gelation behavior, surface tunability, and metal-ion responsiveness underscore the potential of these supramolecular nucleolipid synthons in constructing novel functional materials.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) , Pune Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) , Pune Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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38
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Pi F, Zhang H, Li H, Thiviyanathan V, Gorenstein DG, Sood AK, Guo P. RNA nanoparticles harboring annexin A2 aptamer can target ovarian cancer for tumor-specific doxorubicin delivery. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2017; 13:1183-1193. [PMID: 27890659 PMCID: PMC5426907 DOI: 10.1016/j.nano.2016.11.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022]
Abstract
A novel modified nucleic acid nanoparticle harboring an annexin A2 aptamer for ovarian cancer cell targeting and a GC rich sequence for doxorubicin loading is designed and constructed. The system utilizes a highly stable three-way junction (3WJ) motif from phi29 packaging RNA as a core structure. A phosphorothioate-modified DNA aptamer targeting annexin A2, Endo28, was conjugated to one arm of the 3WJ. The pRNA-3WJ motif retains correct folding of attached aptamer, keeping its functions intact. It is of significant utility for aptamer-mediated targeted delivery. The DNA/RNA hybrid nanoparticles remained intact after systemic injection in mice and strongly bound to tumors with little accumulation in healthy organs 6 h post-injection. The Endo28-3WJ-Sph1/Dox intercalates selectively enhanced toxicity to annexin A2 positive ovarian cancer cells in vitro. The constructed RNA/DNA hybrid nanoparticles can potentially enhance the therapeutic efficiency of doxorubicin at low doses for ovarian cancer treatment through annexin A2 targeted drug delivery.
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Affiliation(s)
- Fengmei Pi
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Hui Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Varatharasa Thiviyanathan
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center, Houston, TX, USA; AM Biotechnologies, Houston, TX, USA
| | - David G Gorenstein
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center, Houston, TX, USA; AM Biotechnologies, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Center for RNA Interference and Non-Coding RNA, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; Department of Physiology & Cell Biology, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
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Lee JH, Ku SH, Kim MJ, Lee SJ, Kim HC, Kim K, Kim SH, Kwon IC. Rolling circle transcription-based polymeric siRNA nanoparticles for tumor-targeted delivery. J Control Release 2017; 263:29-38. [PMID: 28373128 DOI: 10.1016/j.jconrel.2017.03.390] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/09/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023]
Abstract
RNA, one of the major biological macromolecules, has been considered as an attractive building material for bottom-up fabrication of nanostructures in the past few decades due to advancements in RNA biology, RNA chemistry and RNA nanotechnology. Most recently, an isothermal enzymatic nucleic acid amplification method termed rolling circle transcription (RCT), which achieves a large-scale synthesis of RNA nanostructures, has emerged as one of fascinating techniques for RNAi-based therapies. Herein, we proposed a newly designed RCT method for synthesis of polymeric siRNA nanoflower, referred to 'RCT and annealing-generated polymeric siRNA (RAPSI)': (1) Amplification of the antisense strand of siRNA via RCT process and (2) annealing of chimeric sense strand containing 3'-terminal DNA nucleotides that provide enzyme cleavage sites. To verify its potentials in RNAi-based cancer therapy, the newly designed RAPSI nanoflower was further complexed with glycol chitosan (GC) derivatives, and systemically delivered to PC-3 xenograft tumors. The resultant RAPSI nanoparticles exhibited the improved particle stability against polyanion competition or nuclease attack. When the RAPSI nanoparticles reached to the cytoplasmic region, active mono siRNA was liberated and significantly down-regulated the expression of target VEGF gene in PC-3 cells. Excellent tumor-homing efficacy and anti-tumor effects of the RAPSI nanoparticles were further demonstrated. Overall, the proposed RCT-based polymeric siRNA nanoflower formulation can provide a new platform technology that allows further functional modifications via an advanced annealing method for systemic cancer RNAi therapy.
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Affiliation(s)
- Jae Hyeop Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Sook Hee Ku
- Technology Convergence R&D Group, Korea Institute of Industrial Technology, Daegu, Republic of Korea
| | - Min Ju Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
| | - So Jin Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Hyun Cheol Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Kwangmeyung Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Sun Hwa Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.
| | - Ick Chan Kwon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea.
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40
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Jasinski D, Haque F, Binzel DW, Guo P. Advancement of the Emerging Field of RNA Nanotechnology. ACS NANO 2017; 11:1142-1164. [PMID: 28045501 PMCID: PMC5333189 DOI: 10.1021/acsnano.6b05737] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/03/2017] [Indexed: 05/14/2023]
Abstract
The field of RNA nanotechnology has advanced rapidly during the past decade. A variety of programmable RNA nanoparticles with defined shape, size, and stoichiometry have been developed for diverse applications in nanobiotechnology. The rising popularity of RNA nanoparticles is due to a number of factors: (1) removing the concern of RNA degradation in vitro and in vivo by introducing chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; (2) confirming the concept that RNA displays very high thermodynamic stability and is suitable for in vivo trafficking and other applications; (3) obtaining the knowledge to tune the immunogenic properties of synthetic RNA constructs for in vivo applications; (4) increased understanding of the 4D structure and intermolecular interaction of RNA molecules; (5) developing methods to control shape, size, and stoichiometry of RNA nanoparticles; (6) increasing knowledge of regulation and processing functions of RNA in cells; (7) decreasing cost of RNA production by biological and chemical synthesis; and (8) proving the concept that RNA is a safe and specific therapeutic modality for cancer and other diseases with little or no accumulation in vital organs. Other applications of RNA nanotechnology, such as adapting them to construct 2D, 3D, and 4D structures for use in tissue engineering, biosensing, resistive biomemory, and potential computer logic gate modules, have stimulated the interest of the scientific community. This review aims to outline the current state of the art of RNA nanoparticles as programmable smart complexes and offers perspectives on the promising avenues of research in this fast-growing field.
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Affiliation(s)
| | | | - Daniel W Binzel
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Peixuan Guo
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
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41
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Jeong EH, Kim H, Jang B, Cho H, Ryu J, Kim B, Park Y, Kim J, Lee JB, Lee H. Technological development of structural DNA/RNA-based RNAi systems and their applications. Adv Drug Deliv Rev 2016; 104:29-43. [PMID: 26494399 DOI: 10.1016/j.addr.2015.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 01/04/2023]
Abstract
RNA interference (RNAi)-based gene therapy has drawn tremendous attention due to its highly specific gene regulation by selective degradation of any target mRNA. There have been multiple reports regarding the development of various cationic materials for efficient siRNA delivery, however, many studies still suffer from the conventional delivery problems such as suboptimal transfection performance, a lack of tissue specificity, and potential cytotoxicity. Despite the huge therapeutic potential of siRNAs, conventional gene carriers have failed to guarantee successful gene silencing in vivo, thus not warranting clinical trials. The relatively short double-stranded structure of siRNAs has resulted in uncompromising delivery formulations, as well as low transfection efficiency, compared with the conventional nucleic acid drugs such as plasmid DNAs. Recent developments in structural siRNA and RNAi nanotechnology have enabled more refined and reliable in vivo gene silencing with multiple advantages over naked siRNAs. This review focuses on recent progress in the development of structural DNA/RNA-based RNAi systems and their potential therapeutic applications. In addition, an extensive list of prior reports on various RNAi systems is provided and categorized by their distinctive molecular characters.
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42
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Generation of siRNA Nanosheets for Efficient RNA Interference. Sci Rep 2016; 6:25146. [PMID: 27120975 PMCID: PMC4848498 DOI: 10.1038/srep25146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/11/2016] [Indexed: 02/05/2023] Open
Abstract
After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.
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Li X, Zheng F, Ren R. Detecting miRNA by producing RNA: a sensitive assay that combines rolling-circle DNA polymerization and rolling circle transcription. Chem Commun (Camb) 2016; 51:11976-9. [PMID: 26120604 DOI: 10.1039/c5cc01748c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Target miRNA was detected by producing RNA: rolling circle polymerization (RCP) and rolling circle transcription (RCT) were interlinked to provide dual amplification, producing multiplied malachite green (MG) aptamers, and a signal was generated by the SERS (surface-enhanced Raman scattering) quantification of the MG molecules that were bound to the transcripts.
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Affiliation(s)
- Xuemei Li
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China.
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Park Y, Kim H, Lee JB. Self-assembled DNA-Guided RNA Nanovector via Step-wise Dual Enzyme Polymerization (SDEP) for Carrier-free siRNA Delivery. ACS Biomater Sci Eng 2016; 2:616-624. [DOI: 10.1021/acsbiomaterials.5b00554] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yongkuk Park
- Department
of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Hyejin Kim
- Department
of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Jong Bum Lee
- Department
of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
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Nuthanakanti A, Srivatsan SG. Hierarchical self-assembly of switchable nucleolipid supramolecular gels based on environmentally-sensitive fluorescent nucleoside analogs. NANOSCALE 2016; 8:3607-3619. [PMID: 26804191 DOI: 10.1039/c5nr07490h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Exquisite recognition and folding properties have rendered nucleic acids as useful supramolecular synthons for the construction of programmable architectures. Despite their proven applications in nanotechnology, scalability and fabrication of nucleic acid nanostructures still remain a challenge. Here, we describe a novel design strategy to construct new supramolecular nucleolipid synthons by using environmentally-sensitive fluorescent nucleoside analogs, based on 5-(benzofuran-2-yl)uracil and 5-(benzo[b]thiophen-2-yl)uracil cores, as the head group and fatty acids, attached to the ribose sugar, as the lipophilic group. These modified nucleoside-lipid hybrids formed organogels driven by hierarchical structures such as fibers, twisted ribbons, helical ribbons and nanotubes, which depended on the nature of fatty acid chain and nucleobase modification. NMR, single crystal X-ray and powder X-ray diffraction studies revealed the coordinated interplay of various non-covalent interactions invoked by modified nucleobase, sugar and fatty acid chains in setting up the pathway for the gelation process. Importantly, these nucleolipid gels retained or displayed aggregation-induced enhanced emission and their gelation behavior and photophysical properties could be reversibly switched by external stimuli such as temperature, ultrasound and chemicals. Furthermore, the switchable nature of nucleolipid gels to chemical stimuli enabled the selective two channel recognition of fluoride and Hg(2+) ions through visual phase transition and fluorescence change. Fluorescent organogels exhibiting such a combination of useful features is rare, and hence, we expect that this innovative design of fluorescent nucleolipid supramolecular synthons could lead to the emergence of a new family of smart optical materials and probes.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
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Kim H, Park Y, Kim J, Jeong J, Han S, Lee JS, Lee JB. Nucleic Acid Engineering: RNA Following the Trail of DNA. ACS COMBINATORIAL SCIENCE 2016; 18:87-99. [PMID: 26735596 DOI: 10.1021/acscombsci.5b00108] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The self-assembly feature of the naturally occurring biopolymer, DNA, has fascinated researchers in the fields of materials science and bioengineering. With the improved understanding of the chemical and structural nature of DNA, DNA-based constructs have been designed and fabricated from two-dimensional arbitrary shapes to reconfigurable three-dimensional nanodevices. Although DNA has been used successfully as a building block in a finely organized and controlled manner, its applications need to be explored. Hence, with the myriad of biological functions, RNA has recently attracted considerable attention to further the application of nucleic acid-based structures. This Review categorizes different approaches of engineering nucleic acid-based structures and introduces the concepts, principles, and applications of each technique, focusing on how DNA engineering is applied as a guide to RNA engineering.
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Affiliation(s)
- Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Yongkuk Park
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Jieun Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Jaepil Jeong
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Jae Sung Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 130-743, Korea
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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48
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Shu D, Li H, Shu Y, Xiong G, Carson WE, Haque F, Xu R, Guo P. Systemic Delivery of Anti-miRNA for Suppression of Triple Negative Breast Cancer Utilizing RNA Nanotechnology. ACS NANO 2015; 9:9731-40. [PMID: 26387848 PMCID: PMC4723066 DOI: 10.1021/acsnano.5b02471] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/05/2015] [Indexed: 05/20/2023]
Abstract
MicroRNAs play important roles in regulating the gene expression and life cycle of cancer cells. In particular, miR-21, an oncogenic miRNA is a major player involved in tumor initiation, progression, invasion and metastasis in several cancers, including triple negative breast cancer (TNBC). However, delivery of therapeutic miRNA or anti-miRNA specifically into cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miR-21 to block the growth of TNBC in orthotopic mouse models. The 15 nm therapeutic RNA nanoparticles contains the 58-nucleotide (nt) phi29 pRNA-3WJ as a core, a 8-nt sequence complementary to the seed region of miR-21, and a 39-nt epidermal growth factor receptor (EGFR) targeting aptamer for internalizing RNA nanoparticles into cancer cells via receptor mediated endocytosis. The RNase resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection into mice and strongly bound to tumors with little or no accumulation in healthy organs 8 h postinjection, and subsequently repressed tumor growth at low doses. The observed specific cancer targeting and tumor regression is a result of several key attributes of RNA nanoparticles: anionic charge which disallows nonspecific passage across negatively charged cell membrane; "active" targeting using RNA aptamers which increases the homing of RNA nanoparticles to cancer cells; nanoscale size and shape which avoids rapid renal clearance and engulfment by lung macrophages and liver Kupffer cells; favorable biodistribution profiles with little accumulation in healthy organs, which minimizes nonspecific side effects; and favorable pharmacokinetic profiles with extended in vivo half-life. The results demonstrate the clinical potentials of RNA nanotechnology based platform to deliver miRNA based therapeutics for cancer treatment.
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Affiliation(s)
- Dan Shu
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
- Address correspondence to ,
| | - Hui Li
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yi Shu
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Gaofeng Xiong
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - William E. Carson
- OSU Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Ren Xu
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, Kentucky 40536, United States
- Address correspondence to ,
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Li H, Lee T, Dziubla T, Pi F, Guo S, Xu J, Li C, Haque F, Liang XJ, Guo P. RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications. NANO TODAY 2015; 10:631-655. [PMID: 26770259 PMCID: PMC4707685 DOI: 10.1016/j.nantod.2015.09.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The value of polymers is manifested in their vital use as building blocks in material and life sciences. Ribonucleic acid (RNA) is a polynucleic acid, but its polymeric nature in materials and technological applications is often overlooked due to an impression that RNA is seemingly unstable. Recent findings that certain modifications can make RNA resistant to RNase degradation while retaining its authentic folding property and biological function, and the discovery of ultra-thermostable RNA motifs have adequately addressed the concerns of RNA unstability. RNA can serve as a unique polymeric material to build varieties of nanostructures including nanoparticles, polygons, arrays, bundles, membrane, and microsponges that have potential applications in biomedical and material sciences. Since 2005, more than a thousand publications on RNA nanostructures have been published in diverse fields, indicating a remarkable increase of interest in the emerging field of RNA nanotechnology. In this review, we aim to: delineate the physical and chemical properties of polymers that can be applied to RNA; introduce the unique properties of RNA as a polymer; review the current methods for the construction of RNA nanostructures; describe its applications in material, biomedical and computer sciences; and, discuss the challenges and future prospects in this field.
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Affiliation(s)
- Hui Li
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Taek Lee
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Thomas Dziubla
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY 40506, USA
| | - Fengmei Pi
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Sijin Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
| | - Jing Xu
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Chan Li
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Xing-Jie Liang
- Laboratory of Nanomedicine and Nanosafety, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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50
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Self-assembled Messenger RNA Nanoparticles (mRNA-NPs) for Efficient Gene Expression. Sci Rep 2015; 5:12737. [PMID: 26235529 PMCID: PMC4522648 DOI: 10.1038/srep12737] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/12/2015] [Indexed: 01/24/2023] Open
Abstract
Although mRNA has several advantages over plasmid DNA when delivered into cells for gene expression, mRNA transfection is a very rare occurrence in gene delivery. This is mainly because of the labile nature of RNA, resulting in a low expression level of the desired protein. In this study, self-assembled mRNA nanoparticles (mRNA-NPs) packed with multiple repeats of mRNA were synthesized to achieve efficient gene expression. This approach required only a one-step process to synthesize particles with a minimal amount of plasmid DNA to produce the RNA transcripts via rolling circle transcription. Moreover, there are no concerns for cytotoxicity which can be caused by chemical condensates because mRNA-NPs are made entirely of mRNA. An examination of the cells transfected with the mRNA-NPs encoding the green fluorescence protein (GFP) confirmed that the mRNA-NPs can be used as a novel platform for effective gene delivery.
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