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Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T. Aptamer Therapeutics in Cancer: Current and Future. Cancers (Basel) 2018; 10:cancers10030080. [PMID: 29562664 PMCID: PMC5876655 DOI: 10.3390/cancers10030080] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022] Open
Abstract
Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small—approximately one-tenth that of monoclonal antibodies—their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules. Additionally, unlike antibodies, aptamers can be readily chemically synthesized and modified. In addition, aptamers’ long storage period and low immunogenicity are favorable properties for clinical utility. Due to their flexibility of chemical modification, aptamers are conjugated to other chemical entities including chemotherapeutic agents, siRNA, nanoparticles, and solid phase surfaces for therapeutic and diagnostic applications. However, as relatively small sized oligonucleotides, aptamers present several challenges for successful clinical translation. Their short plasma half-lives due to nuclease degradation and rapid renal excretion necessitate further structural modification of aptamers for clinical application. Since the US Food and Drug Administration (FDA) approval of the first aptamer drug, Macugen® (pegaptanib), which treats wet-age-related macular degeneration, several aptamer therapeutics for oncology have followed and shown promise in pre-clinical models as well as clinical trials. This review discusses the advantages and challenges of aptamers and introduces therapeutic aptamers under investigation and in clinical trials for cancer treatments.
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Affiliation(s)
- Yoshihiro Morita
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Macall Leslie
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Hiroyasu Kameyama
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - David E Volk
- McGovern Medical School, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Hermann Pressler, Houston, TX 77030, USA.
| | - Takemi Tanaka
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, 940 SL Young Blvd, Oklahoma City, OK 73104, USA.
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202
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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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203
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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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204
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Churkin A, Retwitzer MD, Reinharz V, Ponty Y, Waldispühl J, Barash D. Design of RNAs: comparing programs for inverse RNA folding. Brief Bioinform 2018; 19:350-358. [PMID: 28049135 PMCID: PMC6018860 DOI: 10.1093/bib/bbw120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.
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Affiliation(s)
- Alexander Churkin
- Shamoon College of Engineering and Physics Department at Ben-Gurion University, Beer-Sheva, Israel
| | | | - Vladimir Reinharz
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
- School of Computer Science, McGill University, Montréal QC, Canada
| | - Yann Ponty
- Laboratoire d’informatique, École Polytechnique, Palaiseau, France
| | | | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva, Israel
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205
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Garg A, Heinemann U. A novel form of RNA double helix based on G·U and C·A + wobble base pairing. RNA (NEW YORK, N.Y.) 2018; 24:209-218. [PMID: 29122970 PMCID: PMC5769748 DOI: 10.1261/rna.064048.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/05/2017] [Indexed: 05/27/2023]
Abstract
Wobble base pairs are critical in various physiological functions and have been linked to local structural perturbations in double-helical structures of nucleic acids. We report a 1.38-Å resolution crystal structure of an antiparallel octadecamer RNA double helix in overall A conformation, which includes a unique, central stretch of six consecutive wobble base pairs (W helix) with two G·U and four rare C·A+ wobble pairs. Four adenines within the W helix are N1-protonated and wobble-base-paired with the opposing cytosine through two regular hydrogen bonds. Combined with the two G·U pairs, the C·A+ base pairs facilitate formation of a half turn of W-helical RNA flanked by six regular Watson-Crick base pairs in standard A conformation on either side. RNA melting experiments monitored by differential scanning calorimetry, UV and circular dichroism spectroscopy demonstrate that the RNA octadecamer undergoes a pH-induced structural transition which is consistent with the presence of a duplex with C·A+ base pairs at acidic pH. Our crystal structure provides a first glimpse of an RNA double helix based entirely on wobble base pairs with possible applications in RNA or DNA nanotechnology and pH biosensors.
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Affiliation(s)
- Ankur Garg
- Crystallography, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie University Berlin, 14195 Berlin, Germany
| | - Udo Heinemann
- Crystallography, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Institute for Chemistry and Biochemistry, Freie University Berlin, 14195 Berlin, Germany
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206
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Roloff A, Nelles DA, Thompson MP, Yeo GW, Gianneschi NC. Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas. Bioconjug Chem 2018; 29:126-135. [PMID: 29286237 PMCID: PMC5993044 DOI: 10.1021/acs.bioconjchem.7b00657] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The intracellular delivery of synthetic nucleic acids represents a major challenge in biotechnology and in biomedicine. Methods to deliver short, double-stranded RNA to living cells are of particular interest because of the potential to engage the RNA interference machinery and to regulate mRNA expression. In this work, we describe novel RNA-polymer amphiphiles that assemble into spherical micellar nanoparticles with diameters of ca. 15-30 nm and efficiently enter live cells without transfection reagents. Each micelle consists of approximately 100 RNA strands forming a densely packed corona around a polymeric core. Importantly, the surface-displayed RNA remains accessible for hybridization with complementary RNA. Chemical modification of the termini of hybridized RNA strands enabled the display of small organic moieties on the outer surface of the micelle corona. We found that some of these modifications can have a tremendous impact on cellular internalization efficiencies. The display of hydrophobic dabcyl or stilbene units dramatically increased cell uptake, whereas hydrophilic neutral hydroxy or anionic phosphate residues were ineffective. Interestingly, neither of these modifications mediated noticeable uptake of free RNA oligonucleotides. We infer that their high density display on micellar nanoparticle surfaces is key for the observed effect; achieved with local effective surface concentrations in the millimolar range. We speculate that weak interactions with cell surface receptors that are amplified by the multivalent presentation of such modifications may be responsible. The installation of small molecule ligands on nanomaterial surfaces via hybridization of chemically modified oligonucleotides offers a simple and straightforward way to modulate cellular uptake of nanoparticles. Biological functionality of micellar RNA was demonstrated through the sequence-specific regulation of mRNA expression in HeLa cells.
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Affiliation(s)
- Alexander Roloff
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - David A. Nelles
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | - Matthew P. Thompson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Gene W. Yeo
- Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, California 92093, United States
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Nathan C. Gianneschi
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry, Materials Science and Engineering, Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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207
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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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208
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Mofazzal Jahromi MA, Sahandi Zangabad P, Moosavi Basri SM, Sahandi Zangabad K, Ghamarypour A, Aref AR, Karimi M, Hamblin MR. Nanomedicine and advanced technologies for burns: Preventing infection and facilitating wound healing. Adv Drug Deliv Rev 2018; 123:33-64. [PMID: 28782570 PMCID: PMC5742034 DOI: 10.1016/j.addr.2017.08.001] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/20/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
Abstract
According to the latest report from the World Health Organization, an estimated 265,000 deaths still occur every year as a direct result of burn injuries. A widespread range of these deaths induced by burn wound happens in low- and middle-income countries, where survivors face a lifetime of morbidity. Most of the deaths occur due to infections when a high percentage of the external regions of the body area is affected. Microbial nutrient availability, skin barrier disruption, and vascular supply destruction in burn injuries as well as systemic immunosuppression are important parameters that cause burns to be susceptible to infections. Topical antimicrobials and dressings are generally employed to inhibit burn infections followed by a burn wound therapy, because systemic antibiotics have problems in reaching the infected site, coupled with increasing microbial drug resistance. Nanotechnology has provided a range of molecular designed nanostructures (NS) that can be used in both therapeutic and diagnostic applications in burns. These NSs can be divided into organic and non-organic (such as polymeric nanoparticles (NPs) and silver NPs, respectively), and many have been designed to display multifunctional activity. The present review covers the physiology of skin, burn classification, burn wound pathogenesis, animal models of burn wound infection, and various topical therapeutic approaches designed to combat infection and stimulate healing. These include biological based approaches (e.g. immune-based antimicrobial molecules, therapeutic microorganisms, antimicrobial agents, etc.), antimicrobial photo- and ultrasound-therapy, as well as nanotechnology-based wound healing approaches as a revolutionizing area. Thus, we focus on organic and non-organic NSs designed to deliver growth factors to burned skin, and scaffolds, dressings, etc. for exogenous stem cells to aid skin regeneration. Eventually, recent breakthroughs and technologies with substantial potentials in tissue regeneration and skin wound therapy (that are as the basis of burn wound therapies) are briefly taken into consideration including 3D-printing, cell-imprinted substrates, nano-architectured surfaces, and novel gene-editing tools such as CRISPR-Cas.
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Affiliation(s)
- Mirza Ali Mofazzal Jahromi
- Department of Advanced Medical Sciences & Technologies, School of Medicine, Jahrom University of Medical Sciences (JUMS), Jahrom, Iran; Research Center for Noncommunicable Diseases, School of Medicine, Jahrom University of Medical Sciences (JUMS), Jahrom, Iran
| | - Parham Sahandi Zangabad
- Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Science (TUOMS), Tabriz, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Bio-Nano-Interfaces: Convergence of Sciences (BNICS), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Masoud Moosavi Basri
- Bio-Nano-Interfaces: Convergence of Sciences (BNICS), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Bioenvironmental Research Center, Sharif University of Technology, Tehran, Iran; Civil & Environmental Engineering Department, Shahid Beheshti University, Tehran, Iran
| | - Keyvan Sahandi Zangabad
- Bio-Nano-Interfaces: Convergence of Sciences (BNICS), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Department of Polymer Engineering, Sahand University of Technology, PO Box 51335-1996, Tabriz, Iran; Nanomedicine Research Association (NRA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ameneh Ghamarypour
- Bio-Nano-Interfaces: Convergence of Sciences (BNICS), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Department of Biology, Science and Research Branch, Islamic Azad university, Tehran, Iran
| | - Amir R Aref
- Department of Medical Oncology, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran; Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran, Iran; Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, USA; Department of Dermatology, Harvard Medical School, Boston, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, USA.
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209
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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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210
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Su H, Wang Y, Gu Y, Bowman L, Zhao J, Ding M. Potential applications and human biosafety of nanomaterials used in nanomedicine. J Appl Toxicol 2018; 38:3-24. [PMID: 28589558 PMCID: PMC6506719 DOI: 10.1002/jat.3476] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 12/18/2022]
Abstract
With the rapid development of nanotechnology, potential applications of nanomaterials in medicine have been widely researched in recent years. Nanomaterials themselves can be used as image agents or therapeutic drugs, and for drug and gene delivery, biological devices, nanoelectronic biosensors or molecular nanotechnology. As the composition, morphology, chemical properties, implant sites as well as potential applications become more and more complex, human biosafety of nanomaterials for clinical use has become a major concern. If nanoparticles accumulate in the human body or interact with the body molecules or chemical components, health risks may also occur. Accordingly, the unique chemical and physical properties, potential applications in medical fields, as well as human biosafety in clinical trials are reviewed in this study. Finally, this article tries to give some suggestions for future work in nanomedicine research. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Hong Su
- Department of Preventative Medicine, Zhejiang Provincial
Key Laboratory of Pathological and Physiological Technology, School of Medicine,
Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang Province 315211,
People’s Republic of China
| | - Yafei Wang
- Department of Preventative Medicine, Zhejiang Provincial
Key Laboratory of Pathological and Physiological Technology, School of Medicine,
Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang Province 315211,
People’s Republic of China
| | - Yuanliang Gu
- Department of Preventative Medicine, Zhejiang Provincial
Key Laboratory of Pathological and Physiological Technology, School of Medicine,
Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang Province 315211,
People’s Republic of China
| | - Linda Bowman
- Toxicology and Molecular Biology Branch, Health Effects
Laboratory Division, National Institute for Occupational Safety and Health,
Morgantown, WV, 26505, USA
| | - Jinshun Zhao
- Department of Preventative Medicine, Zhejiang Provincial
Key Laboratory of Pathological and Physiological Technology, School of Medicine,
Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang Province 315211,
People’s Republic of China
- Toxicology and Molecular Biology Branch, Health Effects
Laboratory Division, National Institute for Occupational Safety and Health,
Morgantown, WV, 26505, USA
| | - Min Ding
- Toxicology and Molecular Biology Branch, Health Effects
Laboratory Division, National Institute for Occupational Safety and Health,
Morgantown, WV, 26505, USA
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211
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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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212
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Kim H, Lee E, Kang YY, Song J, Mok H, Lee JB. Enzymatically Produced miR34a Nanoparticles for Enhanced Antiproliferation Activity. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hyejin Kim
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
| | - Eunju Lee
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Yoon Young Kang
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Jihyun Song
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Hyejung Mok
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 05029 Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering; University of Seoul; Seoul 02504 Republic of Korea
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213
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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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214
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Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:199-214. [PMID: 29499933 PMCID: PMC5862129 DOI: 10.1016/j.omtn.2017.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023]
Abstract
Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
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215
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Copp W, Denisov AY, Xie J, Noronha AM, Liczner C, Safaee N, Wilds CJ, Gehring K. Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA. Nucleic Acids Res 2017; 45:10321-10331. [PMID: 28973475 PMCID: PMC5737284 DOI: 10.1093/nar/gkx713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/17/2017] [Indexed: 12/17/2022] Open
Abstract
Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability.
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Affiliation(s)
- William Copp
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada.,Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada
| | - Alexey Y Denisov
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada.,Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada
| | - Jingwei Xie
- Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada.,Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Anne M Noronha
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada.,Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada
| | - Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada.,Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada
| | - Nozhat Safaee
- Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada.,Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada.,Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada
| | - Kalle Gehring
- Groupe de recherché axé sur la structure des protéines, Montréal, Québec H3G 0B1, Canada.,Department of Biochemistry, McGill University, Montréal, Québec H3G 0B1, Canada
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216
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Smith JA, Braga A, Verheyen J, Basilico S, Bandiera S, Alfaro-Cervello C, Peruzzotti-Jametti L, Shu D, Haque F, Guo P, Pluchino S. RNA Nanotherapeutics for the Amelioration of Astroglial Reactivity. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:103-121. [PMID: 29499926 PMCID: PMC5738063 DOI: 10.1016/j.omtn.2017.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022]
Abstract
In response to injuries to the CNS, astrocytes enter a reactive state known as astrogliosis, which is believed to be deleterious in some contexts. Activated astrocytes overexpress intermediate filaments including glial fibrillary acidic protein (GFAP) and vimentin (Vim), resulting in entangled cells that inhibit neurite growth and functional recovery. Reactive astrocytes also secrete inflammatory molecules such as Lipocalin 2 (Lcn2), which perpetuate reactivity and adversely affect other cells of the CNS. Herein, we report proof-of-concept use of the packaging RNA (pRNA)-derived three-way junction (3WJ) motif as a platform for the delivery of siRNAs to downregulate such reactivity-associated genes. In vitro, siRNA-3WJs induced a significant knockdown of Gfap, Vim, and Lcn2 in a model of astroglial activation, with a concomitant reduction in protein expression. Knockdown of Lcn2 also led to reduced protein secretion from reactive astroglial cells, significantly impeding the perpetuation of inflammation in otherwise quiescent astrocytes. Intralesional injection of anti-Lcn2-3WJs in mice with contusion spinal cord injury led to knockdown of Lcn2 at mRNA and protein levels in vivo. Our results provide evidence for siRNA-3WJs as a promising platform for ameliorating astroglial reactivity, with significant potential for further functionalization and adaptation for therapeutic applications in the CNS.
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Affiliation(s)
- Jayden A Smith
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK.
| | - Alice Braga
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK; Department of Diagnostics and Public Health, University of Verona, Verona 37134, Italy
| | - Jeroen Verheyen
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Silvia Basilico
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Sara Bandiera
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK; Department of Life Sciences, University of Trieste, Trieste 34127, Italy
| | - Clara Alfaro-Cervello
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Luca Peruzzotti-Jametti
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Dan Shu
- 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
| | - Farzin Haque
- 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.
| | - Stefano Pluchino
- Department of Clinical Neurosciences, Division of Stem Cell Neurobiology, Wellcome Trust-Medical Research Council Stem Cell Institute and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK.
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217
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RNA nanoparticle distribution and clearance in the eye after subconjunctival injection with and without thermosensitive hydrogels. J Control Release 2017; 270:14-22. [PMID: 29170141 DOI: 10.1016/j.jconrel.2017.11.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/28/2017] [Accepted: 11/18/2017] [Indexed: 12/15/2022]
Abstract
Thermodynamically and chemically stable RNA nanoparticles derived from the three-way junction (3WJ) of the pRNA from bacteriophage phi29 DNA packaging motor were examined previously for ocular delivery. It was reported that, after subconjunctival injection, RNA nanoparticles with tri-way shape entered the corneal cells but not the retinal cells, whereas particle with four-way shape entered both corneal and retinal cells. The present study evaluated ocular delivery of RNA nanoparticles with various shapes and sizes, and assessed the effect of thermosensitive hydrogels (poly(lactic-co-glycolic acid)-b-poly(ethylene glycol)-b-poly(lactic-co-glycolic acid); PLGA-PEG-PLGA) for increasing the retention of RNA nanoparticles in the eye. Fluorescence imaging of mouse eyes and fluorescence microscopy of dissected eye tissues from the conjunctiva, cornea, retina, and sclera were performed to determine the distribution and clearance of the nanoparticles in the eyes after subconjunctival injection in vivo. RNA nanoparticles entered the cells of the conjunctiva, cornea, retina, and sclera after subconjunctival delivery. The clearance of RNA pentagon was slower than both RNA square and triangle of the same designed edge length (10nm) in the eye, and the clearance of RNA squares of the longer edge lengths (10 and 20nm) was slower than RNA square of the shorter edge length (5nm), thus indicating that the size could affect ocular pharmacokinetics of the nanoparticles. At 24h after the injection, approximately 6-10% of the fluorescence signal from the larger nanoparticles in the study (RNA square of 20nm edge length and RNA pentagon of 10nm edge length) remained in the eye, and up to 70% of the retinal cells contained the nanoparticles. The results suggest that the larger nanoparticles were "gulped" in conjunctival, corneal, retinal, and scleral cells, similar to the behavior observed in macrophages. Additionally, the combination of RNA nanoparticles with the thermosensitive polymers increased the retention of the nanoparticles in the eye.
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218
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Geary C, Chworos A, Verzemnieks E, Voss NR, Jaeger L. Composing RNA Nanostructures from a Syntax of RNA Structural Modules. NANO LETTERS 2017; 17:7095-7101. [PMID: 29039189 PMCID: PMC6363482 DOI: 10.1021/acs.nanolett.7b03842] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Natural stable RNAs fold and assemble into complex three-dimensional architectures by relying on the hierarchical formation of intricate, recurrent networks of noncovalent tertiary interactions. These sequence-dependent networks specify RNA structural modules enabling orientational and topological control of helical struts to form larger self-folding domains. Borrowing concepts from linguistics, we defined an extended structural syntax of RNA modules for programming RNA strands to assemble into complex, responsive nanostructures under both thermodynamic and kinetic control. Based on this syntax, various RNA building blocks promote the multimolecular assembly of objects with well-defined three-dimensional shapes as well as the isothermal folding of long RNAs into complex single-stranded nanostructures during transcription. This work offers a glimpse of the limitless potential of RNA as an informational medium for designing programmable and functional nanomaterials useful for synthetic biology, nanomedicine, and nanotechnology.
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Affiliation(s)
- Cody Geary
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Arkadiusz Chworos
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Erik Verzemnieks
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Neil R. Voss
- Biological, Chemical, and Physical Sciences Department, Roosevelt University, 1400 North Roosevelt Blvd., Schaumburg, Illinois 60173, United States
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
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219
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Johnson MB, Halman JR, Satterwhite E, Zakharov AV, Bui MN, Benkato K, Goldsworthy V, Kim T, Hong E, Dobrovolskaia MA, Khisamutdinov EF, Marriott I, Afonin KA. Programmable Nucleic Acid Based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201701255. [PMID: 28922553 PMCID: PMC6258062 DOI: 10.1002/smll.201701255] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/14/2017] [Indexed: 05/13/2023]
Abstract
In the past few years, the study of therapeutic RNA nanotechnology has expanded tremendously to encompass a large group of interdisciplinary sciences. It is now evident that rationally designed programmable RNA nanostructures offer unique advantages in addressing contemporary therapeutic challenges such as distinguishing target cell types and ameliorating disease. However, to maximize the therapeutic benefit of these nanostructures, it is essential to understand the immunostimulatory aptitude of such tools and identify potential complications. This paper presents a set of 16 nanoparticle platforms that are highly configurable. These novel nucleic acid based polygonal platforms are programmed for controllable self-assembly from RNA and/or DNA strands via canonical Watson-Crick interactions. It is demonstrated that the immunostimulatory properties of these particular designs can be tuned to elicit the desired immune response or lack thereof. To advance the current understanding of the nanoparticle properties that contribute to the observed immunomodulatory activity and establish corresponding designing principles, quantitative structure-activity relationship modeling is conducted. The results demonstrate that molecular weight, together with melting temperature and half-life, strongly predicts the observed immunomodulatory activity. This framework provides the fundamental guidelines necessary for the development of a new library of nanoparticles with predictable immunomodulatory activity.
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Affiliation(s)
- M. Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Emily Satterwhite
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - My N. Bui
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Kheiria Benkato
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Taejin Kim
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Enping Hong
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | | | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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220
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Huang G, Li F, Zhao X, Ma Y, Li Y, Lin M, Jin G, Lu TJ, Genin GM, Xu F. Functional and Biomimetic Materials for Engineering of the Three-Dimensional Cell Microenvironment. Chem Rev 2017; 117:12764-12850. [PMID: 28991456 PMCID: PMC6494624 DOI: 10.1021/acs.chemrev.7b00094] [Citation(s) in RCA: 457] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cell microenvironment has emerged as a key determinant of cell behavior and function in development, physiology, and pathophysiology. The extracellular matrix (ECM) within the cell microenvironment serves not only as a structural foundation for cells but also as a source of three-dimensional (3D) biochemical and biophysical cues that trigger and regulate cell behaviors. Increasing evidence suggests that the 3D character of the microenvironment is required for development of many critical cell responses observed in vivo, fueling a surge in the development of functional and biomimetic materials for engineering the 3D cell microenvironment. Progress in the design of such materials has improved control of cell behaviors in 3D and advanced the fields of tissue regeneration, in vitro tissue models, large-scale cell differentiation, immunotherapy, and gene therapy. However, the field is still in its infancy, and discoveries about the nature of cell-microenvironment interactions continue to overturn much early progress in the field. Key challenges continue to be dissecting the roles of chemistry, structure, mechanics, and electrophysiology in the cell microenvironment, and understanding and harnessing the roles of periodicity and drift in these factors. This review encapsulates where recent advances appear to leave the ever-shifting state of the art, and it highlights areas in which substantial potential and uncertainty remain.
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Affiliation(s)
- Guoyou Huang
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
| | - Fei Li
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
- Department of Chemistry, School of Science,
Xi’an Jiaotong University, Xi’an 710049, People’s Republic
of China
| | - Xin Zhao
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
- Interdisciplinary Division of Biomedical
Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong,
People’s Republic of China
| | - Yufei Ma
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
| | - Yuhui Li
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
| | - Min Lin
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
| | - Guorui Jin
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
| | - Tian Jian Lu
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
- MOE Key Laboratory for Multifunctional Materials
and Structures, Xi’an Jiaotong University, Xi’an 710049,
People’s Republic of China
| | - Guy M. Genin
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
- Department of Mechanical Engineering &
Materials Science, Washington University in St. Louis, St. Louis 63130, MO,
USA
- NSF Science and Technology Center for
Engineering MechanoBiology, Washington University in St. Louis, St. Louis 63130,
MO, USA
| | - Feng Xu
- MOE Key Laboratory of Biomedical Information
Engineering, School of Life Science and Technology, Xi’an Jiaotong
University, Xi’an 710049, People’s Republic of China
- Bioinspired Engineering and Biomechanics Center
(BEBC), Xi’an Jiaotong University, Xi’an 710049, People’s
Republic of China
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221
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Alibakhshi MA, Halman JR, Wilson J, Aksimentiev A, Afonin KA, Wanunu M. Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores. ACS NANO 2017; 11:9701-9710. [PMID: 28841287 PMCID: PMC5959297 DOI: 10.1021/acsnano.7b04923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.
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Affiliation(s)
| | - Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - James Wilson
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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222
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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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223
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Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate. Nat Commun 2017; 8:540. [PMID: 28912471 PMCID: PMC5599586 DOI: 10.1038/s41467-017-00459-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 06/29/2017] [Indexed: 11/22/2022] Open
Abstract
Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA–protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour. Nucleic acid nanotechnology has great potential for future therapeutic applications. Here the authors build protein-driven RNA nanostructures that can function within mammalian cells and regulate the cell fate.
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224
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Sahay R, Radchenko I, Budiman AS, Baji A. Measuring the Pull-Off Force of an Individual Fiber Using a Novel Picoindenter/Scanning Electron Microscope Technique. MATERIALS (BASEL, SWITZERLAND) 2017; 10:ma10091074. [PMID: 28902168 PMCID: PMC5615728 DOI: 10.3390/ma10091074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/10/2017] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
We employed a novel picoindenter (PI)/scanning electron microscopy (SEM) technique to measure the pull-off force of an individual electrospun poly(vinylidene fluoride) (PVDF) fibers. Individual fibers were deposited over a channel in a custom-designed silicon substrate, which was then attached to a picoindenter. The picoindenter was then positioned firmly on the sample stage of the SEM. The picoindenter tip laterally pushed individual fibers to measure the force required to detach it from the surface of substrate. SEM was used to visualize and document the process. The measured pull-off force ranged between 5.8 ± 0.2 μN to ~17.8 ± 0.2 μN for individual fibers with average diameter ranging from 0.8 to 2.3 μm. Thus, this study, a first of its kind, demonstrates the use of a picoindenter to measure the pull-off force of a single micro/nanofiber.
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Affiliation(s)
- Rahul Sahay
- Engineering Product Development (EPD) Pillar, Singapore University of Technology and Design, 8 Somapah Rd, Singapore 487372, Singapore.
| | - Ihor Radchenko
- The Xtreme Materials Laboratory (XML), Singapore University of Technology and Design, 8 Somapah Rd, Singapore 487372, Singapore.
| | - Arief S Budiman
- The Xtreme Materials Laboratory (XML), Singapore University of Technology and Design, 8 Somapah Rd, Singapore 487372, Singapore.
| | - Avinash Baji
- Engineering Product Development (EPD) Pillar, Singapore University of Technology and Design, 8 Somapah Rd, Singapore 487372, Singapore.
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225
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Kiliszek A, Blaszczyk L, Kierzek R, Rypniewski W. Stabilization of RNA hairpins using non-nucleotide linkers and circularization. Nucleic Acids Res 2017; 45:e92. [PMID: 28334744 PMCID: PMC5449636 DOI: 10.1093/nar/gkx122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/09/2017] [Indexed: 12/21/2022] Open
Abstract
An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem. One method involves stilbene diether or hexaethylene glycol linkers and circularization by T4 RNA ligase. Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Leszek Blaszczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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226
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Han S, Kim H, Lee JB. Library siRNA-generating RNA nanosponges for gene silencing by complementary rolling circle transcription. Sci Rep 2017; 7:10005. [PMID: 28855687 PMCID: PMC5577100 DOI: 10.1038/s41598-017-10219-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/04/2017] [Indexed: 12/23/2022] Open
Abstract
Since the discovery of RNA interference (RNAi), small interfering RNA (siRNA) has been powerful tools for gene downregulation in biomedical applications. Despite the outstanding efficacy of siRNA, the development of a therapeutic delivery system remains a challenge owing to the instability of RNA. In this study, we describe a new method for the design of siRNA-generating nanosponges by using complementary rolling circle transcription (cRCT), a technique that requires two complementary circular DNA. The sequences of one of the circular DNA are designed to have complete complementarity to the target mRNA resulting in double stranded RNA (dsRNA) that can be digested to siRNA by cellular Dicer activity. This siRNA design, called 'library siRNA', could be universally applied to fabricate RNA nanosponges targeting any known mRNA sequence.
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Affiliation(s)
- Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul, 02504, Republic of Korea
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul, 02504, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul, 02504, Republic of Korea.
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227
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Wu X, Shaikh AB, Yu Y, Li Y, Ni S, Lu A, Zhang G. Potential Diagnostic and Therapeutic Applications of Oligonucleotide Aptamers in Breast Cancer. Int J Mol Sci 2017; 18:ijms18091851. [PMID: 28841163 PMCID: PMC5618500 DOI: 10.3390/ijms18091851] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is one of the most common causes of cancer related deaths in women. Currently, with the development of early detection, increased social awareness and kinds of treatment options, survival rate has improved in nearly every type of breast cancer patients. However, about one third patients still have increased chances of recurrence within five years and the five-year relative survival rate in patients with metastasis is less than 30%. Breast cancer contains multiple subtypes. Each subtype could cause distinct clinical outcomes and systemic interventions. Thereby, new targeted therapies are of particular importance to solve this major clinical problem. Aptamers, often termed “chemical antibodies”, are functionally similar to antibodies and have demonstrated their superiority of recognizing target with high selectivity, affinity and stability. With these intrinsic properties, aptamers have been widely studied in cancer biology and some are in clinical trials. In this review, we will firstly discuss about the global impacts and mechanisms of breast cancer, then briefly highlight applications of aptamers that have been developed for breast cancer and finally summarize various challenges in clinical translation of aptamers.
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Affiliation(s)
| | - Atik Badshah Shaikh
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yuanyuan Yu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Yongshu Li
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Shuaijian Ni
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Aiping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
| | - Ge Zhang
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China.
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228
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Schön P. Atomic force microscopy of RNA: State of the art and recent advancements. Semin Cell Dev Biol 2017; 73:209-219. [PMID: 28843977 DOI: 10.1016/j.semcdb.2017.08.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022]
Abstract
The atomic force microscope (AFM) has become a powerful tool for the visualization, probing and manipulation of RNA at the single molecule level. AFM measurements can be carried out in buffer solution in a physiological medium, which is crucial to study the structure and function of biomolecules, also allowing studying them at work. Imaging the specimen in its native state is a great advantage compared to other high resolution methods such as electron microscopy and X-ray diffraction. There is no need to stain, freeze or crystallize biological samples. Moreover, compared to NMR spectroscopy for instance, for AFM studies the size of the biomolecules is not limiting. Consequently the AFM allows one also to investigate larger RNA molecules. In particular, structural studies of nucleic acids and assemblies thereof, have been carried out by AFM routinely including ssRNA, dsRNA and nucleoprotein complexes thereof, as well as RNA aggregates and 2D RNA assemblies. These are becoming increasingly important as novel unique building blocks in the emerging field of RNA nanotechnology. In particular by AFM unique information can be obtained on these RNA based assemblies. Moreover, the AFM is of fundamental relevance to study biological relevant RNA interactions and dynamics. In this short review a brief overview will be given on structural studies that have been done related to AFM topographic imaging of RNA, RNA assemblies and aggregates. Finally, an overview on AFM beyond imaging will be provided. This includes force spectroscopy of RNA under physiological conditions in aqueous buffer to probe RNA interaction with proteins and ligands as well as other AFM tip based RNA probing. Important applications include the detection and quantification of RNA in biological samples. A selection of recent highlights and breakthroughs will be provided related to structural and functional studies by AFM. The main intention of this short review to provide the reader with a flavor of what AFM is able to contribute to RNA research and engineering.
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Affiliation(s)
- Peter Schön
- NanoBioInterface Research Group, Research Center Design and Technology, Saxion University of Applied Sciences, 7500 KB Enschede, The Netherlands; Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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229
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Huang BT, Lai WY, Chang YC, Wang JW, Yeh SD, Lin EPY, Yang PC. A CTLA-4 Antagonizing DNA Aptamer with Antitumor Effect. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:520-528. [PMID: 28918052 PMCID: PMC5573796 DOI: 10.1016/j.omtn.2017.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 01/07/2023]
Abstract
The successful translation of cytotoxic T lymphocyte antigen-4 (CTLA-4) blockade has revolutionized the concept of cancer immunotherapy. Although monoclonal antibody therapeutics remain the mainstream in clinical practice, aptamers are synthetic oligonucleotides that encompass antibody-mimicking functions. Here, we report a novel high-affinity CTLA-4-antagonizing DNA aptamer (dissociation constant, 11.84 nM), aptCTLA-4, which was identified by cell-based SELEX and high-throughput sequencing. aptCTLA-4 is relatively stable in serum, promotes lymphocyte proliferation, and inhibits tumor growth in cell and animal models. Our study demonstrates the developmental pipeline of a functional CTLA-4-targeting aptamer and suggests a translational potential for aptCTLA-4.
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Affiliation(s)
- Bo-Tsang Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Yun Lai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Chung Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jen-Wei Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shauh-Der Yeh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Department of Urology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Emily Pei-Ying Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; National Center of Excellence for Clinical Trials and Research Center, Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.
| | - Pan-Chyr Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.
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230
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Kim H, Jeong J, Kim D, Kwak G, Kim SH, Lee JB. Bubbled RNA-Based Cargo for Boosting RNA Interference. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1600523. [PMID: 28852615 PMCID: PMC5566230 DOI: 10.1002/advs.201600523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/17/2017] [Indexed: 05/23/2023]
Abstract
As ribonucleic acid (RNA) nanotechnology has advanced, it has been applied widely in RNA-based therapeutics. Among the range of approaches, enzymatically synthesized RNA structures for inducing RNA interference in cancer cells have potential for silencing genes in a target-specific manner. On the other hand, the efficiency of gene silencing needs to be improved to utilize the RNA-based system for RNAi therapeutics. This paper introduces a new approach for efficient generation of siRNA from bubbled RNA-based cargo (BRC). The presence of bubbles in between to avoid nonfunctional short dsRNAs allows the RNA-based cargoes to contain multiple Dicer-cleavage sites to release the functional siRNAs when introduced to cells. BRCs can be synthesized easily in a one-pot process and be purified by simple centrifugation. Furthermore, efficient target gene silencing by the bubbled structure is confirmed both in vitro and in vivo. Therefore, this bubbled RNA cargo system can be utilized for target-specific RNAi therapeutics with high efficiency in the generation of functional siRNAs in the target cells.
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Affiliation(s)
- Hyejin Kim
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
| | - Jaepil Jeong
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
| | - Dajeong Kim
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
| | - Gijung Kwak
- KU‐KIST Graduate School of Converging Science and TechnologyKorea University145 Anam‐roSeongbuk‐gu, Seoul02841Republic of Korea
- Center for TheragnosisBiomedical Research InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
| | - Sun Hwa Kim
- Center for TheragnosisBiomedical Research InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
| | - Jong Bum Lee
- Department of Chemical EngineeringUniversity of Seoul163 SeoulsiripdaeroDongdaemun‐gu Seoul02504Republic of Korea
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231
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Nuthanakanti A, Srivatsan SG. Surface-Tuned and Metal-Ion-Responsive Supramolecular Gels Based on Nucleolipids. ACS APPLIED MATERIALS & INTERFACES 2017; 9:22864-22874. [PMID: 28614659 DOI: 10.1021/acsami.7b06037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Supramolecular synthons based on nucleic acid components, nucleobases and nucleosides, and their derivatives have been highly useful in constructing wide varieties of nanoarchitectures. While most of the design strategies have focused on developing biocompatible delivery vehicles, the potential of nucleoside hybrids in assembling smart materials with tunable and sensing properties, though challenging, is gaining significant attention. Here, we describe the development of novel functional materials with surface tunability and metal-ion responsiveness by using simple nucleolipid supramolecular synthons derived by attaching various fatty acids to the 3'-O or 3',5'-O positions of the sugar residue of thymidine nucleoside. 3',5'-O-Difatty acid-substituted thymidines formed typical organogels in pure organic solvents, whereas, 3'-O-monofatty acid-substituted thymidine nucleolipids formed water-induced gels. A detailed morphological and structural analysis using microscopy, single-crystal and powder X-ray diffraction, and NMR techniques clearly revealed the molecular interactions invoked by nucleobase, sugar, fatty acid chain, and water in setting up the path for hierarchical self-assembly and gelation of thymidine nucleolipids. Interestingly, the surface property of the xerogel film fabricated using 3'-O-monosubstituted nucleolipid gels could be switched from highly hydrophobic to hydrophilic and vice versa depending on the nature of the organic solvent-water mixture used in the gelation process. On the contrary, the gelation process of disubstituted thymidine nucleolipids was highly sensitive to the presence of Hg2+ ions as the metal ion formed a T-Hg-T base pair, thereby disrupting the H-bonding interactions that favored the gelation. Taken together, straightforward synthesis and modification-dependent gelation behavior, surface tunability, and metal-ion responsiveness underscore the potential of these supramolecular nucleolipid synthons in constructing novel functional materials.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) , Pune Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) , Pune Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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232
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Bao L, Zhang X, Shi YZ, Wu YY, Tan ZJ. Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling. Biophys J 2017; 112:1094-1104. [PMID: 28355538 DOI: 10.1016/j.bpj.2017.02.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 01/16/2023] Open
Abstract
The flexibility of double-stranded (ds) RNA and dsDNA is crucial for their biological functions. Recent experiments have shown that the flexibility of dsRNA and dsDNA can be distinctively different in the aspects of stretching and twist-stretch coupling. Although various studies have been performed to understand the flexibility of dsRNA and dsDNA, there is still a lack of deep understanding of the distinctive differences in the flexibility of dsRNA and dsDNA helices as pertains to their stretching and twist-stretch coupling. In this work, we have explored the relative flexibility in stretching and twist-stretch coupling between dsRNA and dsDNA by all-atom molecular dynamics simulations. The calculated stretch modulus and twist-stretch coupling are in good accordance with the existing experiments. Our analyses show that the differences in stretching and twist-stretch coupling between dsRNA and dsDNA helices are mainly attributed to their different (A- and B-form) helical structures. Stronger basepair inclination and slide in dsRNA is responsible for the apparently weaker stretching rigidity versus that of dsDNA, and the opposite twist-stretch coupling for dsRNA and dsDNA is also attributed to the stronger basepair inclination in dsRNA than in dsDNA. Our calculated macroscopic elastic parameters and microscopic analyses are tested and validated by different force fields for both dsRNA and dsDNA.
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Affiliation(s)
- Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China; College of Physical Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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233
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Sun W, Song W, Guo X, Wang Z. Ultrasensitive detection of nucleic acids and proteins using quartz crystal microbalance and surface plasmon resonance sensors based on target-triggering multiple signal amplification strategy. Anal Chim Acta 2017; 978:42-47. [DOI: 10.1016/j.aca.2017.04.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 01/12/2023]
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234
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Dršata T, Réblová K, Beššeová I, Šponer J, Lankaš F. rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif. J Chem Theory Comput 2017; 13:3359-3371. [DOI: 10.1021/acs.jctc.7b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomáš Dršata
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC—Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivana Beššeová
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- CEITEC—Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Filip Lankaš
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- Laboratory
of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
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235
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Halman J, Satterwhite E, Smollett J, Bindewald E, Parlea L, Viard M, Zakrevsky P, Kasprzak WK, Afonin KA, Shapiro BA. Triggerable RNA nanodevices. RNA & DISEASE 2017; 4:e1349. [PMID: 34307841 PMCID: PMC8301261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The targeted and conditional activation of pharmaceuticals is an increasingly important feature in modern personalized medicine. Nucleic acid nanoparticles show tremendous potential in this exploit due to their programmability and biocompatibility. Among the most powerful nucleic acid specific treatments is RNA interference-based therapeutics. RNA interference is a naturally occurring phenomenon in which specific genes are effectively silenced. Recently we have developed two different strategies based on customized multivalent nucleic acid nanoparticles with the ability to conditionally activate RNA interference in diseased cells as well as elicit detectable fluorescent responses.[1,2] These novel technologies can be further utilized for the simultaneous delivery and conditional intracellular activation of multiple therapeutic and biosensing functions to combat various diseases.
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Affiliation(s)
- Justin Halman
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte 28223, North Carolina, USA
| | - Emily Satterwhite
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte 28223, North Carolina, USA
| | - Jaclyn Smollett
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte 28223, North Carolina, USA
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
| | - Lorena Parlea
- Gene Regulation Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
| | - Mathias Viard
- Gene Regulation Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
- Basic Science Program, Leidos Biomedical Research, Inc., Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
| | - Paul Zakrevsky
- Gene Regulation Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
| | - Kirill A. Afonin
- Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte 28223, North Carolina, USA
| | - Bruce A. Shapiro
- Gene Regulation Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick 21702, Maryland, USA
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236
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Nagamune T. Biomolecular engineering for nanobio/bionanotechnology. NANO CONVERGENCE 2017; 4:9. [PMID: 28491487 PMCID: PMC5401866 DOI: 10.1186/s40580-017-0103-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/29/2017] [Indexed: 05/02/2023]
Abstract
Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.
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Affiliation(s)
- Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
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237
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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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238
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Onizuka K, Hazemi ME, Thomas JM, Monteleone LR, Yamada K, Imoto S, Beal PA, Nagatsugi F. Synthesis of native-like crosslinked duplex RNA and study of its properties. Bioorg Med Chem 2017; 25:2191-2199. [PMID: 28268052 PMCID: PMC5969911 DOI: 10.1016/j.bmc.2017.02.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 02/08/2023]
Abstract
A variety of enzymes have been found to interact with double-stranded RNA (dsRNA) in order to carry out its functions. We have endeavored to prepare the covalently crosslinked native-like duplex RNA, which could be useful for biochemical studies and RNA nanotechnology. In this study, the interstrand covalently linked duplex RNA was formed by a crosslinking reaction between vinylpurine (VP) and the target cytosine or uracil in RNA. We measured melting temperatures and CD spectra to identify the properties of the VP crosslinked duplex RNA. The crosslinking formation increased the thermodynamic stability without disturbing the natural conformation of dsRNA. In addition, a competitive binding experiment with the duplex RNA binding enzyme, ADAR2, showed the crosslinked dsRNA bound the protein with nearly the same binding affinity as the natural dsRNA, confirming that it has finely preserved the natural traits of duplex RNA.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Madoka E Hazemi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Justin M Thomas
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Leanna R Monteleone
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Shuhei Imoto
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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239
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Synthesizing topological structures containing RNA. Nat Commun 2017; 8:14936. [PMID: 28361879 PMCID: PMC5381007 DOI: 10.1038/ncomms14936] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/15/2017] [Indexed: 12/27/2022] Open
Abstract
Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontrivial RNA molecules. Here we show that topological structures containing single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by configuring RNA-DNA hybrid four-way junctions or by template-directed synthesis with a single-stranded DNA (ssDNA) topological structure. By using a constructed ssRNA knot as a highly sensitive topological probe, we find that Escherichia coli DNA topoisomerase I has low RNA topoisomerase activity and that the R173A point mutation abolishes the unknotting activity for ssRNA, but not for ssDNA. Furthermore, we discover the topological inhibition of reverse transcription (RT) and obtain different RT-PCR patterns for an ssRNA knot and circle of the same sequence.
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240
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Lee JH, Ku SH, Kim MJ, Lee SJ, Kim HC, Kim K, Kim SH, Kwon IC. Rolling circle transcription-based polymeric siRNA nanoparticles for tumor-targeted delivery. J Control Release 2017; 263:29-38. [PMID: 28373128 DOI: 10.1016/j.jconrel.2017.03.390] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/09/2017] [Accepted: 03/26/2017] [Indexed: 02/06/2023]
Abstract
RNA, one of the major biological macromolecules, has been considered as an attractive building material for bottom-up fabrication of nanostructures in the past few decades due to advancements in RNA biology, RNA chemistry and RNA nanotechnology. Most recently, an isothermal enzymatic nucleic acid amplification method termed rolling circle transcription (RCT), which achieves a large-scale synthesis of RNA nanostructures, has emerged as one of fascinating techniques for RNAi-based therapies. Herein, we proposed a newly designed RCT method for synthesis of polymeric siRNA nanoflower, referred to 'RCT and annealing-generated polymeric siRNA (RAPSI)': (1) Amplification of the antisense strand of siRNA via RCT process and (2) annealing of chimeric sense strand containing 3'-terminal DNA nucleotides that provide enzyme cleavage sites. To verify its potentials in RNAi-based cancer therapy, the newly designed RAPSI nanoflower was further complexed with glycol chitosan (GC) derivatives, and systemically delivered to PC-3 xenograft tumors. The resultant RAPSI nanoparticles exhibited the improved particle stability against polyanion competition or nuclease attack. When the RAPSI nanoparticles reached to the cytoplasmic region, active mono siRNA was liberated and significantly down-regulated the expression of target VEGF gene in PC-3 cells. Excellent tumor-homing efficacy and anti-tumor effects of the RAPSI nanoparticles were further demonstrated. Overall, the proposed RCT-based polymeric siRNA nanoflower formulation can provide a new platform technology that allows further functional modifications via an advanced annealing method for systemic cancer RNAi therapy.
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Affiliation(s)
- Jae Hyeop Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Sook Hee Ku
- Technology Convergence R&D Group, Korea Institute of Industrial Technology, Daegu, Republic of Korea
| | - Min Ju Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
| | - So Jin Lee
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Hyun Cheol Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Kwangmeyung Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Sun Hwa Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.
| | - Ick Chan Kwon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea.
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241
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Pelaz B, Alexiou C, Alvarez-Puebla RA, Alves F, Andrews AM, Ashraf S, Balogh LP, Ballerini L, Bestetti A, Brendel C, Bosi S, Carril M, Chan WCW, Chen C, Chen X, Chen X, Cheng Z, Cui D, Du J, Dullin C, Escudero A, Feliu N, Gao M, George M, Gogotsi Y, Grünweller A, Gu Z, Halas NJ, Hampp N, Hartmann RK, Hersam MC, Hunziker P, Jian J, Jiang X, Jungebluth P, Kadhiresan P, Kataoka K, Khademhosseini A, Kopeček J, Kotov NA, Krug HF, Lee DS, Lehr CM, Leong KW, Liang XJ, Ling Lim M, Liz-Marzán LM, Ma X, Macchiarini P, Meng H, Möhwald H, Mulvaney P, Nel AE, Nie S, Nordlander P, Okano T, Oliveira J, Park TH, Penner RM, Prato M, Puntes V, Rotello VM, Samarakoon A, Schaak RE, Shen Y, Sjöqvist S, Skirtach AG, Soliman MG, Stevens MM, Sung HW, Tang BZ, Tietze R, Udugama BN, VanEpps JS, Weil T, Weiss PS, Willner I, Wu Y, Yang L, Yue Z, Zhang Q, Zhang Q, Zhang XE, Zhao Y, Zhou X, Parak WJ. Diverse Applications of Nanomedicine. ACS NANO 2017; 11:2313-2381. [PMID: 28290206 PMCID: PMC5371978 DOI: 10.1021/acsnano.6b06040] [Citation(s) in RCA: 748] [Impact Index Per Article: 106.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 04/14/2023]
Abstract
The design and use of materials in the nanoscale size range for addressing medical and health-related issues continues to receive increasing interest. Research in nanomedicine spans a multitude of areas, including drug delivery, vaccine development, antibacterial, diagnosis and imaging tools, wearable devices, implants, high-throughput screening platforms, etc. using biological, nonbiological, biomimetic, or hybrid materials. Many of these developments are starting to be translated into viable clinical products. Here, we provide an overview of recent developments in nanomedicine and highlight the current challenges and upcoming opportunities for the field and translation to the clinic.
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Affiliation(s)
- Beatriz Pelaz
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Christoph Alexiou
- ENT-Department, Section of Experimental Oncology & Nanomedicine
(SEON), Else Kröner-Fresenius-Stiftung-Professorship for Nanomedicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Ramon A. Alvarez-Puebla
- Department of Physical Chemistry, Universitat Rovira I Virgili, 43007 Tarragona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Frauke Alves
- Department of Haematology and Medical Oncology, Department of Diagnostic
and Interventional Radiology, University
Medical Center Göttingen, 37075 Göttingen Germany
- Department of Molecular Biology of Neuronal Signals, Max-Planck-Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Anne M. Andrews
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Sumaira Ashraf
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Lajos P. Balogh
- AA Nanomedicine & Nanotechnology Consultants, North Andover, Massachusetts 01845, United States
| | - Laura Ballerini
- International School for Advanced Studies (SISSA/ISAS), 34136 Trieste, Italy
| | - Alessandra Bestetti
- School of Chemistry & Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cornelia Brendel
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Susanna Bosi
- Department of Chemical
and Pharmaceutical Sciences, University
of Trieste, 34127 Trieste, Italy
| | - Monica Carril
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
| | - Warren C. W. Chan
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Xiaodong Chen
- School of Materials
Science and Engineering, Nanyang Technological
University, Singapore 639798
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine,
National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhen Cheng
- Molecular
Imaging Program at Stanford and Bio-X Program, Canary Center at Stanford
for Cancer Early Detection, Stanford University, Stanford, California 94305, United States
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument
Science and Engineering, School of Electronic Information and Electronical
Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Jianzhong Du
- Department of Polymeric Materials, School of Materials
Science and Engineering, Tongji University, Shanghai, China
| | - Christian Dullin
- Department of Haematology and Medical Oncology, Department of Diagnostic
and Interventional Radiology, University
Medical Center Göttingen, 37075 Göttingen Germany
| | - Alberto Escudero
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
- Instituto
de Ciencia de Materiales de Sevilla. CSIC, Universidad de Sevilla, 41092 Seville, Spain
| | - Neus Feliu
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Mingyuan Gao
- Institute of Chemistry, Chinese
Academy of Sciences, 100190 Beijing, China
| | | | - Yury Gogotsi
- Department of Materials Science and Engineering and A.J. Drexel Nanomaterials
Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Arnold Grünweller
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Zhongwei Gu
- College of Polymer Science and Engineering, Sichuan University, 610000 Chengdu, China
| | - Naomi J. Halas
- Departments of Physics and Astronomy, Rice
University, Houston, Texas 77005, United
States
| | - Norbert Hampp
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Roland K. Hartmann
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Mark C. Hersam
- Departments of Materials Science and Engineering, Chemistry,
and Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Patrick Hunziker
- University Hospital, 4056 Basel, Switzerland
- CLINAM,
European Foundation for Clinical Nanomedicine, 4058 Basel, Switzerland
| | - Ji Jian
- Department of Polymer Science and Engineering and Center for
Bionanoengineering and Department of Chemical and Biological Engineering, Zhejiang University, 310027 Hangzhou, China
| | - Xingyu Jiang
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Philipp Jungebluth
- Thoraxklinik Heidelberg, Universitätsklinikum
Heidelberg, 69120 Heidelberg, Germany
| | - Pranav Kadhiresan
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | | | | | - Jindřich Kopeček
- Biomedical Polymers Laboratory, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nicholas A. Kotov
- Emergency Medicine, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Harald F. Krug
- EMPA, Federal Institute for Materials
Science and Technology, CH-9014 St. Gallen, Switzerland
| | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical
Sciences and School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
| | - Claus-Michael Lehr
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- HIPS - Helmhotz Institute for Pharmaceutical Research Saarland, Helmholtz-Center for Infection Research, 66123 Saarbrücken, Germany
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York City, New York 10027, United States
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS), 100190 Beijing, China
| | - Mei Ling Lim
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Luis M. Liz-Marzán
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
- Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine, Ciber-BBN, 20014 Donostia - San Sebastián, Spain
| | - Xiaowei Ma
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS), 100190 Beijing, China
| | - Paolo Macchiarini
- Laboratory of Bioengineering Regenerative Medicine (BioReM), Kazan Federal University, 420008 Kazan, Russia
| | - Huan Meng
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Helmuth Möhwald
- Department of Interfaces, Max-Planck
Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Paul Mulvaney
- School of Chemistry & Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andre E. Nel
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Shuming Nie
- Emory University, Atlanta, Georgia 30322, United States
| | - Peter Nordlander
- Departments of Physics and Astronomy, Rice
University, Houston, Texas 77005, United
States
| | - Teruo Okano
- Tokyo Women’s Medical University, Tokyo 162-8666, Japan
| | | | - Tai Hyun Park
- Department of Molecular Medicine and Biopharmaceutical
Sciences and School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Advanced Institutes of Convergence Technology, Suwon, South Korea
| | - Reginald M. Penner
- Department of Chemistry, University of
California, Irvine, California 92697, United States
| | - Maurizio Prato
- Department of Chemical
and Pharmaceutical Sciences, University
of Trieste, 34127 Trieste, Italy
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
| | - Victor Puntes
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Institut Català de Nanotecnologia, UAB, 08193 Barcelona, Spain
- Vall d’Hebron University Hospital
Institute of Research, 08035 Barcelona, Spain
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Amila Samarakoon
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Raymond E. Schaak
- Department of Chemistry, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Youqing Shen
- Department of Polymer Science and Engineering and Center for
Bionanoengineering and Department of Chemical and Biological Engineering, Zhejiang University, 310027 Hangzhou, China
| | - Sebastian Sjöqvist
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Andre G. Skirtach
- Department of Interfaces, Max-Planck
Institute of Colloids and Interfaces, 14476 Potsdam, Germany
- Department of Molecular Biotechnology, University of Ghent, B-9000 Ghent, Belgium
| | - Mahmoud G. Soliman
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Molly M. Stevens
- Department of Materials,
Department of Bioengineering, Institute for Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hsing-Wen Sung
- Department of Chemical Engineering and Institute of Biomedical
Engineering, National Tsing Hua University, Hsinchu City, Taiwan,
ROC 300
| | - Ben Zhong Tang
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Hong Kong, China
| | - Rainer Tietze
- ENT-Department, Section of Experimental Oncology & Nanomedicine
(SEON), Else Kröner-Fresenius-Stiftung-Professorship for Nanomedicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Buddhisha N. Udugama
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - J. Scott VanEpps
- Emergency Medicine, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Tanja Weil
- Institut für
Organische Chemie, Universität Ulm, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
| | - Paul S. Weiss
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Itamar Willner
- Institute of Chemistry, The Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Yuzhou Wu
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | | | - Zhao Yue
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Qian Zhang
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Qiang Zhang
- School of Pharmaceutical Science, Peking University, 100191 Beijing, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules,
CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Yuliang Zhao
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wolfgang J. Parak
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
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242
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Bottai G, Truffi M, Corsi F, Santarpia L. Progress in nonviral gene therapy for breast cancer and what comes next? Expert Opin Biol Ther 2017; 17:595-611. [DOI: 10.1080/14712598.2017.1305351] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Giulia Bottai
- Oncology Experimental Therapeutics, IRCCS Clinical and Research Institute Humanitas, Rozzano (Milan), Italy
| | - Marta Truffi
- Laboratory of Nanomedicine, Department of Biomedical and Clinical Sciences University of Milan, “Luigi Sacco” Hospital, Milano, Italy
| | - Fabio Corsi
- Laboratory of Nanomedicine, Surgery Division, Department of Biomedical and Clinical Sciences University of Milan, “Luigi Sacco” Hospital, Milan, Italy
| | - Libero Santarpia
- Oncology Experimental Therapeutics, IRCCS Clinical and Research Institute Humanitas, Rozzano (Milan), Italy
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243
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Rajendran A, Nakata E, Nakano S, Morii T. Nucleic-Acid-Templated Enzyme Cascades. Chembiochem 2017; 18:696-716. [DOI: 10.1002/cbic.201600703] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Indexed: 11/08/2022]
Affiliation(s)
| | - Eiji Nakata
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Shun Nakano
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
| | - Takashi Morii
- Institute of Advanced Energy; Kyoto University; Uji Kyoto 611-0011 Japan
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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246
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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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247
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Halman JR, Satterwhite E, Roark B, Chandler M, Viard M, Ivanina A, Bindewald E, Kasprzak WK, Panigaj M, Bui MN, Lu JS, Miller J, Khisamutdinov EF, Shapiro BA, Dobrovolskaia MA, Afonin KA. Functionally-interdependent shape-switching nanoparticles with controllable properties. Nucleic Acids Res 2017; 45:2210-2220. [PMID: 28108656 PMCID: PMC5389727 DOI: 10.1093/nar/gkx008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/22/2016] [Accepted: 01/03/2017] [Indexed: 12/18/2022] Open
Abstract
We introduce a new concept that utilizes cognate nucleic acid nanoparticles which are fully complementary and functionally-interdependent to each other. In the described approach, the physical interaction between sets of designed nanoparticles initiates a rapid isothermal shape change which triggers the activation of multiple functionalities and biological pathways including transcription, energy transfer, functional aptamers and RNA interference. The individual nanoparticles are not active and have controllable kinetics of re-association and fine-tunable chemical and thermodynamic stabilities. Computational algorithms were developed to accurately predict melting temperatures of nanoparticles of various compositions and trace the process of their re-association in silico. Additionally, tunable immunostimulatory properties of described nanoparticles suggest that the particles that do not induce pro-inflammatory cytokines and high levels of interferons can be used as scaffolds to carry therapeutic oligonucleotides, while particles with strong interferon and mild pro-inflammatory cytokine induction may qualify as vaccine adjuvants. The presented concept provides a simple, cost-effective and straightforward model for the development of combinatorial regulation of biological processes in nucleic acid nanotechnology.
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Affiliation(s)
- Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Emily Satterwhite
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Brandon Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Mathias Viard
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna Ivanina
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, 041 54, Slovak Republic
| | - My N. Bui
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Jacob S. Lu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Johann Miller
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | | | - Bruce A. Shapiro
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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248
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Guo Y, Li S, Wang Y, Zhang S. Diagnosis–Therapy Integrative Systems Based on Magnetic RNA Nanoflowers for Co-drug Delivery and Targeted Therapy. Anal Chem 2017; 89:2267-2274. [DOI: 10.1021/acs.analchem.6b03346] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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
| | - 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
| | - Yujie Wang
- 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, Shandong Normal University, Jinan 250014, P. R. China
| | - Shusheng Zhang
- 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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249
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Antimisiaris S, Mourtas S, Papadia K. Targeted si-RNA with liposomes and exosomes (extracellular vesicles): How to unlock the potential. Int J Pharm 2017; 525:293-312. [PMID: 28163221 DOI: 10.1016/j.ijpharm.2017.01.056] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
Abstract
The concept of RNA interference therapeutics has been initiated 18 years ago, and the main bottleneck for translation of the technology into therapeutic products remains the delivery of functional RNA molecules into the cell cytoplasm. In the present review article after an introduction about the theoretical basis of RNAi therapy and the main challenges encountered for its realization, an overview of the different types of delivery systems or carriers, used as potential systems to overcome RNAi delivery issues, will be provided. Characteristic examples or results obtained with the most promising systems will be discussed. Focus will be given mostly on the applications of liposomes or other types of lipid carriers, such as exosomes, towards improved delivery of RNAi to therapeutic targets. Finally the approach of integrating the advantages of these two vesicular systems, liposomes and exosomes, as a potential solution to realize RNAi therapy, will be proposed.
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Affiliation(s)
- Sophia Antimisiaris
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, Rio 26504, Greece; Institute of Chemical Engineering, FORTH/ICE-HT, Rio 26504, Greece.
| | - Spyridon Mourtas
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, Rio 26504, Greece
| | - Konstantina Papadia
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, Rio 26504, Greece
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250
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Takeuchi Y, Endo M, Suzuki Y, Hidaka K, Durand G, Dausse E, Toulmé JJ, Sugiyama H. Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure. Biomater Sci 2017; 4:130-5. [PMID: 26438892 DOI: 10.1039/c5bm00274e] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.
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Affiliation(s)
- Yosuke Takeuchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Yuki Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Guillaume Durand
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Jean-Jacques Toulmé
- ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
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