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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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2
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Pang HH, Huang CY, Chen PY, Li NS, Hsu YP, Wu JK, Fan HF, Wei KC, Yang HW. Bioengineered Bacteriophage-Like Nanoparticles as RNAi Therapeutics to Enhance Radiotherapy against Glioblastomas. ACS NANO 2023; 17:10407-10422. [PMID: 37120837 DOI: 10.1021/acsnano.3c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Since glioblastomas (GBMs) are radioresistant malignancies and most GBM recurrences occur in radiotherapy, increasing the effectiveness of radiotherapy by gene-silencing has recently attracted attention. However, the difficulty in precisely tuning the composition and RNA loading in nanoparticles leads to batch-to-batch variations of the RNA therapeutics, thus significantly restricting their clinical translation. Here, we bioengineer bacteriophage Qβ particles with a designed broccoli light-up three-way junction (b-3WJ) RNA scaffold (contains two siRNA/miRNA sequences and one light-up aptamer) packaging for the silencing of genes in radioresistant GBM cells. The in vitro results demonstrate that the cleavage of de novo designed b-3WJ RNA by Dicer enzyme can be easily monitored in real-time using fluorescence microscopy, and the TrQβ@b-3WJLet-7gsiEGFR successfully knocks down EGFR and IKKα simultaneously and thereby inactivates NF-κB signaling to inhibit DNA repair. Delivery of TrQβ@b-3WJLet-7gsiEGFR through convection-enhanced delivery (CED) infusion followed by 2Gy X-ray irradiation demonstrated that the median survival was prolonged to over 60 days compared with the 2Gy X-ray irradiated group (median survival: 31 days). Altogether, the results of this study could be critical for the design of RNAi-based genetic therapeutics, and CED infusion serves as a powerful delivery system for promoting radiotherapy against GBMs without evidence of systemic toxicity.
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Affiliation(s)
- Hao-Han Pang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
| | - Chiung-Yin Huang
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
| | - Pin-Yuan Chen
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
- School of Medicine, Chang Gung University, 259 Wenhua 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, 222 Maijin Rd., Keelung 20401, Taiwan
| | - Nan-Si Li
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
| | - Ying-Pei Hsu
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
- Department of Materials and Optoelectronic Science, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Jan-Kai Wu
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Hsiu-Fang Fan
- Department of Chemistry, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Kuo-Chen Wei
- Department of Neurosurgery, Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou, 5 Fuxing St., Guishan Dist., Taoyuan 33305, Taiwan
- School of Medicine, Chang Gung University, 259 Wenhua 1st Rd., Guishan Dist., Taoyuan 33302, Taiwan
- Department of Neurosurgery, New Taipei Municipal TuCheng Hospital, 6, Sec 2, JunCheng Rd., New Taipei City 23652, Taiwan
| | - Hung-Wei Yang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, No. 1, University Rd., Tainan 70101, Taiwan
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3
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022; 20:6120-6137. [PMID: 36420155 PMCID: PMC9672130 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
The International Society of RNA Nanotechnology and Nanomedicine (ISRNN) serves to further the development of a wide variety of functional nucleic acids and other related nanotechnology platforms. To aid in the dissemination of the most recent advancements, a biennial discussion focused on biomotors, viral assembly, and RNA nanobiotechnology has been established where international experts in interdisciplinary fields such as structural biology, biophysical chemistry, nanotechnology, cell and cancer biology, and pharmacology share their latest accomplishments and future perspectives. The results summarized here highlight advancements in our understanding of viral biology and the structure-function relationship of frame-shifting elements in genomic viral RNA, improvements in the predictions of SHAPE analysis of 3D RNA structures, and the understanding of dynamic RNA structures through a variety of experimental and computational means. Additionally, recent advances in the drug delivery, vaccine design, nanopore technologies, biomotor and biomachine development, DNA packaging, RNA nanotechnology, and drug delivery are included in this critical review. We emphasize some of the novel accomplishments, major discussion topics, and present current challenges and perspectives of these emerging fields.
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Mg2+ Ions Regulating 3WJ-PRNA to Construct Controllable RNA Nanoparticle Drug Delivery Platforms. Pharmaceutics 2022; 14:pharmaceutics14071413. [PMID: 35890308 PMCID: PMC9320661 DOI: 10.3390/pharmaceutics14071413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/13/2022] [Accepted: 06/24/2022] [Indexed: 02/01/2023] Open
Abstract
RNA nanotechnology has shown great progress over the past decade. Diverse controllable and multifunctional RNA nanoparticles have been developed for various applications in many areas. For example, RNA nanoparticles can participate in the construction of drug delivery nanoplatforms. Recently, a three-way junction packaging RNA (3WJ-pRNA) has been exploited for its characteristics of self-assembly and ultrahigh stability in many aspects. 3WJ-pRNA is the 3WJ part of bacteriophage φ29 pRNA and joins different components of φ29 as a linker element. In this work, we used all-atom MD simulation to study the thermal stability of 3WJ-pRNA and the underlying mechanisms. While 3WJ-pRNA can remain in its original structure without Mg2+ ions at room temperature, only Mg-bound 3WJ-pRNA still maintains its initial three-way junction structure at a higher temperature (T = 400 K). The Mg-free 3WJ-pRNA undergoes dramatic deformation under high temperature condition. The contribution of Mg ions can be largely attributed to the protective effect of two Mg clamps on the hydrogen bond and base stacking interactions in helices. Taken together, our results reveal the extraordinary thermal stability of 3WJ-pRNA, which can be regulated by Mg2+ ions. Comprehensive depictions of thermal stability of pRNA and the regulation mechanism are helpful for the further development of controllable RNA nanoparticle drug delivery platforms.
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6
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Hill A, van Leeuwen D, Schlösser V, Behera A, Mateescu B, Hall J. Chemically synthesized, self-assembling small interfering RNA-prohead RNA molecules trigger Dicer-independent gene silencing. Chemistry 2021; 28:e202103995. [PMID: 34879171 PMCID: PMC9305526 DOI: 10.1002/chem.202103995] [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: 11/05/2021] [Indexed: 11/07/2022]
Abstract
RNA interference (RNAi) mediated by small interfering RNA (siRNA) duplexes is a powerful therapeutic modality, but the translation of siRNAs from the bench into clinical application has been hampered by inefficient delivery in vivo. An innovative delivery strategy involves fusing siRNAs to a three‐way junction (3WJ) motif derived from the phi29 bacteriophage prohead RNA (pRNA). Chimeric siRNA‐3WJ molecules are presumed to enter the RNAi pathway through Dicer cleavage. Here, we fused siRNAs to the phi29 3WJ and two phylogenetically related 3WJs. We confirmed that the siRNA‐3WJs are substrates for Dicer in vitro. However, our results reveal that siRNA‐3WJs transfected into Dicer‐deficient cell lines trigger potent gene silencing. Interestingly, siRNA‐3WJs transfected into an Argonaute 2‐deficient cell line also retain some gene silencing activity. siRNA‐3WJs are most efficient when the antisense strand of the siRNA duplex is positioned 5′ of the 3WJ (5′‐siRNA‐3WJ) relative to 3′ of the 3WJ (3′‐siRNA‐3WJ). This work sheds light on the functional properties of siRNA‐3WJs and offers a design rule for maximizing their potency in the human RNAi pathway.
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Affiliation(s)
- Alyssa Hill
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, SWITZERLAND
| | - Daniël van Leeuwen
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Verena Schlösser
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Alok Behera
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
| | - Bogdan Mateescu
- ETH Zürich D-BIOL: Eidgenossische Technische Hochschule Zurich Departement Biologie, Department of Biology, SWITZERLAND
| | - Jonathan Hall
- ETH Zurich D-CHAB: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Department of Chemistry and Applied Biosciences, SWITZERLAND
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7
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Rational design for controlled release of Dicer-substrate siRNA harbored in phi29 pRNA-based nanoparticles. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 25:524-535. [PMID: 34589275 PMCID: PMC8463318 DOI: 10.1016/j.omtn.2021.07.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Small interfering RNA (siRNA) for silencing genes and treating disease has been a dream since ranking as a top Breakthrough of the Year in 2002 by Science. With the recent FDA approval of four siRNA-based drugs, the potential of RNA therapeutics to become the third milestone in pharmaceutical drug development has become a reality. However, the field of RNA interference (RNAi) therapeutics still faces challenges such as specificity in targeting, intracellular processing, and endosome trapping after targeted delivery. Dicer-substrate siRNAs included onto RNA nanoparticles may be able to overcome these challenges. Here, we show that pRNA-based nanoparticles can be designed to efficiently harbor the Dicer-substrate siRNAs in vitro and in vivo to the cytosol of tumor cells and release the siRNA. The structure optimization and chemical modification for controlled release of Dicer-substrate siRNAs in tumor cells were also evaluated through molecular beacon analysis. Studies on the length requirement of the overhanging siRNA revealed that at least 23 nucleotides at the dweller's arm were needed for dicer processing. The above sequence parameters and structure optimization were confirmed in recent studies demonstrating the release of functional Survivin siRNA from the pRNA-based nanoparticles for cancer inhibition in non-small-cell lung, breast, and prostate cancer animal models.
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Blanco Carcache PJ, Guo S, Li H, Zhang K, Xu C, Chiu W, Guo P. Regulation of reversible conformational change, size switching, and immunomodulation of RNA nanocubes. RNA (NEW YORK, N.Y.) 2021; 27:971-980. [PMID: 34193550 PMCID: PMC8370748 DOI: 10.1261/rna.078718.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 05/20/2023]
Abstract
In biological systems, conformational changes and allosteric modulation play pivotal roles in regulating biological functions, such as the dynamic change of protein molecules, in response to binding or interacting with other factors such as pH, voltage, salt, light, or ligand. RNA can be manipulated and tuned with a level of simplicity that is characteristic of DNA or polymers, while displaying versatility in structure, diversity in function, and adaptability in a configuration similar to proteins. In the past, the work on the investigation of conformational change mainly focused on protein. The induced-fit and conformational capture in RNA have also been explored, such as in the study of riboswitches. Herein, we report the engineering of three-dimensional RNA nanocubes and demonstrated the operation and regulation for its configuration. We demonstrate the operation of reconfigurable RNA nanocubes whose shapes change precisely and reversibly in response to a specific trigger strand. The shape, size, and conformation can be regulated precisely and reversibly in response to the specific triggering signals. The shape and conformational conversion were observed by cryo-EM and gel electrophoresis, respectively. Harnessing the size, shape, conformation, and self-assembly capabilities of the RNA nanocube can provide a new potential use of this technology as nanocarriers for the treatment of various diseases.
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Affiliation(s)
- Peter J Blanco Carcache
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kaiming Zhang
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, California 94305, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
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Binzel DW, Li X, Burns N, Khan E, Lee WJ, Chen LC, Ellipilli S, Miles W, Ho YS, Guo P. Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. Chem Rev 2021; 121:7398-7467. [PMID: 34038115 DOI: 10.1021/acs.chemrev.1c00009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA nanotechnology is the bottom-up self-assembly of nanometer-scale architectures, resembling LEGOs, composed mainly of RNA. The ideal building material should be (1) versatile and controllable in shape and stoichiometry, (2) spontaneously self-assemble, and (3) thermodynamically, chemically, and enzymatically stable with a long shelf life. RNA building blocks exhibit each of the above. RNA is a polynucleic acid, making it a polymer, and its negative-charge prevents nonspecific binding to negatively charged cell membranes. The thermostability makes it suitable for logic gates, resistive memory, sensor set-ups, and NEM devices. RNA can be designed and manipulated with a level of simplicity of DNA while displaying versatile structure and enzyme activity of proteins. RNA can fold into single-stranded loops or bulges to serve as mounting dovetails for intermolecular or domain interactions without external linking dowels. RNA nanoparticles display rubber- and amoeba-like properties and are stretchable and shrinkable through multiple repeats, leading to enhanced tumor targeting and fast renal excretion to reduce toxicities. It was predicted in 2014 that RNA would be the third milestone in pharmaceutical drug development. The recent approval of several RNA drugs and COVID-19 mRNA vaccines by FDA suggests that this milestone is being realized. Here, we review the unique properties of RNA nanotechnology, summarize its recent advancements, describe its distinct attributes inside or outside the body and discuss potential applications in nanotechnology, medicine, and material science.
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Affiliation(s)
- Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nicolas Burns
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wen-Jui Lee
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Li-Ching Chen
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Satheesh Ellipilli
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Wayne Miles
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, College of Medicine, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuan Soon Ho
- TMU Research Center of Cancer Translational Medicine, School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Dorothy M. Davis Heart and Lung Research Institute, James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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Yoo JY, Yeh M, Kaur B, Lee TJ. Targeted delivery of small noncoding RNA for glioblastoma. Cancer Lett 2020; 500:274-280. [PMID: 33176185 DOI: 10.1016/j.canlet.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/16/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Aberrant expression of certain genes and microRNAs (miRNAs) has been shown to drive cancer development and progression, thus the modification of aberrant gene and miRNA expression presents an opportunity for therapeutic targeting. Ectopic modulation of a single dysregulated miRNA has the potential to revert therapeutically unfavorable gene expression in cancer cells by targeting multiple genes simultaneously. Although the use of noncoding RNA-based cancer therapy is a promising approach, the lack of a feasible delivery platform for small noncoding RNAs has hindered the development of this therapeutic modality. Recently, however, there has been an evolution in RNA nanotechnology, in which small noncoding RNA is loaded onto nanoparticles derived from the pRNA-3WJ viral RNA motif of the bacteriophage phi29. Preclinical studies have shown the capacity of this technology to specifically target tumor cells by conjugating these nanoparticles with ligands specific for cancer cells and resulting in the endocytic delivery of siRNA and miRNA inhibitors directly into the cell. Here we provide a systematic review of the various strategies, which have been utilized for miRNA delivery with a specific focus on the preclinical evaluation of promising RNA nanoparticles for glioblastoma (GBM) targeted therapy.
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Affiliation(s)
- Ji Young Yoo
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Margaret Yeh
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Balveen Kaur
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Tae Jin Lee
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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Li X, Vieweger M, Guo P. Self-assembly of four generations of RNA dendrimers for drug shielding with controllable layer-by-layer release. NANOSCALE 2020; 12:16514-16525. [PMID: 32729600 PMCID: PMC7448292 DOI: 10.1039/d0nr02614j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chemical dendrimers have been shown to be a promising drug delivery platform due to their advantageous properties such as monodispersity, multivalency and branched structure. Taking advantage of self-assembly and its intrinsic negative charge, we used RNA as the building block for dendrimer construction to eliminate complex synthesis procedures and cationic charge-related toxicity. Oligo ribonucleotides produced by solid phase chemical synthesis allow the large-scale manufacture of homologous RNA dendrimers. Employing concepts from RNA nanotechnology enabled the controllable production of dendrimers with generations from G1, G2, G3, to G4 with layer-by-layer release capability. The conjugation of functional groups into individual RNA strands and the incorporation of functionalized RNA strands into the dendrimers at different sites have been reported. Anticancer drugs loaded into RNA dendrimers showed comparable cancer cell inhibition effect to free drugs. Encapsulation of cell binding ligands and hydrophobic drugs within the dendrimer significantly reduced the efficiency of cell binding and protein binding respectively, demonstrating the shielding effect of RNA dendrimers. The results imply a potential application of RNA dendrimer for delivery, shielding and controlled release of hydrophobic drugs in vivo.
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Affiliation(s)
- Xin Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA.
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12
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Ishiguro K, Yan IK, Lewis-Tuffin L, Patel T. Targeting Liver Cancer Stem Cells Using Engineered Biological Nanoparticles for the Treatment of Hepatocellular Cancer. Hepatol Commun 2020; 4:298-313. [PMID: 32025612 PMCID: PMC6996342 DOI: 10.1002/hep4.1462] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022] Open
Abstract
By exploiting their biological functions, the use of biological nanoparticles such as extracellular vesicles can provide an efficient and effective approach for hepatic delivery of RNA‐based therapeutics for the treatment of liver cancers such as hepatocellular cancer (HCC). Targeting liver cancer stem cells (LCSC) within HCC provide an untapped opportunity to improve outcomes by enhancing therapeutic responses. Cells with tumor‐initiating capabilities such as LCSC can be identified by expression of markers such as epithelial cell adhesion molecule (EpCAM) on their cell surface. EpCAM is a target of Wnt/β‐catenin signaling, a fundamental pathway in stem‐cell growth. Moreover, mutations in the β‐catenin gene are frequently observed in HCC and can be associated with constitutive activation of the Wnt/β‐catenin pathway. However, targeting these pathways for the treatment of HCC has been challenging. Using RNA nanotechnology, we developed engineered biological nanoparticles capable of specific and effective delivery of RNA therapeutics targeting β‐catenin to LCSC. Extracellular vesicles isolated from milk were loaded with small interfering RNA to β‐catenin and decorated with RNA scaffolds to incorporate RNA aptamers capable of binding to EpCAM. Cellular uptake of these EpCAM‐targeting therapeutic milk‐derived nanovesicles in vitro resulted in loss of β‐catenin expression and decreased proliferation. The uptake and therapeutic efficacy of these engineered biological nanotherapeutics was demonstrated in vivo using tumor xenograft mouse models. Conclusion: β‐catenin can be targeted directly to control the proliferation of hepatic cancer stem cells using small interfering RNA delivered using target‐specific biological nanoparticles. Application of this RNA nanotechnology–based approach to engineer biological nanotherapeutics provides a platform for developing cell‐surface molecule–directed targeted therapeutics.
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Affiliation(s)
- Kaori Ishiguro
- Department of Transplantation Mayo Clinic Jacksonville FL.,Department of Cancer Biology Mayo Clinic Jacksonville FL
| | - Irene K Yan
- Department of Transplantation Mayo Clinic Jacksonville FL.,Department of Cancer Biology Mayo Clinic Jacksonville FL
| | | | - Tushar Patel
- Department of Transplantation Mayo Clinic Jacksonville FL.,Department of Cancer Biology Mayo Clinic Jacksonville FL
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13
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Piao X, Yin H, Guo S, Wang H, Guo P. RNA Nanotechnology to Solubilize Hydrophobic Antitumor Drug for Targeted Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900951. [PMID: 31763137 PMCID: PMC6864502 DOI: 10.1002/advs.201900951] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/06/2019] [Indexed: 05/15/2023]
Abstract
Small-molecule drugs are used extensively in clinics for cancer treatment; however, many antitumor chemical drugs dissolve poorly in aqueous solution. Their poor solubility and nonselective delivery in vivo often cause severe side effects. Here, the application of RNA nanotechnology to enhance the solubility of hydrophobic drugs, using camptothecin (CPT) for proof-of-concept in targeted delivery for cancer treatment is reported. Multiple CPT prodrug molecules are conjugated to RNA oligos via a click reaction, and the resulting CPT-RNA conjugates efficiently self-assemble into thermodynamically stable RNA three-way junction (3WJ) nanoparticles. The RNA 3WJ is covalently linked with seven hydrophobic CPT prodrug molecules through cleavable ester bonds and a folic acid ligand for specific tumor targeting while remaining soluble in aqueous solutions without detectable aggregation at therapeutic dose. This CPT-RNA nanoparticle exhibits efficient and specific cell binding and internalization, leading to cell apoptosis. Tumor growth is effectively inhibited by CPT-RNA nanoparticles; the targeted delivery, strengthened by tumor ligand, further enhances tumor suppression. Compared with the traditional formulation, solubilization of CPT in aqueous buffer using RNA nanoparticles as a carrier is found to be safe and efficacious, demonstrating that RNA nanoparticles are a promising platform for the solubilization and the delivery of hydrophobic antitumor drugs.
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Affiliation(s)
- Xijun Piao
- Center for RNA Nanobiotechnology and NanomedicineThe Ohio State UniversityColumbusOH43210USA
- College of PharmacyDivision of Pharmaceutics and PharmacologyThe Ohio State UniversityColumbusOH43210USA
| | - Hongran Yin
- Center for RNA Nanobiotechnology and NanomedicineThe Ohio State UniversityColumbusOH43210USA
- College of PharmacyDivision of Pharmaceutics and PharmacologyThe Ohio State UniversityColumbusOH43210USA
| | - Sijin Guo
- Center for RNA Nanobiotechnology and NanomedicineThe Ohio State UniversityColumbusOH43210USA
- College of PharmacyDivision of Pharmaceutics and PharmacologyThe Ohio State UniversityColumbusOH43210USA
| | - Hongzhi Wang
- Center for RNA Nanobiotechnology and NanomedicineThe Ohio State UniversityColumbusOH43210USA
- College of PharmacyDivision of Pharmaceutics and PharmacologyThe Ohio State UniversityColumbusOH43210USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and NanomedicineThe Ohio State UniversityColumbusOH43210USA
- College of PharmacyDivision of Pharmaceutics and PharmacologyThe Ohio State UniversityColumbusOH43210USA
- College of MedicineDorothy M. Davis Heart and Lung Research InstituteThe Ohio State UniversityColumbusOH43210USA
- James Comprehensive Cancer CenterThe Ohio State UniversityColumbusOH43210USA
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14
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Valsangkar VA, Chandrasekaran AR, Zhuo L, Mao S, Lee GW, Kizer M, Wang X, Halvorsen K, Sheng J. Click and photo-release dual-functional nucleic acid nanostructures. Chem Commun (Camb) 2019; 55:9709-9712. [PMID: 31353371 PMCID: PMC6687541 DOI: 10.1039/c9cc03806j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We functionalize nucleic acid nanostructures with click chemistry (for attachment of cargos) and a photocleavable linker (for release). We demonstrate cargo attachment using a fluorescein dye and release using UV trigger from an RNA three-way junction, a DNA star motif and a DNA tetrahedron. Such multifunctional nucleic acid nanostructures have potential in targeted drug delivery.
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Affiliation(s)
- Vibhav A Valsangkar
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | | | - Lifeng Zhuo
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Song Mao
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Goh Woon Lee
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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15
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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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16
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Xu C, Li H, Zhang K, Binzel DW, Yin H, Chiu W, Guo P. Photo-controlled release of paclitaxel and model drugs from RNA pyramids. NANO RESEARCH 2019; 12:41-48. [PMID: 31258852 PMCID: PMC6599617 DOI: 10.1007/s12274-018-2174-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Stimuli-responsive release of drugs from a nanocarrier in spatial-, temporal-, and dosage-controlled fashions is of great interest in the pharmaceutical industry. Paclitaxel is one of the most effective and popular chemotherapeutic drugs against a number of cancers such as metastatic or nonmetastatic breast cancer, non-small cell lung cancer, refractory ovarian cancer, AIDS-related Kaposi's sarcoma, and head and neck cancers. Here, by taking the advantage of RNA nanotechnology in biomedical and material science, we developed a three-dimensional pyramid-shaped RNA nanocage for a photocontrolled release of cargo, using paclitaxel as a model drug. The light-triggered release of paclitaxel or fluorophore Cy5 was achieved by incorporation of photocleavable spacers into the RNA nanoparticles. Upon irradiation with ultraviolet light, cargos were rapidly released (within 5 min). In vitro treatment of breast cancer cells with the RNA nanoparticles harboring photocleavable paclitaxel showed higher cytotoxicity as compared to RNA nanoparticles without the photocleavable spacer. The methodology provides proof of concept for the application of the light-triggered controlled release of drugs from RNA nanocages.
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Affiliation(s)
- Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kaiming Zhang
- Departments of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hongran Yin
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Wah Chiu
- Departments of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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17
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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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18
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Shu Y, Yin H, Rajabi M, Li H, Vieweger M, Guo S, Shu D, Guo P. RNA-based micelles: A novel platform for paclitaxel loading and delivery. J Control Release 2018; 276:17-29. [PMID: 29454064 PMCID: PMC5964609 DOI: 10.1016/j.jconrel.2018.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022]
Abstract
RNA can serve as powerful building blocks for bottom-up fabrication of nanostructures for biotechnological and biomedical applications. In addition to current self-assembly strategies utilizing base pairing, motif piling and tertiary interactions, we reported for the first time the formation of RNA based micellar nanoconstruct with a cholesterol molecule conjugated onto one helical end of a branched pRNA three-way junction (3WJ) motif. The resulting amphiphilic RNA micelles consist of a hydrophilic RNA head and a covalently linked hydrophobic lipid tail that can spontaneously assemble in aqueous solution via hydrophobic interaction. Taking advantage of pRNA 3WJ branched structure, the assembled RNA micelles are capable of escorting multiple functional modules. As a proof of concept for delivery for therapeutics, Paclitaxel was loaded into the RNA micelles with significantly improved water solubility. The successful construction of the drug loaded RNA micelles was confirmed and characterized by agarose gel electrophoresis, atomic force microscopy (AFM), dynamic light scattering (DLS), and fluorescence Nile Red encapsulation assay. The estimate critical micelle formation concentration ranges from 39 nM to 78 nM. The Paclitaxel loaded RNA micelles can internalize into cancer cells and inhibit their proliferation. Further studies showed that the Paclitaxel loaded RNA micelles induced cancer cell apoptosis in a Caspase-3 dependent manner but RNA micelles alone exhibited low cytotoxicity. Finally, the Paclitaxel loaded RNA micelles targeted to tumor in vivo without accumulation in healthy tissues and organs. There is also no or very low induction of pro-inflammatory response. Therefore, multivalence, cancer cell permeability, combined with controllable assembly, low or non toxic nature, and tumor targeting are all promising features that make our pRNA micelles a suitable platform for potential drug delivery.
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Affiliation(s)
- Yi Shu
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences/College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Hongran Yin
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Mehdi Rajabi
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences/College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States; Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences/College of Pharmacy, University of Kentucky, Lexington, KY 40536, United States
| | - Mario Vieweger
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Dan Shu
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry/College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State Universtiy, Columbus, OH 43210, United States.
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19
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Benkato K, O'Brien B, Bui MN, Jasinski DL, Guo P, Khisamutdinov EF. Evaluation of Thermal Stability of RNA Nanoparticles by Temperature Gradient Gel Electrophoresis (TGGE) in Native Condition. Methods Mol Biol 2018; 1632:123-133. [PMID: 28730436 DOI: 10.1007/978-1-4939-7138-1_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Temperature gradient gel electrophoresis (TGGE) is a powerful tool used to analyze the thermal stabilities of nucleic acids. While TGGE is a decades-old technique, it has recently gained favor in the field of RNA nanotechnology, notably in assessing the thermal stabilities of RNA nanoparticles (NPs). With TGGE, an electrical current and a linear temperature gradient are applied simultaneously to NP-loaded polyacrylamide gel, separating the negatively charged NPs based on their thermal behavior (a more stable RNA complex will remain intact through higher temperature ranges). The linear temperature gradient can be set either perpendicular or parallel to the electrical current, as either will make the NPs undergo a transition from native to denatured conformations. Often, the melting transition is influenced by sequence variations, secondary/tertiary structures, concentrations, and external factors such as the presence of a denaturing agent (e.g., urea), the presence of monovalent or divalent metal ions, and the pH of the solvent. In this chapter, we describe the experimental setup and the analysis of the thermal stability of RNA NPs in native conditions using a modified version of a commercially available TGGE system.
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Affiliation(s)
- Kheiria Benkato
- Department of Chemistry, Ball State University, 2000 W. University Ave., Muncie, IN, 47306, USA
| | - Benjamin O'Brien
- Department of Chemistry, Ball State University, 2000 W. University Ave., Muncie, IN, 47306, USA
| | - My N Bui
- Department of Chemistry, Ball State University, 2000 W. University Ave., Muncie, IN, 47306, USA
| | - Daniel L Jasinski
- Department of Physiology and Cell Biology, College of Pharmacy, The Ohio State University, 300 W 10th Ave, Columbus, OH, 43210, USA
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Department of Physiology and Cell Biology, College of Pharmacy, The Ohio State University, 300 W 10th Ave, Columbus, OH, 43210, USA
| | - Emil F Khisamutdinov
- Department of Chemistry, Ball State University, 2000 W. University Ave., Muncie, IN, 47306, USA.
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20
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Guo S, Piao X, Li H, Guo P. Methods for construction and characterization of simple or special multifunctional RNA nanoparticles based on the 3WJ of phi29 DNA packaging motor. Methods 2018. [PMID: 29530505 DOI: 10.1016/j.ymeth.2018.02.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The field of RNA nanotechnology has developed rapidly over the last decade, as more elaborate RNA nanoarchitectures and therapeutic RNA nanoparticles have been constructed, and their applications have been extensively explored. Now it is time to offer different levels of RNA construction methods for both the beginners and the experienced researchers or enterprisers. The first and second parts of this article will provide instructions on basic and simple methods for the assembly and characterization of RNA nanoparticles, mainly based on the pRNA three-way junction (pRNA-3WJ) of phi29 DNA packaging motor. The third part of this article will focus on specific methods for the construction of more sophisticated multivalent RNA nanoparticles for therapeutic applications. In these parts, some simple protocols are provided to facilitate the initiation of the RNA nanoparticle construction in labs new to the field of RNA nanotechnology. This article is intended to serve as a general reference aimed at both apprentices and senior scientists for their future design, construction and characterization of RNA nanoparticles based on the pRNA-3WJ of phi29 DNA packaging motor.
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Affiliation(s)
- Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Xijun Piao
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
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21
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Jasinski DL, Li H, Guo P. The Effect of Size and Shape of RNA Nanoparticles on Biodistribution. Mol Ther 2018; 26:784-792. [PMID: 29402549 PMCID: PMC5910665 DOI: 10.1016/j.ymthe.2017.12.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/12/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022] Open
Abstract
Drugs with ideal pharmacokinetic profile require long half-life but little organ accumulation. Generally, PK and organ accumulation are contradictory factors: smaller size leads to faster excretion and shorter half-lives and thus a lower tendency to reach targets; larger size leads to longer circulation but stronger organ accumulation that leads to toxicity. Organ accumulation has been reported to be size dependent due in large part to engulfing by macrophages. However, publications on the size effect are inconsistent because of complication by the effect of shape that varies from nanoparticle to nanoparticle. Unique to RNA nanotechnology, size could be tuned without a change in shape, resulting in a true size comparison. Here we investigated size effects using RNA squares of identical shape but varying size and shape effects using RNA triangles, squares, and pentagons of identical size but varying shape. We found that circulation time increased with increasing RNA nanoparticle size from 5-25 nm, which is the common size range of therapeutic RNA nanoparticles. Most particles were cleared from the body within 2 hr after systemic injection. Undetectable organ accumulation was found at any time for 5 nm particles. For 20 nm particles, weak signal was found after 24 hr, while accumulation in tumor was strongest during the entire study.
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Affiliation(s)
- Daniel L Jasinski
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, USA; College of Medicine, Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; NCI Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Hui Li
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, USA; College of Medicine, Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; NCI 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
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH, USA; College of Medicine, Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; NCI 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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22
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Hoosen Y, Pradeep P, Kumar P, du Toit LC, Choonara YE, Pillay V. Nanotechnology and Glycosaminoglycans: Paving the Way Forward for Ovarian Cancer Intervention. Int J Mol Sci 2018; 19:E731. [PMID: 29510526 PMCID: PMC5877592 DOI: 10.3390/ijms19030731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer (OC) has gained a great deal of attention due to its aggressive proliferative capabilities, high death rates and poor treatment outcomes, rendering the disease the ultimate lethal gynaecological cancer. Nanotechnology provides a promising avenue to combat this malignancy by the niche fabrication of optimally-structured nanomedicines that ensure potent delivery of chemotherapeutics to OC, employing nanocarriers to act as "intelligent" drug delivery vehicles, functionalized with active targeting approaches for precision delivery of chemotherapeutics to overexpressed biomarkers on cancer cells. Recently, much focus has been implemented to optimize these active targeting mechanisms for treatment/diagnostic purposes employing nanocarriers. This two-part article aims to review the latest advances in active target-based OC interventions, where the impact of the newest antibody, aptamer and folate functionalization on OC detection and treatment is discussed in contrast to the limitations of this targeting mechanism. Furthermore, we discuss the latest advances in nanocarrier based drug delivery in OC, highlighting their commercial/clinical viability of these systems beyond the realms of research. Lastly, in the second section of this review, we comprehensively discussed a focus shift in OC targeting from the well-studied OC cells to the vastly neglected extracellular matrix and motivate the potential for glycosaminoglycans (GAGs) as a more focused extracellular molecular target.
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Affiliation(s)
- Yasar Hoosen
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
| | - Priyamvada Pradeep
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
| | - Pradeep Kumar
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
| | - Lisa C du Toit
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
| | - Yahya E Choonara
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
| | - Viness Pillay
- Wits Advanced Drug Delivery Platform Research Unit, Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 7 York Road, Parktown 2193, South Africa.
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23
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Haque F, Pi F, Zhao Z, Gu S, Hu H, Yu H, Guo P. RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:10.1002/wrna.1452. [PMID: 29105333 PMCID: PMC5739991 DOI: 10.1002/wrna.1452] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 12/23/2022]
Abstract
In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry. Many structural motifs have been discovered and characterized over the years and the crystal structures of many of these motifs are available for nanoparticle construction. For example, using the flexibility and versatility of RNA structure, RNA triangles, squares, pentagons, and hexagons can be constructed from phi29 pRNA three-way-junction (3WJ) building block. This review will focus on 2D RNA triangles, squares, and hexamers; 3D and 4D structures built from basic RNA building blocks; and their prospective applications in vivo as imaging or therapeutic agents via specific delivery and targeting. Methods for intracellular cloning and expression of RNA molecules and the in vivo assembly of RNA nanoparticles will also be reviewed. WIREs RNA 2018, 9:e1452. doi: 10.1002/wrna.1452 This article is categorized under: RNA Methods > RNA Nanotechnology RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Farzin Haque
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Fengmei Pi
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Zhengyi Zhao
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Shanqing Gu
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Haibo Hu
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Hang Yu
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, Ohio, USA
| | - Peixuan Guo
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute; Comprehensive Cancer Center; and Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
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24
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Piao X, Wang H, Binzel DW, Guo P. Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2'-F RNA, and LNA in the context of Phi29 pRNA 3WJ. RNA (NEW YORK, N.Y.) 2018; 24:67-76. [PMID: 29051199 PMCID: PMC5733572 DOI: 10.1261/rna.063057.117] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 05/27/2023]
Abstract
The question of whether RNA is more stable or unstable compared to DNA or other nucleic acids has long been a subject of extensive scrutiny and public attention. Recently, thermodynamically stable and degradation-resistant RNA motifs have been utilized in RNA nanotechnology to build desired architectures and integrate multiple functional groups. Here we report the effects of phosphorothioate deoxyribonucleotides (PS-DNA), deoxyribonucleotides (DNA), ribonucleotides (RNA), 2'-F nucleotides (2'-F), and locked nucleic acids (LNA) on the thermal and in vivo stability of the three-way junction (3WJ) of bacteriophage phi29 motor packaging RNA. It was found that the thermal stability gradually increased following the order of PS-DNA/PS-DNA < DNA/DNA < DNA/RNA < RNA/RNA < RNA/2'-F RNA < 2'-F RNA/2'-F RNA < 2'-F RNA/LNA < LNA/LNA. This proposition is supported by studies on strand displacement and the melting of homogeneous and heterogeneous 3WJs. By simply mixing different chemically modified oligonucleotides, the thermal stability of phi29 pRNA 3WJ can be tuned to cover a wide range of melting temperatures from 21.2°C to over 95°C. The 3WJLNA was resistant to boiling temperature denaturation, urea denaturation, and 50% serum degradation. Intravenous injection of fluorescent LNA/2'-F hybrid 3WJs into mice revealed its exceptional in vivo stability and presence in urine. It is thus concluded that incorporation of LNA nucleotides, alone or in combination with 2'-F, into RNA nanoparticles derived from phi29 pRNA 3WJ can extend the half-life of the RNA nanoparticles in vivo and improve their pharmacokinetics profile.
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Affiliation(s)
- Xijun Piao
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hongzhi Wang
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, Ohio 43210, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
- College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; The Ohio State University, Columbus, Ohio 43210, USA
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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25
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Pi F, Binzel DW, Lee TJ, Li Z, Sun M, Rychahou P, Li H, Haque F, Wang S, Croce CM, Guo B, Evers BM, Guo P. Nanoparticle orientation to control RNA loading and ligand display on extracellular vesicles for cancer regression. NATURE NANOTECHNOLOGY 2018; 13:82-89. [PMID: 29230043 PMCID: PMC5762263 DOI: 10.1038/s41565-017-0012-z] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/04/2017] [Indexed: 05/07/2023]
Abstract
Nanotechnology offers many benefits, and here we report an advantage of applying RNA nanotechnology for directional control. The orientation of arrow-shaped RNA was altered to control ligand display on extracellular vesicle membranes for specific cell targeting, or to regulate intracellular trafficking of small interfering RNA (siRNA) or microRNA (miRNA). Placing membrane-anchoring cholesterol at the tail of the arrow results in display of RNA aptamer or folate on the outer surface of the extracellular vesicle. In contrast, placing the cholesterol at the arrowhead results in partial loading of RNA nanoparticles into the extracellular vesicles. Taking advantage of the RNA ligand for specific targeting and extracellular vesicles for efficient membrane fusion, the resulting ligand-displaying extracellular vesicles were capable of specific delivery of siRNA to cells, and efficiently blocked tumour growth in three cancer models. Extracellular vesicles displaying an aptamer that binds to prostate-specific membrane antigen, and loaded with survivin siRNA, inhibited prostate cancer xenograft. The same extracellular vesicle instead displaying epidermal growth-factor receptor aptamer inhibited orthotopic breast cancer models. Likewise, survivin siRNA-loaded and folate-displaying extracellular vesicles inhibited patient-derived colorectal cancer xenograft.
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Affiliation(s)
- Fengmei Pi
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Daniel W Binzel
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Tae Jin Lee
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhefeng Li
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Meiyan Sun
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - Piotr Rychahou
- Markey Cancer Center, Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Hui Li
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Farzin Haque
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Shaoying Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Bin Guo
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA
| | - B Mark Evers
- Markey Cancer Center, Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, OH, USA.
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA.
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, USA.
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26
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Guo S, Li H, Ma M, Fu J, Dong Y, Guo P. Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 9:399-408. [PMID: 29246318 PMCID: PMC5701797 DOI: 10.1016/j.omtn.2017.10.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/14/2017] [Accepted: 10/14/2017] [Indexed: 02/01/2023]
Abstract
RNA molecules have emerged as promising therapeutics. Like all other drugs, the safety profile and immune response are important criteria for drug evaluation. However, the literature on RNA immunogenicity has been controversial. Here, we used the approach of RNA nanotechnology to demonstrate that the immune response of RNA nanoparticles is size, shape, and sequence dependent. RNA triangle, square, pentagon, and tetrahedron with same shape but different sizes, or same size but different shapes were used as models to investigate the immune response. The levels of pro-inflammatory cytokines induced by these RNA nanoarchitectures were assessed in macrophage-like cells and animals. It was found that RNA polygons without extension at the vertexes were immune inert. However, when single-stranded RNA with a specific sequence was extended from the vertexes of RNA polygons, strong immune responses were detected. These immunostimulations are sequence specific, because some other extended sequences induced little or no immune response. Additionally, larger-size RNA square induced stronger cytokine secretion. 3D RNA tetrahedron showed stronger immunostimulation than planar RNA triangle. These results suggest that the immunogenicity of RNA nanoparticles is tunable to produce either a minimal immune response that can serve as safe therapeutic vectors, or a strong immune response for cancer immunotherapy or vaccine adjuvants.
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Affiliation(s)
- Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Mengshi Ma
- Center for Research on Environmental Disease, College of Medicine, Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Jian Fu
- Center for Research on Environmental Disease, College of Medicine, Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Yizhou Dong
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; NCI Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA; College of Medicine, The Ohio State University, Columbus, OH 43210, USA; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; NCI Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
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27
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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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28
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Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo. ACS Synth Biol 2017; 6:1710-1721. [PMID: 28548488 PMCID: PMC5603824 DOI: 10.1021/acssynbio.7b00059] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
RNA–RNA
assembly governs key biological processes and is
a powerful tool for engineering synthetic genetic circuits. Characterizing
RNA assembly in living cells often involves monitoring fluorescent
reporter proteins, which are at best indirect measures of underlying
RNA–RNA hybridization events and are subject to additional
temporal and load constraints associated with translation and activation
of reporter proteins. In contrast, RNA aptamers that sequester small
molecule dyes and activate their fluorescence are increasingly utilized
in genetically encoded strategies to report on RNA-level events. Split-aptamer
systems have been rationally designed to generate signal upon hybridization
of two or more discrete RNA transcripts, but none directly function
when expressed in vivo. We reasoned that the improved
physiological properties of the Broccoli aptamer enable construction
of a split-aptamer system that could function in living cells. Here
we present the Split-Broccoli system, in which self-assembly is nucleated
by a thermostable, three-way junction RNA architecture and fluorescence
activation requires both strands. Functional assembly of the system
approximately follows second-order kinetics in vitro and improves when cotranscribed, rather than when assembled from
purified components. Split-Broccoli fluorescence
is digital in vivo and retains functional modularity
when fused to RNAs that regulate circuit function through RNA–RNA
hybridization, as demonstrated with an RNA Toehold switch. Split-Broccoli represents the first functional split-aptamer
system to operate in vivo. It offers a genetically
encoded and nondestructive platform to monitor and exploit RNA–RNA
hybridization, whether as an all-RNA, stand-alone AND gate or as a
tool for monitoring assembly of RNA–RNA hybrids.
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Affiliation(s)
- Khalid K. Alam
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kwaku D. Tawiah
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Matthew F. Lichte
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - David Porciani
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, United States
| | - Donald H. Burke
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, United States
- Department
of Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
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29
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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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30
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Hill AC, Schroeder SJ. Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA. RNA (NEW YORK, N.Y.) 2017; 23:521-529. [PMID: 28069889 PMCID: PMC5340915 DOI: 10.1261/rna.059220.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions. A comparison of our data with free energies predicted by currently available RNA secondary structure prediction programs shows that these programs do not accurately predict multibranch loop stabilities. These results will expand the existing parameters used for RNA secondary structure prediction from sequence in order to better inform RNA structure-function hypotheses and guide the rational design of functional RNA supramolecular assemblies.
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Affiliation(s)
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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31
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Bui MN, Brittany Johnson M, Viard M, Satterwhite E, Martins AN, Li Z, Marriott I, Afonin KA, Khisamutdinov EF. Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2017; 13:1137-1146. [PMID: 28064006 PMCID: PMC6637421 DOI: 10.1016/j.nano.2016.12.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/20/2016] [Accepted: 12/23/2016] [Indexed: 12/21/2022]
Abstract
RNA nanotechnology employs synthetically modified ribonucleic acid (RNA) to engineer highly stable nanostructures in one, two, and three dimensions for medical applications. Despite the tremendous advantages in RNA nanotechnology, unmodified RNA itself is fragile and prone to enzymatic degradation. In contrast to use traditionally modified RNA strands e.g. 2'-fluorine, 2'-amine, 2'-methyl, we studied the effect of RNA/DNA hybrid approach utilizing a computer-assisted RNA tetra-uracil (tetra-U) motif as a toolkit to address questions related to assembly efficiency, versatility, stability, and the production costs of hybrid RNA/DNA nanoparticles. The tetra-U RNA motif was implemented to construct four functional triangles using RNA, DNA and RNA/DNA mixtures, resulting in fine-tunable enzymatic and thermodynamic stabilities, immunostimulatory activity and RNAi capability. Moreover, the tetra-U toolkit has great potential in the fabrication of rectangular, pentagonal, and hexagonal NPs, representing the power of simplicity of RNA/DNA approach for RNA nanotechnology and nanomedicine community.
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Affiliation(s)
- My N Bui
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - M Brittany Johnson
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mathias Viard
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Emily Satterwhite
- Nanoscale Science Program, University of North Carolina at Charlotte, The Center for Biomedical Engineering and Science, Charlotte, NC 28223, USA
| | - Angelica N Martins
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zhihai Li
- Department of Chemistry, Ball State University, Muncie, IN, USA
| | - Ian Marriott
- Department of Biology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- Nanoscale Science Program, University of North Carolina at Charlotte, The Center for Biomedical Engineering and Science, Charlotte, NC 28223, USA
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32
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Doyle F, Lapsia S, Spadaro S, Wurz ZE, Bhaduri-McIntosh S, Tenenbaum SA. Engineering Structurally Interacting RNA (sxRNA). Sci Rep 2017; 7:45393. [PMID: 28350000 PMCID: PMC5368982 DOI: 10.1038/srep45393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/22/2017] [Indexed: 01/01/2023] Open
Abstract
RNA-based three-way junctions (3WJs) are naturally occurring structures found in many functional RNA molecules including rRNA, tRNA, snRNA and ribozymes. 3WJs are typically characterized as resulting from an RNA molecule folding back on itself in cis but could also form in trans when one RNA, for instance a microRNA binds to a second structured RNA, such as a mRNA. Trans-3WJs can influence the final shape of one or both of the RNA molecules and can thus provide a means for modulating the availability of regulatory motifs including potential protein or microRNA binding sites. Regulatory 3WJs generated in trans represent a newly identified regulatory category that we call structurally interacting RNA or sxRNA for convenience. Here we show that they can be rationally designed using familiar cis-3WJ examples as a guide. We demonstrate that an sxRNA "bait" sequence can be designed to interact with a specific microRNA "trigger" sequence, creating a regulatable RNA-binding protein motif that retains its functional activity. Further, we show that when placed downstream of a coding sequence, sxRNA can be used to switch "ON" translation of that sequence in the presence of the trigger microRNA and the amount of translation corresponded with the amount of microRNA present.
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Affiliation(s)
- Francis Doyle
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA
| | - Sameer Lapsia
- Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Salvatore Spadaro
- Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Zachary E. Wurz
- HocusLocus, LLC, 253 Fuller Road, Nanofab North, Albany NY 12203, USA
| | - Sumita Bhaduri-McIntosh
- Pediatric Infectious Diseases, Departments of Pediatrics and Molecular Genetics and Microbiology, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Scott A. Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA
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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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Haque F, Xu C, Jasinski DL, Li H, Guo P. Using Planar Phi29 pRNA Three-Way Junction to Control Size and Shape of RNA Nanoparticles for Biodistribution Profiling in Mice. Methods Mol Biol 2017; 1632:359-380. [PMID: 28730451 DOI: 10.1007/978-1-4939-7138-1_23] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
RNA is rapidly emerging as a versatile building block for nanoparticle assembly due to its simplicity in base pairing, while exhibiting diversity in function such as enzymatic activity similar to some proteins. Recent advances in RNA nanotechnology have generated significant interests in applying RNA nanoparticles for various applications in nanotechnology and nanomedicine. In particular, assessing the effect of size and shape on cell entry and intracellular trafficking as well as in vivo biodistribution of nanoparticles is challenging due to the lack of nanoparticles rich in structure while varying in size and shape. RNA nanotechnology exemplified by the packaging RNA (pRNA) of bacteriophage phi29 DNA packaging motor has provided a different prospect in nanoparticle designs. Of note, there is a robust three-way junction (3WJ) motif in pRNA which can serve as an adaptable scaffold to construct thermodynamically stable 2D planar and 3D globular RNA architectures with tunable shapes and sizes, and harboring various targeting, therapeutic, and imaging modules. This chapter focuses on the methods for constructing pRNA-3WJ based nanoparticles with controllable sizes and shapes, and assessment of their biodistribution profiles in cancer mouse models after systemic injection and ocular mouse models following subconjunctival injection.
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Affiliation(s)
- Farzin Haque
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Congcong Xu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel L Jasinski
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Hui Li
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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35
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Binzel DW, Khisamutdinov E, Vieweger M, Ortega J, Li J, Guo P. Mechanism of three-component collision to produce ultrastable pRNA three-way junction of Phi29 DNA-packaging motor by kinetic assessment. RNA (NEW YORK, N.Y.) 2016; 22:1710-1718. [PMID: 27672132 PMCID: PMC5066623 DOI: 10.1261/rna.057646.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/09/2016] [Indexed: 05/27/2023]
Abstract
RNA nanotechnology is rapidly emerging. Due to advantageous pharmacokinetics and favorable in vivo biodistribution, RNA nanoparticles have shown promise in targeted delivery of therapeutics. RNA nanotechnology applies bottom-up assembly, thus elucidation of the mechanism of interaction between multiple components is of fundamental importance. The tendency of diminishing concern about RNA instability has accelerated by the finding of the novel thermostable three-way junction (3WJ) motif of the phi29 DNA-packaging motor. The kinetics of these three components, each averaging 18 nucleotides (nt), was investigated to elucidate the mechanism for producing the stable 3WJ. The three fragments coassembled into the 3WJ with extraordinary speed and affinity via a two-step reaction mechanism, 3WJb + 3WJc ↔ 3WJbc + 3WJa ↔ 3WJabc The first step of reaction between 3WJb and 3WJc is highly dynamic since these two fragments only contain 8 nt for complementation. In the second step, the 3WJa, which contains 17 nt complementary to the 3WJbc complex, locks the unstable 3WJbc complex into a highly stable 3WJ. The resulting pRNA-3WJ is more stable than any of the dimer species as shown in the much more rapid association rates and slowest dissociation rate constant. The second step occurs at a very high association rate that is difficult to quantify, resulting in a rapid formation of a stable 3WJ. Elucidation of the mechanism of three-component collision in producing the ultrastable 3WJ proves a promising platform for bottom-up assembly of RNA nanoparticles as a new class of anion polymers for material science, electronic elements, or therapeutic reagents.
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Affiliation(s)
- Daniel W Binzel
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Emil Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, USA
| | - Mario Vieweger
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
| | - Janice Ortega
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky 40536, USA
| | - Jingyuan Li
- Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China, 1000049
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy
- Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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36
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Li H, Zhang K, Pi F, Guo S, Shlyakhtenko L, Chiu W, Shu D, Guo P. Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:7501-7. [PMID: 27322097 PMCID: PMC5059845 DOI: 10.1002/adma.201601976] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/11/2016] [Indexed: 05/20/2023]
Abstract
RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be extended to construct higher-order polyhedral RNA architectures for various applications such as targeted cancer imaging and therapy.
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Affiliation(s)
- Hui Li
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kaiming Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fengmei Pi
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Sijin Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Luda Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Shu
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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37
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Binzel DW, Shu Y, Li H, Sun M, Zhang Q, Shu D, Guo B, Guo P. Specific Delivery of MiRNA for High Efficient Inhibition of Prostate Cancer by RNA Nanotechnology. Mol Ther 2016; 24:1267-77. [PMID: 27125502 PMCID: PMC5088763 DOI: 10.1038/mt.2016.85] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/07/2016] [Indexed: 12/19/2022] Open
Abstract
Both siRNA and miRNA can serve as powerful gene-silencing reagents but their specific delivery to 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-miRNA seed-targeting sequence to block the growth of prostate cancer in mouse models. Utilizing the thermodynamically ultra-stable three-way junction of the pRNA of phi29 DNA packaging motor, RNA nanoparticles were constructed by bottom-up self-assembly containing the anti-prostate-specific membrane antigen (PSMA) RNA aptamer as a targeting ligand and anti-miR17 or anti-miR21 as therapeutic modules. The 16 nm RNase-resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection in mice and strongly bound to tumors with little or no accumulation in healthy organs 8 hours postinjection, and subsequently repressed tumor growth at low doses with high efficiency.
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Affiliation(s)
- Daniel W Binzel
- 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, The Ohio State University, Columbus, Ohio, USA
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Yi Shu
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Hui Li
- 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, The Ohio State University, Columbus, Ohio, USA
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Meiyan Sun
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Qunshu Zhang
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Dan Shu
- 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, The Ohio State University, Columbus, Ohio, USA
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Bin Guo
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Peixuan Guo
- 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, The Ohio State University, Columbus, Ohio, USA
- Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
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Afonin KA, Viard M, Tedbury P, Bindewald E, Parlea L, Howington M, Valdman M, Johns-Boehme A, Brainerd C, Freed EO, Shapiro BA. The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities. NANO LETTERS 2016; 16:1746-53. [PMID: 26926382 PMCID: PMC6345527 DOI: 10.1021/acs.nanolett.5b04676] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA-DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds.
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Affiliation(s)
- Kirill A. Afonin
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Mathias Viard
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Philip Tedbury
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Lorena Parlea
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Marshall Howington
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Melissa Valdman
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Alizah Johns-Boehme
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Cara Brainerd
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Eric O. Freed
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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39
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Sharma A, Haque F, Pi F, Shlyakhtenko LS, Evers BM, Guo P. Controllable self-assembly of RNA dendrimers. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2015; 12:835-844. [PMID: 26656633 DOI: 10.1016/j.nano.2015.11.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/09/2015] [Accepted: 11/14/2015] [Indexed: 10/22/2022]
Abstract
UNLABELLED We report programmable self-assembly of branched, 3D globular, monodisperse and nanoscale sized dendrimers using RNA as building blocks. The central core and repeating units of the RNA dendrimer are derivatives of the ultrastable three-way junction (3WJ) motif from the bacteriophage phi29 motor pRNA. RNA dendrimers were constructed by step-wise self-assembly of modular 3WJ building blocks initiating with a single 3WJ core (Generation-0) with overhanging sticky end and proceeding in a radial manner in layers up to Generation-4. The final constructs were generated under control without any structural defects in high yield and purity, as demonstrated by gel electrophoresis and AFM imaging. Upon incorporation of folate on the peripheral branches of the RNA dendrimers, the resulting constructs showed high binding and internalization into cancer cells. RNA dendrimers are envisioned to have a major impact in targeting, disease therapy, molecular diagnostics and bioelectronics in the near future. FROM THE CLINICAL EDITOR Dendrimers are gaining importance as a carrier platform for diagnosis and therapeutics. The authors here reported building of their dendrimer molecules using RNA as building blocks. The addition of folate also allowed recognition and subsequent binding to tumor cells. This new construct may prove to be useful in many clinical settings.
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Affiliation(s)
- Ashwani Sharma
- College of Pharmacy, College of Medicine/Department of Physiology & Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA; Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Farzin Haque
- College of Pharmacy, College of Medicine/Department of Physiology & Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA; Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
| | - Fengmei Pi
- College of Pharmacy, College of Medicine/Department of Physiology & Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA; Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Lyudmila S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - B Mark Evers
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA; Markey Cancer Center, University of Kentucky, Lexington, KY, USA; Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- College of Pharmacy, College of Medicine/Department of Physiology & Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA; Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA; Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
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40
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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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41
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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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42
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Lee T, Yagati AK, Pi F, Sharma A, Choi JW, Guo P. Construction of RNA-Quantum Dot Chimera for Nanoscale Resistive Biomemory Application. ACS NANO 2015; 9:6675-82. [PMID: 26135474 PMCID: PMC4642448 DOI: 10.1021/acsnano.5b03269] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
RNA nanotechnology offers advantages to construct thermally and chemically stable nanoparticles with well-defined shape and structure. Here we report the development of an RNA-QD (quantum dot) chimera for resistive biomolecular memory application. Each QD holds two copies of the pRNA three-way junction (pRNA-3WJ) of the bacteriophage phi29 DNA packaging motor. The fixed quantity of two RNAs per QD was achieved by immobilizing the pRNA-3WJ with a Sephadex aptamer for resin binding. Two thiolated pRNA-3WJ serve as two feet of the chimera that stand on the gold plate. The RNA nanostructure served as both an insulator and a mediator to provide defined distance between the QD and gold. Immobilization of the chimera nanoparticle was confirmed with scanning tunneling microscopy. As revealed by scanning tunneling spectroscopy, the conjugated pRNA-3WJ-QD chimera exhibited an excellent electrical bistability signal for biomolecular memory function, demonstrating great potential for the development of resistive biomolecular memory and a nano-bio-inspired electronic device for information processing and computing.
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Affiliation(s)
- Taek Lee
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ajay Kumar Yagati
- Department of Biomedical Engineering, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 406-799, Republic of Korea
| | - Fengmei Pi
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Ashwani Sharma
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jeong-Woo Choi
- Department of Biomedical Engineering, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 406-799, Republic of Korea
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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43
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Li H, Rychahou PG, Cui Z, Pi F, Evers BM, Shu D, Guo P, Luo W. RNA Nanoparticles Derived from Three-Way Junction of Phi29 Motor pRNA Are Resistant to I-125 and Cs-131 Radiation. Nucleic Acid Ther 2015; 25:188-97. [PMID: 26017686 DOI: 10.1089/nat.2014.0525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Radiation reagents that specifically target tumors are in high demand for the treatment of cancer. The emerging field of RNA nanotechnology might provide new opportunities for targeted radiation therapy. This study investigates whether chemically modified RNA nanoparticles derived from the packaging RNA (pRNA) three-way junction (3WJ) of phi29 DNA-packaging motor are resistant to potent I-125 and Cs-131 radiation, which is a prerequisite for utilizing these RNA nanoparticles as carriers for targeted radiation therapy. pRNA 3WJ nanoparticles were constructed and characterized, and the stability of these nanoparticles under I-125 and Cs-131 irradiation with clinically relevant doses was examined. RNA nanoparticles derived from the pRNA 3WJ targeted tumors specifically and they were stable under irradiation of I-125 and Cs-131 with clinically relevant doses ranging from 1 to 90 Gy over a significantly long time up to 20 days, while control plasmid DNA was damaged at 20 Gy or higher.
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Affiliation(s)
- Hui Li
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky
| | - Piotr G Rychahou
- 3 Department of Surgery, Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Zheng Cui
- 2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky
| | - Fengmei Pi
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky
| | - B Mark Evers
- 4 Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Dan Shu
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky.,4 Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Peixuan Guo
- 1 Nanobiotechnology Center, University of Kentucky , Lexington, Kentucky.,2 Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky.,4 Markey Cancer Center, University of Kentucky , Lexington, Kentucky
| | - Wei Luo
- 5 Department of Radiation Medicine, Markey Cancer Center, University of Kentucky , Lexington, Kentucky
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44
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Afonin KA, Viard M, Kagiampakis I, Case CL, Dobrovolskaia MA, Hofmann J, Vrzak A, Kireeva M, Kasprzak WK, KewalRamani VN, Shapiro BA. Triggering of RNA interference with RNA-RNA, RNA-DNA, and DNA-RNA nanoparticles. ACS NANO 2015; 9:251-9. [PMID: 25521794 PMCID: PMC4310632 DOI: 10.1021/nn504508s] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/11/2014] [Indexed: 05/08/2023]
Abstract
Control over cellular delivery of different functionalities and their synchronized activation is a challenging task. We report several RNA and RNA/DNA-based nanoparticles designed to conditionally activate the RNA interference in various human cells. These nanoparticles allow precise control over their formulation, stability in blood serum, and activation of multiple functionalities. Importantly, interferon and pro-inflammatory cytokine activation assays indicate the significantly lower responses for DNA nanoparticles compared to the RNA counterparts, suggesting greater potential of these molecules for therapeutic use.
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Affiliation(s)
- Kirill A. Afonin
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mathias Viard
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic Science Program, Leidos Biomedical Research, Inc., NCI Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ioannis Kagiampakis
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Christopher L. Case
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Jen Hofmann
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ashlee Vrzak
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Maria Kireeva
- Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, NCI, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech K. Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., NCI Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Vineet N. KewalRamani
- HIV Drug Resistance Program, NCI, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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45
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Haque F, Guo P. Overview of methods in RNA nanotechnology: synthesis, purification, and characterization of RNA nanoparticles. Methods Mol Biol 2015; 1297:1-19. [PMID: 25895992 DOI: 10.1007/978-1-4939-2562-9_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149-155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833-842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860-921, 2001) that used to be called "junk DNA" actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.
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Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, Departmentof Pharmaceutical Sciences, University of Kentucky, 789 S Limestone Ave, 576 Biopharm Complex, Lexington, KY, 40536, USA,
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46
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Khisamutdinov EF, Bui MNH, Jasinski D, Zhao Z, Cui Z, Guo P. Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°. Methods Mol Biol 2015; 1316:181-93. [PMID: 25967062 DOI: 10.1007/978-1-4939-2730-2_15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Precise shape control of architectures at the nanometer scale is an intriguing but extremely challenging facet. RNA has recently emerged as a unique material and thermostable building block for use in nanoparticle construction. Here, we describe a simple method from design to synthesis of RNA triangle, square, and pentagon by stretching RNA 3WJ native angle from 60° to 90° and 108°, using the three-way junction (3WJ) of the pRNA from bacteriophage phi29 dsDNA packaging motor. These methods for the construction of elegant polygons can be applied to other RNA building blocks including the utilization and application of RNA 4-way, 5-way, and other multi-way junctions.
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Affiliation(s)
- Emil F Khisamutdinov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA,
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47
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Jasinski DL, Khisamutdinov EF, Lyubchenko YL, Guo P. Physicochemically tunable polyfunctionalized RNA square architecture with fluorogenic and ribozymatic properties. ACS NANO 2014; 8:7620-9. [PMID: 24971772 PMCID: PMC4148160 DOI: 10.1021/nn502160s] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/27/2014] [Indexed: 05/22/2023]
Abstract
Recent advances in RNA nanotechnology allow the rational design of various nanoarchitectures. Previous methods utilized conserved angles from natural RNA motifs to form geometries with specific sizes. However, the feasibility of producing RNA architecture with variable sizes using native motifs featuring fixed sizes and angles is limited. It would be advantageous to display RNA nanoparticles of diverse shape and size derived from a given primary sequence. Here, we report an approach to construct RNA nanoparticles with tunable size and stability. Multifunctional RNA squares with a 90° angle were constructed by tuning the 60° angle of the three-way junction (3WJ) motif from the packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor. The physicochemical properties and size of the RNA square were also easily tuned by modulating the “core” strand and adjusting the length of the sides of the square via predictable design. Squares of 5, 10, and 20 nm were constructed, each showing diverse thermodynamic and chemical stabilities. Four “arms” extending from the corners of the square were used to incorporate siRNA, ribozyme, and fluorogenic RNA motifs. Unique intramolecular contact using the pre-existing intricacy of the 3WJ avoids relatively weaker intermolecular interactions via kissing loops or sticky ends. Utilizing the 3WJ motif, we have employed a modular design technique to construct variable-size RNA squares with controllable properties and functionalities for diverse and versatile applications with engineering, pharmaceutical, and medical potential. This technique for simple design to finely tune physicochemical properties adds a new angle to RNA nanotechnology.
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Affiliation(s)
- Daniel L. Jasinski
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Emil F. Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Address correspondence to
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48
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Khisamutdinov EF, Li H, Jasinski DL, Chen J, Fu J, Guo P. Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles. Nucleic Acids Res 2014; 42:9996-10004. [PMID: 25092921 PMCID: PMC4150753 DOI: 10.1093/nar/gku516] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Modulation of immune response is important in cancer immunotherapy, vaccine adjuvant development and inflammatory or immune disease therapy. Here we report the development of new immunomodulators via control of shape transition among RNA triangle, square and pentagon. Changing one RNA strand in polygons automatically induced the stretching of the interior angle from 60° to 90° or 108°, resulting in self-assembly of elegant RNA triangles, squares and pentagons. When immunological adjuvants were incorporated, their immunomodulation effect for cytokine TNF-α and IL-6 induction was greatly enhanced in vitro and in animals up to 100-fold, while RNA polygon controls induced unnoticeable effect. The RNA nanoparticles were delivered to macrophages specifically. The degree of immunostimulation greatly depended on the size, shape and number of the payload per nanoparticles. Stronger immune response was observed when the number of adjuvants per polygon was increased, demonstrating the advantage of shape transition from triangle to pentagon.
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Affiliation(s)
- Emil F Khisamutdinov
- Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center, Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA
| | - Hui Li
- Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center, Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA
| | - Daniel L Jasinski
- Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center, Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA
| | - Jiao Chen
- Center for Research on Environmental Disease, Graduate Center for Toxicology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Jian Fu
- Center for Research on Environmental Disease, Graduate Center for Toxicology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Peixuan Guo
- Department of Pharmaceutical Sciences, College of Pharmacy, Markey Cancer Center, Nanobiotechnology Center, University of Kentucky, Lexington, KY 40536, USA
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49
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De-Donatis GM, Zhao Z, Wang S, Huang LP, Schwartz C, Tsodikov OV, Zhang H, Haque F, Guo P. Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size. Cell Biosci 2014; 4:30. [PMID: 24940480 PMCID: PMC4060578 DOI: 10.1186/2045-3701-4-30] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/16/2014] [Indexed: 12/03/2022] Open
Abstract
Background Double-stranded DNA translocation is ubiquitous in living systems. Cell mitosis, bacterial binary fission, DNA replication or repair, homologous recombination, Holliday junction resolution, viral genome packaging and cell entry all involve biomotor-driven dsDNA translocation. Previously, biomotors have been primarily classified into linear and rotational motors. We recently discovered a third class of dsDNA translocation motors in Phi29 utilizing revolution mechanism without rotation. Analogically, the Earth rotates around its own axis every 24 hours, but revolves around the Sun every 365 days. Results Single-channel DNA translocation conductance assay combined with structure inspections of motor channels on bacteriophages P22, SPP1, HK97, T7, T4, Phi29, and other dsDNA translocation motors such as bacterial FtsK and eukaryotic mimiviruses or vaccinia viruses showed that revolution motor is widespread. The force generation mechanism for revolution motors is elucidated. Revolution motors can be differentiated from rotation motors by their channel size and chirality. Crystal structure inspection revealed that revolution motors commonly exhibit channel diameters larger than 3 nm, while rotation motors that rotate around one of the two separated DNA strands feature a diameter smaller than 2 nm. Phi29 revolution motor translocated double- and tetra-stranded DNA that occupied 32% and 64% of the narrowest channel cross-section, respectively, evidencing that revolution motors exhibit channel diameters significantly wider than the dsDNA. Left-handed oriented channels found in revolution motors drive the right-handed dsDNA via anti-chiral interaction, while right-handed channels observed in rotation motors drive the right-handed dsDNA via parallel threads. Tethering both the motor and the dsDNA distal-end of the revolution motor does not block DNA packaging, indicating that no rotation is required for motors of dsDNA phages, while a small-angle left-handed twist of dsDNA that is aligned with the channel could occur due to the conformational change of the phage motor channels from a left-handed configuration for DNA entry to a right-handed configuration for DNA ejection for host cell infection. Conclusions The revolution motor is widespread among biological systems, and can be distinguished from rotation motors by channel size and chirality. The revolution mechanism renders dsDNA void of coiling and torque during translocation of the lengthy helical chromosome, thus resulting in more efficient motor energy conversion.
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Affiliation(s)
- Gian Marco De-Donatis
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zhengyi Zhao
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Shaoying Wang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Lisa P Huang
- Current address: Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., Hamilton, NJ 08690, USA
| | - Chad Schwartz
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Hui Zhang
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Farzin Haque
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Peixuan Guo
- Nanobiotechnology Center, University of Kentucky, Lexington, KY, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,William Farish Endowed Chair in Nanobiotechnology, School of Pharmacy, University of Kentucky, 565 Biopharmaceutical Complex, 789 S. Limestone Street, Lexington, KY 40536, USA
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