1
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Zhu L, Luo J, Ren K. Nucleic acid-based artificial nanocarriers for gene therapy. J Mater Chem B 2023; 11:261-279. [PMID: 36524395 DOI: 10.1039/d2tb01179d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.
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Affiliation(s)
- Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Jun Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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2
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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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3
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Han Z, Hilburg SL, Alexander-Katz A. Forced Unfolding of Protein-Inspired Single-Chain Random Heteropolymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c02411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zexiang Han
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shayna L. Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Zhuo B, Ou X, Li J. Structure and Mechanical Stabilities of the Three-Way Junction Motifs in Prohead RNA. J Phys Chem B 2021; 125:12125-12134. [PMID: 34719230 DOI: 10.1021/acs.jpcb.1c04681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The core structure of phi29 prohead RNA (pRNA) is composed of three major helices organized into three-way junction pRNA (3WJ-pRNA) and has stout structural rigidity along the coaxial helices. Prohead RNAs of the other Bacillus subtilis bacteriophages such as GA1 and SF5 share similar secondary structure and function with phi29; whether these pRNAs have similar mechanical rigidity remains to be elucidated. In this study, we constructed the tertiary structures of GA1 and SF5 3WJ-pRNAs by comparative modeling. Both GA1 and SF5 3WJ-pRNAs adopt a similar structure, in which three helices are organized as the three-way junction and two of the three helices are stacked coaxially. Moreover, detailed structural features of GA1 and SF5 3WJ-pRNAs are also similar to those of phi29 3WJ-pRNA: all of the bases of the coaxial helices are paired, and all of the adenines in the junction region are paired, which eliminates the interference of A-minor tertiary interactions. Hence, the coaxial helices tightly join to each other, and the major groove between them is very narrow. Two Mg2+ ions can thus fit into this major groove and form double Mg clamps. A steered molecular dynamics simulation was used to study the mechanical properties of these 3WJ-pRNAs. Both GA1 and SF5 3WJ-pRNAs show strong resistance to applied force in the direction of their coaxial helices. Such mechanical stability can be attributed to the Mg clamps.
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Affiliation(s)
- Boyang Zhuo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jingyuan Li
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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5
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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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6
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Li C, Yuan X, Li N, Wang J, Yu S, Zeng H, Zhang J, Wu Q, Ding Y. Isolation and Characterization of Bacillus cereus Phage vB_BceP-DLc1 Reveals the Largest Member of the Φ29-Like Phages. Microorganisms 2020; 8:E1750. [PMID: 33171789 PMCID: PMC7695010 DOI: 10.3390/microorganisms8111750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Bacillus phage φ29 and its relatives have been considered as one of the most important model organisms for DNA replication, transcription, morphogenesis, DNA packaging studies, and nanotechnology applications. Here, we isolated and characterized a new member of the φ29-like phage, named Bacillus cereus phage vB_BceP-DLc1. This phage, with a unique inserted gene cluster, has the largest genome among known φ29-like phages. DLc1 can use the surface carbohydrate structures of the host cell as receptors and only infects the most related B. cereus strains, showing high host-specificity. The adsorption rate constant and life cycle of DLc1 under experimental conditions were also determined. Not only stable under temperatures below 55 °C and pH range from 5 to 11, the new phage also showed tolerance to high concentrations of NaCl, 75% ethanol, chloroform, and mechanical vortex, which is preferable for practical use in the food and pharmaceutical industries.
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Affiliation(s)
- Chun Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
| | - Xiaoming Yuan
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Na Li
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510642, China;
| | - Shubo Yu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Haiyan Zeng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jumei Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, College of Science & Engineering, Jinan University, Guangzhou 510632, China; (C.L.); (X.Y.); (N.L.)
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (S.Y.); (H.Z.); (J.Z.); (Q.W.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
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7
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Niu X, Liu Q, Xu Z, Chen Z, Xu L, Xu L, Li J, Fang X. Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs). Nat Commun 2020; 11:5496. [PMID: 33127896 PMCID: PMC7603331 DOI: 10.1038/s41467-020-19260-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Mechanical anisotropy is an essential property for many biomolecules to assume their structures, functions and applications, however, the mechanisms for their direction-dependent mechanical responses remain elusive. Herein, by using a single-molecule nanopore sensing technique, we explore the mechanisms of directional mechanical stability of the xrRNA1 RNA from ZIKA virus (ZIKV), which forms a complex ring-like architecture. We reveal extreme mechanical anisotropy in ZIKV xrRNA1 which highly depends on Mg2+ and the key tertiary interactions. The absence of Mg2+ and disruption of the key tertiary interactions strongly affect the structural integrity and attenuate mechanical anisotropy. The significance of ring structures in RNA mechanical anisotropy is further supported by steered molecular dynamics simulations in combination with force distribution analysis. We anticipate the ring structures can be used as key elements to build RNA-based nanostructures with controllable mechanical anisotropy for biomaterial and biomedical applications.
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Affiliation(s)
- Xiaolin Niu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiuhan Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zhonghe Xu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhifeng Chen
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Linghui Xu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lilei Xu
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinghong Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, 100084, China.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structfural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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8
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Zou A, Lee S, Li J, Zhou R. Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp Structure. J Phys Chem B 2020; 124:701-707. [DOI: 10.1021/acs.jpcb.9b06428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Sangyun Lee
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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9
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Prevelige PE, Cortines JR. Phage assembly and the special role of the portal protein. Curr Opin Virol 2018; 31:66-73. [PMID: 30274853 DOI: 10.1016/j.coviro.2018.09.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/16/2018] [Accepted: 09/21/2018] [Indexed: 12/18/2022]
Abstract
Virus infections are ultimately dependent on a successful viral genome delivery to the host cell. The bacteriophage family Caudovirales evolved specialized machinery that fulfills this function: the portal proteins complex. The complexes are arranged as dodecameric rings and are a structural part of capsids incorporated at a five-fold vertex. They are involved in crucial aspects of viral replication, such as virion assembly, DNA packaging and DNA delivery. This review focuses on the organization and the mechanism through which these portal complexes achieve viral genome delivery and their similarities to other viral portal complexes.
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Affiliation(s)
- Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, 35294, United States
| | - Juliana R Cortines
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Brazil.
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10
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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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11
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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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12
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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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13
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Zhang X, Zhang D, Zhao C, Tian K, Shi R, Du X, Burcke AJ, Wang J, Chen SJ, Gu LQ. Nanopore electric snapshots of an RNA tertiary folding pathway. Nat Commun 2017; 8:1458. [PMID: 29133841 PMCID: PMC5684407 DOI: 10.1038/s41467-017-01588-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/29/2017] [Indexed: 12/22/2022] Open
Abstract
The chemical properties and biological mechanisms of RNAs are determined by their tertiary structures. Exploring the tertiary structure folding processes of RNA enables us to understand and control its biological functions. Here, we report a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master equation analysis to elucidate the folding of an RNA pseudoknot structure. In this approach, single RNA molecules captured by the nanopore can freely fold from the unstructured state without constraint and can be programmed to terminate their folding process at different intermediates. By identifying the nanopore signatures and measuring their time-dependent populations, we can “visualize” a series of kinetically important intermediates, track the kinetics of their inter-conversions, and derive the RNA pseudoknot folding pathway. This approach can potentially be developed into a single-molecule toolbox to investigate the biophysical mechanisms of RNA folding and unfolding, its interactions with ligands, and its functions. While RNA folding is critical for its function, study of this process is challenging. Here, the authors combine nanopore single-molecule manipulation with theoretical analysis to follow the folding of an RNA pseudoknot, monitoring the intermediate states and the kinetics of their interconversion.
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Affiliation(s)
- Xinyue Zhang
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dong Zhang
- Department of Physics, University of Missouri, Columbia, MO, 65211, USA
| | - Chenhan Zhao
- Department of Physics, University of Missouri, Columbia, MO, 65211, USA
| | - Kai Tian
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ruicheng Shi
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Xiao Du
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Andrew J Burcke
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Jing Wang
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA. .,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
| | - Li-Qun Gu
- Department of Bioengineering, University of Missouri, Columbia, MO, 65211, USA. .,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.
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14
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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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15
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Sun Y, Di W, Li Y, Huang W, Wang X, Qin M, Wang W, Cao Y. Mg2+-Dependent High Mechanical Anisotropy of Three-Way-Junction pRNA as Revealed by Single-Molecule Force Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yang Sun
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Weishuai Di
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Yiran Li
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Xin Wang
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
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16
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Sun Y, Di W, Li Y, Huang W, Wang X, Qin M, Wang W, Cao Y. Mg 2+ -Dependent High Mechanical Anisotropy of Three-Way-Junction pRNA as Revealed by Single-Molecule Force Spectroscopy. Angew Chem Int Ed Engl 2017. [PMID: 28631866 DOI: 10.1002/anie.201704113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mechanical anisotropy is ubiquitous in biological tissues but is hard to reproduce in synthetic biomaterials. Developing molecular building blocks with anisotropic mechanical response is the key towards engineering anisotropic biomaterials. The three-way-junction (3WJ) pRNA, derived from ϕ29 DNA packaging motor, shows strong mechanical anisotropy upon Mg2+ binding. In the absence of Mg2+ , 3WJ-pRNA is mechanically weak without noticeable mechanical anisotropy. In the presence of Mg2+ , the unfolding forces can differ by more than 4-fold along different pulling directions, ranging from about 47 pN to about 219 pN. Mechanical anisotropy of 3WJ-pRNA stems from pulling direction dependent cooperativity for the rupture of two Mg2+ binding sites, which is a novel mechanism for the mechanical anisotropy of biomacromolecules. It is anticipated that 3WJ-pRNA can be used as a key element for the construction of biomaterials with controllable mechanical anisotropy.
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Affiliation(s)
- Yang Sun
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Weishuai Di
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Yiran Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Xin Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
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