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Shanaa OA, Rumyantsev A, Sambuk E, Padkina M. In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects. Molecules 2021; 26:molecules26051422. [PMID: 33800717 PMCID: PMC7961669 DOI: 10.3390/molecules26051422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.
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Affiliation(s)
- Ousama Al Shanaa
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Atomic Energy Commission of Syria, Damascus P.O.B 6091, Syria
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
| | - Andrey Rumyantsev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Elena Sambuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Marina Padkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
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102
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Ni S, Zhuo Z, Pan Y, Yu Y, Li F, Liu J, Wang L, Wu X, Li D, Wan Y, Zhang L, Yang Z, Zhang BT, Lu A, Zhang G. Recent Progress in Aptamer Discoveries and Modifications for Therapeutic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9500-9519. [PMID: 32603135 DOI: 10.1021/acsami.0c05750] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are oligonucleotide sequences with a length of about 25-80 bases which have abilities to bind to specific target molecules that rival those of monoclonal antibodies. They are attracting great attention in diverse clinical translations on account of their various advantages, including prolonged storage life, little batch-to-batch differences, very low immunogenicity, and feasibility of chemical modifications for enhancing stability, prolonging the half-life in serum, and targeted delivery. In this Review, we demonstrate the emerging aptamer discovery technologies in developing advanced techniques for producing aptamers with high performance consistently and efficiently as well as requiring less cost and resources but offering a great chance of success. Further, the diverse modifications of aptamers for therapeutic applications including therapeutic agents, aptamer-drug conjugates, and targeted delivery materials are comprehensively summarized.
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Affiliation(s)
- Shuaijian Ni
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanyuan Yu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Fangfei Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Jin Liu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Luyao Wang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Xiaoqiu Wu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Dijie Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Youyang Wan
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Aiping Lu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Ge Zhang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
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103
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Dong H, Zhang W, Zhou S, Huang J, Wang P. Engineering bioscaffolds for enzyme assembly. Biotechnol Adv 2021; 53:107721. [PMID: 33631185 DOI: 10.1016/j.biotechadv.2021.107721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/04/2021] [Accepted: 02/14/2021] [Indexed: 12/27/2022]
Abstract
With the demand for green, safe, and continuous biocatalysis, bioscaffolds, compared with synthetic scaffolds, have become a desirable candidate for constructing enzyme assemblages because of their biocompatibility and regenerability. Biocompatibility makes bioscaffolds more suitable for safe and green production, especially in food processing, production of bioactive agents, and diagnosis. The regenerability can enable the engineered biocatalysts regenerate through simple self-proliferation without complex re-modification, which is attractive for continuous biocatalytic processes. In view of the unique biocompatibility and regenerability of bioscaffolds, they can be classified into non-living (polysaccharide, nucleic acid, and protein) and living (virus, bacteria, fungi, spore, and biofilm) bioscaffolds, which can fully satisfy these two unique properties, respectively. Enzymes assembled onto non-living bioscaffolds are based on single or complex components, while enzymes assembled onto living bioscaffolds are based on living bodies. In terms of their unique biocompatibility and regenerability, this review mainly covers the current advances in the research and application of non-living and living bioscaffolds with focus on engineering strategies for enzyme assembly. Finally, the future development of bioscaffolds for enzyme assembly is also discussed. Hopefully, this review will attract the interest of researchers in various fields and empower the development of biocatalysis, biomedicine, environmental remediation, therapy, and diagnosis.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN 55108, USA.
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104
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Abstract
Novel RNA motif design is of great practical importance for technology and medicine. Increasingly, computational design plays an important role in such efforts. Our coarse-grained RAG (RNA-As-Graphs) framework offers strategies for enumerating the universe of RNA 2D folds, selecting "RNA-like" candidates for design, and determining sequences that fold onto these candidates. In RAG, RNA secondary structures are represented as tree or dual graphs. Graphs with known RNA structures are called "existing", and the others are labeled "hypothetical". By using simplified features for RNA graphs, we have clustered the hypothetical graphs into "RNA-like" and "non-RNA-like" groups and proposed RNA-like graphs as candidates for design. Here, we propose a new way of designing graph features by using Fiedler vectors. The new features reflect graph shapes better, and they lead to a more clustered organization of existing graphs. We show significant increases in K-means clustering accuracy by using the new features (e.g., up to 95% and 98% accuracy for tree and dual graphs, respectively). In addition, we propose a scoring model for top graph candidate selection. This scoring model allows users to set a threshold for candidates, and it incorporates weighing of existing graphs based on their corresponding number of known RNAs. We include a list of top scored RNA-like candidates, which we hope will stimulate future novel RNA design.
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Affiliation(s)
- Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Tamar Schlick
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P. R. China
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105
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Mousazadeh H, Pilehvar-Soltanahmadi Y, Dadashpour M, Zarghami N. Cyclodextrin based natural nanostructured carbohydrate polymers as effective non-viral siRNA delivery systems for cancer gene therapy. J Control Release 2021; 330:1046-1070. [DOI: 10.1016/j.jconrel.2020.11.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
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106
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Zhang W, Guan X, Tang J. The long non-coding RNA landscape in triple-negative breast cancer. Cell Prolif 2021; 54:e12966. [PMID: 33314471 PMCID: PMC7848969 DOI: 10.1111/cpr.12966] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a type of breast cancer that has a higher risk of distant recurrence and metastasis, leading to a relatively aggressive biological behaviour and poor outcome. So far, the clinical management of TNBC is challenging because of its heterogeneity and paucity of specific targeted therapy. Recently, various studies have identified a lot of differently expressed long non-coding RNAs (lncRNAs) in TNBC. Those lncRNAs have been reported to play important roles in the multistep process of TNBC tumorigenesis. Here, we review the biological characteristics of lncRNAs, and present the current state of knowledge concerning the expression, function and regulation of lncRNAs in TNBC. Accumulating studies explored the potential lncRNAs-based therapeutics in TNBC, including the techniques of genetic modification using antisense oligonucleotides, locked nucleic acid and RNA nanotechnology. In current review, we also discuss the future prospects of studies about lncRNAs in TNBC and development of lncRNA-based strategies for clinical TNBC patients.
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Affiliation(s)
- Wenwen Zhang
- Department of OncologyNanjing First Hospital, Nanjing Medical UniversityNanjingChina
| | - Xiaoxiang Guan
- Department of OncologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinhai Tang
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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107
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Kim T, Hyun HN, Heo R, Nam K, Yang K, Kim YM, Lee YS, An JY, Park JH, Choi KY, Roh YH. Dual-targeting RNA nanoparticles for efficient delivery of polymeric siRNA to cancer cells. Chem Commun (Camb) 2021; 56:6624-6627. [PMID: 32463029 DOI: 10.1039/d0cc01848a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new dual-targeting polymeric siRNA nanoparticle (Dual-PSNP) was developed via multiple processes: rolling circle transcription, condensation, electrostatic deposition, and click chemistry. The Dual-PSNP showed significantly improved cancer-specific intracellular delivery, gene knockdown efficacy, and apoptosis-mediated cytotoxicity through additive receptor-mediated interactions of the two ligands.
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Affiliation(s)
- Taehyung Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Ha Na Hyun
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Roun Heo
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Kyungjik Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Yoon Suk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Jae Yoon An
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Jae Hyung Park
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea and School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Ki Young Choi
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, 679 Saimdang-ro, Gangneung-si, Gangwon-do 25451, Republic of Korea.
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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108
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Marin-Gonzalez A, Aicart-Ramos C, Marin-Baquero M, Martín-González A, Suomalainen M, Kannan A, Vilhena JG, Greber UF, Moreno-Herrero F, Pérez R. Double-stranded RNA bending by AU-tract sequences. Nucleic Acids Res 2021; 48:12917-12928. [PMID: 33245767 PMCID: PMC7736806 DOI: 10.1093/nar/gkaa1128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/08/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Sequence-dependent structural deformations of the DNA double helix (dsDNA) have been extensively studied, where adenine tracts (A-tracts) provide a striking example for global bending in the molecule. However, in contrast to dsDNA, sequence-dependent structural features of dsRNA have received little attention. In this work, we demonstrate that the nucleotide sequence can induce a bend in a canonical Watson-Crick base-paired dsRNA helix. Using all-atom molecular dynamics simulations, we identified a sequence motif consisting of alternating adenines and uracils, or AU-tracts, that strongly bend the RNA double-helix. This finding was experimentally validated using atomic force microscopy imaging of dsRNA molecules designed to display macroscopic curvature via repetitions of phased AU-tract motifs. At the atomic level, this novel phenomenon originates from a localized compression of the dsRNA major groove and a large propeller twist at the position of the AU-tract. Moreover, the magnitude of the bending can be modulated by changing the length of the AU-tract. Altogether, our results demonstrate the possibility of modifying the dsRNA curvature by means of its nucleotide sequence, which may be exploited in the emerging field of RNA nanotechnology and might also constitute a natural mechanism for proteins to achieve recognition of specific dsRNA sequences.
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Affiliation(s)
- Alberto Marin-Gonzalez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Mikel Marin-Baquero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Maarit Suomalainen
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abhilash Kannan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.,Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.,IFIMAC - Condensed Matter Physics Center, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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109
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Manibalan S, Thirukumaran K, Varshni M, Shobana A, Achary A. Report on biopharmaceutical profile of recent biotherapeutics and insilco docking studies on target bindings of known aptamer biotherapeutics. Biotechnol Genet Eng Rev 2021; 36:57-80. [PMID: 33393433 DOI: 10.1080/02648725.2020.1858395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Accumulated Toxicity, disease recurrence and drug resistivity problems have been observed due to the synthetic and semisynthetic therapeutic practices, which alternatively led to focus on Bio-therapeutics production than xenobiotics. Quick plasma clearance and high potency are the reasons for trending research with huge pharma market of numerous Bio-therapeutics than ever before. Researchers proved that most of the nano and micro Bio-therapeutics have multiple beneficial therapeutic effects. We have analyzed the past, and present scenario of some notable clinically approved Bio-therapeutics to identify the future formulation needs with advanced techniques. Protein-related drugs are the foremost Bio-therapeutics such as antibodies, enzymes, and short, fragmented polypeptides show aggregation properties during storage, naked peptide moieties are resisted by the polar cell membrane, and also the antidrug antibodies were reported. Even though Nucleic acid nano-bodies are excellent target binders than proteins, they had only a few minutes of half-life. Maintaining homogeneousness upon storage of Bio-therapeutics is still a significant challenge in industrial-scale formulation. Notably, plant systems are identified as most useful cost-effective hosts to produce human enzymes than animal systems without any possible viral loads. Irrespective of numerous advancements in routes of administration and additives, subcutaneous is still a golden one to achieve better dynamics. Additionally, the interactions and effective bonds made by each class of well-known aptamer biotherapeutics which are considered as future drugs were studied.
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Affiliation(s)
- Subramaniyan Manibalan
- Center for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology , Madurai, India
| | - Kandasamy Thirukumaran
- Center for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology , Madurai, India
| | - Mathimaran Varshni
- Center for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology , Madurai, India
| | - Ayyasamy Shobana
- Center for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology , Madurai, India
| | - Anant Achary
- Center for Research, Department of Biotechnology, Kamaraj College of Engineering and Technology , Madurai, India
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110
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Wang J, Li Y, Nie G. Multifunctional biomolecule nanostructures for cancer therapy. NATURE REVIEWS. MATERIALS 2021; 6:766-783. [PMID: 34026278 PMCID: PMC8132739 DOI: 10.1038/s41578-021-00315-x] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 05/08/2023]
Abstract
Biomolecule-based nanostructures are inherently multifunctional and harbour diverse biological activities, which can be explored for cancer nanomedicine. The supramolecular properties of biomolecules can be precisely programmed for the design of smart drug delivery vehicles, enabling efficient transport in vivo, targeted drug delivery and combinatorial therapy within a single design. In this Review, we discuss biomolecule-based nanostructures, including polysaccharides, nucleic acids, peptides and proteins, and highlight their enormous design space for multifunctional nanomedicines. We identify key challenges in cancer nanomedicine that can be addressed by biomolecule-based nanostructures and survey the distinct biological activities, programmability and in vivo behaviour of biomolecule-based nanostructures. Finally, we discuss challenges in the rational design, characterization and fabrication of biomolecule-based nanostructures, and identify obstacles that need to be overcome to enable clinical translation.
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Affiliation(s)
- Jing Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yiye Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Guangjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
- GBA Research Innovation Institute for Nanotechnology, Guangdong, China
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, China
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111
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Gerrits L, Hammink R, Kouwer PHJ. Semiflexible polymer scaffolds: an overview of conjugation strategies. Polym Chem 2021. [DOI: 10.1039/d0py01662d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Semiflexible polymers are excellent scaffolds for the presentation of a wide variety of (bio)molecules. This manuscript reviews advantages and challenges of the most common conjugation strategies for the major classes of semiflexible polymers.
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Affiliation(s)
- Lotte Gerrits
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
| | - Roel Hammink
- Department of Tumor Immunology
- Radboud Institute for Molecular Life Sciences
- Radboud University Medical Center
- 6525 GA Nijmegen
- The Netherlands
| | - Paul H. J. Kouwer
- Institute for Molecules and Materials
- Radboud University
- 6525 AJ Nijmegen
- The Netherlands
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112
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Abstract
Nanotechnology has been widely applied to medical interventions for prevention, diagnostics, and therapeutics of diseases, and the application of nanotechnology for medical purposes, which is called as a term "nanomedicine" has received tremendous attention. In particular, the design and development of nanoparticle for biosensors have received a great deal of attention, since those are most impactful area of clinical translation showing potential breakthrough in early diagnosis of diseases such as cancers and infections. For example, the nanoparticles that have intrinsic unique features such as magnetic responsive characteristics or photoluminescence can be utilized for noninvasive visualization of inner body. Drug delivery that makes use of drug-containing nanoparticles as a carrier is another field of study, in which the particulate form nanomedicine is given by parenteral administration for further systemic targeting to pathological tissues. In addition, encapsulation into nanoparticles gives the opportunity to secure the sensitive therapeutic payloads that are readily degraded or deactivated until reached to the target in biological environments, or to provide sufficient solubilization (e.g., to deliver compounds which have physicochemical properties that strongly limit their aqueous solubility and therefore systemic bioavailability). The nanomedicine is further intended to enhance the targeting index such as increased specificity and reduced false binding, thus improve the diagnostic and therapeutic performances. In this chapter, principles of nanomaterials for medicine will be thoroughly covered with applications for imaging-based diagnostics and therapeutics.
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Affiliation(s)
- Jinmyoung Joo
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
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113
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Ordikhani F, Zandi N, Mazaheri M, Luther GA, Ghovvati M, Akbarzadeh A, Annabi N. Targeted nanomedicines for the treatment of bone disease and regeneration. Med Res Rev 2020; 41:1221-1254. [PMID: 33347711 DOI: 10.1002/med.21759] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/14/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022]
Abstract
Targeted delivery by either passive or active targeting of therapeutics to the bone is an attractive treatment for various bone related diseases such as osteoporosis, osteosarcoma, multiple myeloma, and metastatic bone tumors. Engineering novel drug delivery carriers can increase therapeutic efficacy and minimize the risk of side effects. Developmnet of nanocarrier delivery systems is an interesting field of ongoing studies with opportunities to provide more effective therapies. In addition, preclinical nanomedicine research can open new opportunities for preclinical bone-targeted drug delivery; nevertheless, further research is needed to progress these therapies towards clinical applications. In the present review, the latest advancements in targeting moieties and nanocarrier drug delivery systems for the treatment of bone diseases are summarized. We also review the regeneration capability and effective delivery of nanomedicines for orthopedic applications.
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Affiliation(s)
- Farideh Ordikhani
- Transplantation Research Center, Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nooshin Zandi
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran.,Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Mozhdeh Mazaheri
- Department of Materials Science and Engineering, Sharif University of Technology, Tehran, Iran
| | - Gaurav A Luther
- Department of Orthopedic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mahsa Ghovvati
- Department of Chemical and Biomolecular Engineering, University of California- Los Angeles, California, Los Angeles, USA
| | - Abolfazl Akbarzadeh
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, USA.,Department of Medical Nanotechnology, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasim Annabi
- Department of Chemical and Biomolecular Engineering, University of California- Los Angeles, California, Los Angeles, USA
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114
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Multivalent rubber-like RNA nanoparticles for targeted co-delivery of paclitaxel and MiRNA to silence the drug efflux transporter and liver cancer drug resistance. J Control Release 2020; 330:173-184. [PMID: 33316298 DOI: 10.1016/j.jconrel.2020.12.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Analogous to the border customs, liver mainly functions as a filter to detoxify chemicals and metabolite administered orally or intravenously. Besides, the liver cancer cells overexpress the drug exporters which cause high drug effluxion from liver cancer cells, leading to chemoresistance and a diminished chemotherapeutic effect on liver cancer. Recently, we found that RNA nanoparticles display rubber-like property that can rapidly deliver therapeutics to tumor site efficiently and the rest of the RNA nanoparticle were cleared by renal excretion within half hour after systemic injection. Therefore, we designed a new multivalent RNA nanoparticle harboring three copies of hepatocyte targeting-ligands, one copy of miR122, and 24 copies of Paclitaxel to overcome the drug effluxion and chemoresistance thus, synergistically treating HCC. The hepatocyte targeting ligands introduce tumor specificity to the RNA nanoparticles as they selectively bind and internalize into liver cancer cells. The rubber-like RNA nanoparticles allow for enhanced targeting ability to the HCC tumors. The RNA nanoparticles carrying miR122 and PTX were delivered to the liver cancer cells efficiently due to their rubber-like property to enhance their EPR as well as the receptor-mediated endocytosis by hepatocyte targeting-ligands. The miR122 efficiently silenced the drug exporters and the oncogenic proteins. The synergistic effect between miR122 and PTX was confirmed by HSA (Highest Single Agent) synergy model. IC50 was determined to be 460 nM. In vivo studies on mice xenografts revealed that the RNA nanoparticle predominantly accumulated in HCC tumor sites and efficiently inhibited the tumor growth after multiple IV injection. This demonstrates the potential of the rubber-like multivalent RNA nanoparticles to conquest the liver cancer, a currently incurable lethal disease.
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115
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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116
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Bhandari PJ, Sandanaraj BS. Programmed and Sequential Disassembly of Multi-responsive Supramolecular Protein Nanoassemblies: A Detailed Mechanistic Investigation. Chembiochem 2020; 22:876-887. [PMID: 33073455 DOI: 10.1002/cbic.202000581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/18/2020] [Indexed: 12/19/2022]
Abstract
The rational design of a multi-responsive protein-based supramolecular system that can predictably respond to more than one stimulus remains an essential but highly challenging goal in biomolecular engineering. Herein, we report a novel chemical method for the construction of multi-responsive supramolecular nanoassemblies using custom-designed facially amphiphilic monodisperse protein-dendron bioconjugates. The macromolecular synthons contain a globular hydrophilic protein domain site-specifically conjugated to photo-responsive hydrophobic benzyl-ether dendrons of different generations through oligo(ethylene glycol) linkers of defined length. The size of the protein nanoassemblies can be systematically tuned by choosing an appropriate dendron or linker of defined length. Exposure of protein nanoassemblies to light results in partial rather than complete disassembly of the complex. The newly formed protein nanoparticle no longer responds to light but could be disassembled into constitutive monomers under acidic conditions or by further treatment with a small molecule. More interestingly, the distribution ratio of the assembled versus disassembled states of protein nanoassemblies after photochemical reaction does not depend on dendron generation, the nature of the linker functionality or the identity of the protein, but is heavily influenced by the linker length. In sum, this work discloses a new chemical method for the rational design of a monodisperse multi-responsive protein-based supramolecular system with exquisite control over the disassembly process.
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Affiliation(s)
- Pavankumar Janardhan Bhandari
- Department of Chemistry, Indian Institute of Science Education and Research, 100 Homi Bhabha Road, Pune, 411008, India
| | - Britto S Sandanaraj
- Department of Chemistry, Indian Institute of Science Education and Research, 100 Homi Bhabha Road, Pune, 411008, India.,Department of Biology, Indian Institute of Science Education and Research, 100 Homi Bhabha Road, Pune, 411008, India
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117
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Chakraborty S, Khamrui R, Ghosh S. Redox responsive activity regulation in exceptionally stable supramolecular assembly and co-assembly of a protein. Chem Sci 2020; 12:1101-1108. [PMID: 34163877 PMCID: PMC8179030 DOI: 10.1039/d0sc05312k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/14/2020] [Indexed: 11/23/2022] Open
Abstract
Supramolecular assembly of biomolecules/macromolecules stems from the desire to mimic complex biological structures and functions of living organisms. While DNA nanotechnology is already in an advanced stage, protein assembly is still in its infancy as it is a significantly difficult task due to their large molecular weight, conformational complexity and structural instability towards variation in temperature, pH or ionic strength. This article reports highly stable redox-responsive supramolecular assembly of a protein Bovine serum albumin (BSA) which is functionalized with a supramolecular structure directing unit (SSDU). The SSDU consists of a benzamide functionalized naphthalene-diimide (NDI) chromophore which is attached with the protein by a bio-reducible disulfide linker. The SSDU attached protein (NDI-BSA) exhibits spontaneous supramolecular assembly in water by off-set π-stacking among the NDI chromophores, leading to the formation of spherical nanoparticles (diameter: 150-200 nm). The same SSDU when connected with a small hydrophilic wedge (NDI-1) instead of the large globular protein, exhibits a different π-stacking mode with relatively less longitudinal displacement which results in a fibrillar network and hydrogelation. Supramolecular co-assembly of NDI-BSA and NDI-1 (3 : 7) produces similar π-stacking and an entangled 1D morphology. Both the spherical assembly of NDI-BSA or the fibrillar co-assembly of NDI-BSA + NDI-1 (3 : 7) provide sufficient thermal stability to the protein as its thermal denaturation could be completely surpassed while the secondary structure remained intact. However, the esterase like activity of the protein reduced significantly as a result of such supramolecular assembly indicating limited access by the substrate to the active site of the enzyme located in the confined environment. In the presence of glutathione (GSH), a biologically important tri-peptide, due to the cleavage of the disulfide bond, the protein became free and was released, resulting in fully regaining its enzymatic activity. Such supramolecular assembly provided excellent protection to the protein against enzymatic hydrolysis as the relative hydrolysis was estimated to be <30% for the co-assembled protein with respect to the free protein under identical conditions. Similar to bioactivity, the enzymatic hydrolysis also became prominent after GSH-treatment, confirming that the lack of hydrolysis in the supramolecularly assembled state is indeed related to the confinement of the protein in the nanostructure assembly.
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Affiliation(s)
- Saptarshi Chakraborty
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Rajesh Khamrui
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science 2A and 2B Raja S. C. Mullick Road Kolkata India-700032
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118
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Kim YM, Lee YS, Kim T, Yang K, Nam K, Choe D, Roh YH. Cationic cellulose nanocrystals complexed with polymeric siRNA for efficient anticancer drug delivery. Carbohydr Polym 2020; 247:116684. [DOI: 10.1016/j.carbpol.2020.116684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023]
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119
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Ghimire C, Wang H, Li H, Vieweger M, Xu C, Guo P. RNA Nanoparticles as Rubber for Compelling Vessel Extravasation to Enhance Tumor Targeting and for Fast Renal Excretion to Reduce Toxicity. ACS NANO 2020; 14:13180-13191. [PMID: 32902260 PMCID: PMC7799665 DOI: 10.1021/acsnano.0c04863] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Rubber is a fascinating material in both industry and daily life. The development of elastomeric material in nanotechnology is imperative due to its economic and technological potential. By virtue of their distinctive physicochemical properties, nucleic acids have been extensively explored in material science. The Phi29 DNA packaging motor contains a 3WJ with three angles of 97°, 125°, and 138°. Here, the rubber-like property of RNA architectures was investigated using optical tweezers and in vivo imaging technologies. The 3WJ 97° interior angle was contracted or stretched to 60°, 90°, and 108° at will to build elegant RNA triangles, squares, pentagons, cubes, tetrahedrons, dendrimers, and prisms. RNA nanoarchitecture was stretchable and shrinkable by optical tweezer with multiple extension and relaxation repeats like a rubber. Comparing to gold and iron nanoparticles with the same size, RNA nanoparticles display stronger cancer-targeting outcomes, while less accumulation in healthy organs. Generally, the upper limit of renal excretion is 5.5 nm; however, the 5, 10, and 20 nm RNA nanoparticles passed the renal filtration and resumed their original structure identified in urine. These findings solve two previous mysteries: (1) Why RNA nanoparticles have an unusually high tumor targeting efficiency since their rubber or amoeba-like deformation property enables them to squeeze out of the leaky vasculature to improve the EPR effect; and (2) why RNA nanoparticles remain non-toxic since they can be rapidly cleared from the body via renal excretion into urine with little accumulation in the body. Considering its controllable shape and size plus its rubber-like property, RNA holds great promises for industrial and biomedical applications especially in cancer therapeutics delivery.
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Affiliation(s)
| | | | | | - Mario Vieweger
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; College of Pharmacy; College of Medicine; Dorothy M. Davis Heart and Lung Research Institute; and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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120
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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121
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Yasmeen F, Seo H, Javaid N, Kim MS, Choi S. Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers. Pharmaceutics 2020; 12:pharmaceutics12100955. [PMID: 33050544 PMCID: PMC7600108 DOI: 10.3390/pharmaceutics12100955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/03/2020] [Accepted: 10/04/2020] [Indexed: 12/25/2022] Open
Abstract
The immune system plays a crucial role in the body's defense system against various pathogens, such as bacteria, viruses, and parasites, as well as recognizes non-self- and self-molecules. The innate immune system is composed of special receptors known as pattern recognition receptors, which play a crucial role in the identification of pathogen-associated molecular patterns from diverse microorganisms. Any disequilibrium in the activation of a particular pattern recognition receptor leads to various inflammatory, autoimmune, or immunodeficiency diseases. Aptamers are short single-stranded deoxyribonucleic acid or ribonucleic acid molecules, also termed "chemical antibodies," which have tremendous specificity and affinity for their target molecules. Their features, such as stability, low immunogenicity, ease of manufacturing, and facile screening against a target, make them preferable as therapeutics. Immune-system-targeting aptamers have a great potential as a targeted therapeutic strategy against immune diseases. This review summarizes components of the innate immune system, aptamer production, pharmacokinetic characteristics of aptamers, and aptamers related to innate-immune-system diseases.
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122
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Knutson SD, Sanford AA, Swenson CS, Korn MM, Manuel BA, Heemstra JM. Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging. J Am Chem Soc 2020; 142:17766-17781. [PMID: 33017148 DOI: 10.1021/jacs.0c08996] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Controlling the structure and activity of nucleic acids dramatically expands their potential for application in therapeutics, biosensing, nanotechnology, and biocomputing. Several methods have been developed to impart responsiveness of DNA and RNA to small-molecule and light-based stimuli. However, heat-triggered control of nucleic acids has remained largely unexplored, leaving a significant gap in responsive nucleic acid technology. Moreover, current technologies have been limited to natural nucleic acids and are often incompatible with polymerase-generated sequences. Here we show that glyoxal, a well-characterized compound that covalently attaches to the Watson-Crick-Franklin face of several nucleobases, addresses these limitations by thermoreversibly modulating the structure and activity of virtually any nucleic acid scaffold. Using a variety of DNA and RNA constructs, we demonstrate that glyoxal modification is easily installed and potently disrupts nucleic acid structure and function. We also characterize the kinetics of decaging and show that activity can be restored via tunable thermal removal of glyoxal adducts under a variety of conditions. We further illustrate the versatility of this approach by reversibly caging a 2'-O-methylated RNA aptamer as well as synthetic threose nucleic acid (TNA) and peptide nucleic acid (PNA) scaffolds. Glyoxal caging can also be used to reversibly disrupt enzyme-nucleic acid interactions, and we show that caging of guide RNA allows for tunable and reversible control over CRISPR-Cas9 activity. We also demonstrate glyoxal caging as an effective method for enhancing PCR specificity, and we cage a biostable antisense oligonucleotide for time-release activation and titration of gene expression in living cells. Together, glyoxalation is a straightforward and scarless method for imparting reversible thermal responsiveness to theoretically any nucleic acid architecture, addressing a significant need in synthetic biology and offering a versatile new tool for constructing programmable nucleic acid components in medicine, nanotechnology, and biocomputing.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aimee A Sanford
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Megan M Korn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Brea A Manuel
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Juneja R, Vadarevu H, Halman J, Tarannum M, Rackley L, Dobbs J, Marquez J, Chandler M, Afonin K, Vivero-Escoto JL. Combination of Nucleic Acid and Mesoporous Silica Nanoparticles: Optimization and Therapeutic Performance In Vitro. ACS APPLIED MATERIALS & INTERFACES 2020; 12:38873-38886. [PMID: 32805923 PMCID: PMC7748385 DOI: 10.1021/acsami.0c07106] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Programmable nucleic acid nanoparticles (NANPs) with precisely controlled functional compositions can regulate the conditional activation of various biological pathways and responses in human cells. However, the intracellular delivery of NANPs alone is hindered by their susceptibility to nuclease activity and inefficient crossing of biological membranes. In this work, we optimized the internalization and therapeutic performance of several representative NANPs delivered with mesoporous silica nanoparticles (MSNPs) tailored for efficient electrostatic association with NANPs. We compared the immunostimulatory properties of different NA-MS-NP complexes formed with globular, planar, and fibrous NANPs and demonstrated the maximum immunostimulation for globular NANPs. As a proof of concept, we assessed the specific gene silencing by NA-MS-NP complexes functionalized with siRNA targeting green fluorescent protein expressed in triple-negative human breast cancer cells. We showed that the fibrous NANPs have the highest silencing efficiency when compared to globular or planar counterparts. Finally, we confirmed the multimodal ability of MSNPs to co-deliver a chemotherapy drug, doxorubicin, and NANPs targeting apoptosis regulator gene BCL2 in triple-negative breast cancer and melanoma cell lines. Overall, the combination of NANPs and MSNPs may become a new promising approach to efficiently treat cancer and other diseases via the simultaneous targeting of various pathways.
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Affiliation(s)
- Ridhima Juneja
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Hemapriyadarshini Vadarevu
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Justin Halman
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Mubin Tarannum
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Lauren Rackley
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jacob Dobbs
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jose Marquez
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Morgan Chandler
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill Afonin
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Nanoscale Science Program, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, The University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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Koji K, Yoshinaga N, Mochida Y, Hong T, Miyazaki T, Kataoka K, Osada K, Cabral H, Uchida S. Bundling of mRNA strands inside polyion complexes improves mRNA delivery efficiency in vitro and in vivo. Biomaterials 2020; 261:120332. [PMID: 32877764 DOI: 10.1016/j.biomaterials.2020.120332] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 01/08/2023]
Abstract
RNA nanotechnology has promise for developing mRNA carriers with enhanced physicochemical and functional properties. However, the potential synergy for mRNA delivery of RNA nanotechnology in cooperation with established carrier systems remains unknown. This study proposes a combinational system of RNA nanotechnology and mRNA polyplexes, by focusing on mRNA steric structure inside the polyplexes. Firstly, several mRNA strands are bundled through hybridization with RNA oligonucleotide crosslinkers to obtain tight mRNA structure, and then the bundled mRNA is mixed with poly(ethylene glycol) (PEG)-polycation block copolymers to prepare PEG-coated polyplex micelles (PMs). mRNA bundling results in highly condensed mRNA packaging inside PM core with dense PEG chains on the surface, thereby, improving PM stability against polyion exchange reaction and ribonuclease (RNase) attack. Importantly, such stabilization effects are attributed to bundled structure of mRNA rather than the increase in total mRNA amount encapsulated in the PMs, as encapsulation of long mRNA strands without bundling fails to improve PM stability. Consequently, PMs loading bundled mRNA exhibit enhanced stability in mouse blood circulation, and induce efficient protein expression in cultured cells and mouse brain.
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Affiliation(s)
- Kyoko Koji
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Naoto Yoshinaga
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuki Mochida
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan
| | - Taehun Hong
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takuya Miyazaki
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa, 243-0435, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan; Policy Alternatives Research Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kensuke Osada
- Department of Molecular Imaging and Theranostics, Quantum Medical Science Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba, 263-8555, Japan
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.
| | - Satoshi Uchida
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.
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Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
- BCAM-Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
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Braga A, Bandiera S, Verheyen J, Hamel R, Rutigliani C, Edenhofer F, Smith JA, Pluchino S. Combination of In Situ Lcn2 pRNA-RNAi Nanotherapeutics and iNSC Transplantation Ameliorates Experimental SCI in Mice. Mol Ther 2020; 28:2677-2690. [PMID: 32877696 DOI: 10.1016/j.ymthe.2020.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/05/2020] [Accepted: 08/02/2020] [Indexed: 01/19/2023] Open
Abstract
Spinal cord injury (SCI) is a debilitating neurological condition characterized by different cellular and molecular mechanisms that interplay in exacerbating the progression of the pathology. No fully restorative therapies are yet available, and it is thus becoming recognized that combinatorial approaches aimed at addressing different aspects of SCI will likely results in greater functional outcomes. Here we employed packaging RNA-mediated RNA interference (pRNA-RNAi) nanotherapeutics to downregulate in situ the expression of lipocalin 2 (Lcn2), a known mediator of neuroinflammation and autocrine mediator of reactive astrogliosis, and to create a more amenable niche for the subsequent transplantation of induced neural stem cells (iNSCs). To our knowledge, this is the first approach that takes advantage of the modular and multifunctional pRNA three-way junction platform in the SCI niche, while also exploiting the therapeutic potential of immune-compatible and feasible iNSC transplants. We show the combination of such treatments in a mouse model of contusion thoracic SCI leads to significant improvement of locomotor function, albeit not better than single pRNA-RNAi treatment, and results in synergistic histopathological effects, such as reduction of glial scar volume, diminished pro-inflammatory response, and promotion of neuronal survival. Our results provide evidence for a novel combinatorial approach for treating SCI.
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Affiliation(s)
- Alice Braga
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK
| | - Sara Bandiera
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK
| | - Jeroen Verheyen
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK
| | - Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK
| | - Carola Rutigliani
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK
| | - Frank Edenhofer
- Department of Molecular Biology & CMBI, Genomics, Stem Cell Biology & Regenerative Medicine, Leopold-Franzens-University Innsbruck, 6020 Innsbruck, Austria
| | - Jayden Aaron Smith
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK; Cambridge Innovation Technologies Consulting, Ltd., CB4 0WS Cambridge, UK.
| | - Stefano Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, CB2 0HA Cambridge, UK.
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Torelli E, Kozyra J, Shirt-Ediss B, Piantanida L, Voïtchovsky K, Krasnogor N. Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami. ACS Synth Biol 2020; 9:1682-1692. [PMID: 32470289 DOI: 10.1021/acssynbio.0c00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which, for the first time, all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple strands able to correctly fold in a high synthesis yield into the nanoribbon. Synthesis is successfully confirmed by atomic force microscopy, and the unpurified transcription reaction mixture is analyzed by an in gel-imaging assay where the transcribed RNA nanoribbons are able to capture the specific dye through the reconstituted split Broccoli aptamer showing a clear green fluorescent band. Finally, we simulate the RNA origami in silico using the nucleotide-level coarse-grained model oxRNA to investigate the thermodynamic stability of the assembled nanostructure in isothermal conditions over a period of time. Our work suggests that the scaffolded origami technique is a viable, and potentially more powerful, assembly alternative to the single-stranded origami technique for future in vivo applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Jerzy Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Ben Shirt-Ediss
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RX, United Kingdom
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Lee TJ, Yuan X, Kerr K, Yoo JY, Kim DH, Kaur B, Eltzschig HK. Strategies to Modulate MicroRNA Functions for the Treatment of Cancer or Organ Injury. Pharmacol Rev 2020; 72:639-667. [PMID: 32554488 PMCID: PMC7300323 DOI: 10.1124/pr.119.019026] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cancer and organ injury-such as that occurring in the perioperative period, including acute lung injury, myocardial infarction, and acute gut injury-are among the leading causes of death in the United States and impose a significant impact on quality of life. MicroRNAs (miRNAs) have been studied extensively during the last two decades for their role as regulators of gene expression, their translational application as diagnostic markers, and their potential as therapeutic targets for disease treatment. Despite promising preclinical outcomes implicating miRNA targets in disease treatment, only a few miRNAs have reached clinical trials. This likely relates to difficulties in the delivery of miRNA drugs to their targets to achieve efficient inhibition or overexpression. Therefore, understanding how to efficiently deliver miRNAs into diseased tissues and specific cell types in patients is critical. This review summarizes current knowledge on various approaches to deliver therapeutic miRNAs or miRNA inhibitors and highlights current progress in miRNA-based disease therapy that has reached clinical trials. Based on ongoing advances in miRNA delivery, we believe that additional therapeutic approaches to modulate miRNA function will soon enter routine medical treatment of human disease, particularly for cancer or perioperative organ injury. SIGNIFICANCE STATEMENT: MicroRNAs have been studied extensively during the last two decades in cancer and organ injury, including acute lung injury, myocardial infarction, and acute gut injury, for their regulation of gene expression, application as diagnostic markers, and therapeutic potentials. In this review, we specifically emphasize the pros and cons of different delivery approaches to modulate microRNAs, as well as the most recent exciting progress in the field of therapeutic targeting of microRNAs for disease treatment in patients.
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Affiliation(s)
- Tae Jin Lee
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Xiaoyi Yuan
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Keith Kerr
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Ji Young Yoo
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Dong H Kim
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Balveen Kaur
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Holger K Eltzschig
- Departments of Neurosurgery (T.J.L., K.K., J.Y.Y., D.H.K., B.K.) and Anesthesiology (X.Y., H.K.E.), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
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Zhang TX, Zhang ZZ, Yue YX, Hu XY, Huang F, Shi L, Liu Y, Guo DS. A General Hypoxia-Responsive Molecular Container for Tumor-Targeted Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1908435. [PMID: 32459030 DOI: 10.1002/adma.201908435] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
Enhanced drug delivery can improve the therapeutic efficacy of drugs and help overcome side effects. However, many reported drug-delivery systems are too complex and irreproducible for practical use. In this work, the design of a hypoxia-responsive molecular container based on calixarene, called CAC4A, which presents a significant advance in practical, hypoxia-targeted drug-delivery, is reported. CAC4A enables a wide variety of clinical drugs to be quantitatively loaded to improve their solubility and stability, as well as enable the administration of reduced doses. Furthermore, as a result of its azo functional groups, which are sensitive to reduction within a hypoxic environment, it is possible to achieve tumor-targeted drug-release with reduced side effects. CAC4A fulfils all essential requirements for a drug-delivery system in addition to multiple advantages, including facile preparation, well-defined molecular weight, and structure, and universal applicability. Such features collectively enable supramolecular prodrugs to be formulated simply and reproducibly, with potential for bench-to-bedside translation. Moreover, CAC4A is amenable to other therapy modalities and can be facilely decorated with functional groups and hybridized with nanomaterials, providing ample possibilities for its role in future drug-delivery systems.
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Affiliation(s)
- Tian-Xing Zhang
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Zhan-Zhan Zhang
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Yu-Xin Yue
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Xin-Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Fan Huang
- Institute of Radiation Medicine, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, 300192, China
| | - Linqi Shi
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Yang Liu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
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Acebes-Fernández V, Landeira-Viñuela A, Juanes-Velasco P, Hernández AP, Otazo-Perez A, Manzano-Román R, Gongora R, Fuentes M. Nanomedicine and Onco-Immunotherapy: From the Bench to Bedside to Biomarkers. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1274. [PMID: 32610601 PMCID: PMC7407304 DOI: 10.3390/nano10071274] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022]
Abstract
The broad relationship between the immune system and cancer is opening a new hallmark to explore for nanomedicine. Here, all the common and synergy points between both areas are reviewed and described, and the recent approaches which show the progress from the bench to the beside to biomarkers developed in nanomedicine and onco-immunotherapy.
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Affiliation(s)
- Vanessa Acebes-Fernández
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
| | - Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
| | - Angela-Patricia Hernández
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
| | - Andrea Otazo-Perez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain;
| | - Rafael Gongora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC CB16/12/00400, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (V.A.-F.); (A.L.-V.); (P.J.-V.); (A.-P.H.); (A.O.-P.); (R.G.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain;
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Translation of the long-term fundamental studies on viral DNA packaging motors into nanotechnology and nanomedicine. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1103-1129. [DOI: 10.1007/s11427-020-1752-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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133
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Kim T, Viard M, Afonin KA, Gupta K, Popov M, Salotti J, Johnson PF, Linder C, Heldman E, Shapiro BA. Characterization of Cationic Bolaamphiphile Vesicles for siRNA Delivery into Tumors and Brain. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:359-372. [PMID: 32200271 PMCID: PMC7090283 DOI: 10.1016/j.omtn.2020.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/19/2019] [Accepted: 02/23/2020] [Indexed: 12/27/2022]
Abstract
Small interfering RNAs (siRNAs) are potential therapeutic substances due to their gene silencing capability as exemplified by the recent approval by the US Food and Drug Administration (FDA) of the first siRNA therapeutic agent (patisiran). However, the delivery of naked siRNAs is challenging because of their short plasma half-lives and poor cell penetrability. In this study, we used vesicles made from bolaamphiphiles (bolas), GLH-19 and GLH-20, to investigate their ability to protect siRNA from degradation by nucleases while delivering it to target cells, including cells in the brain. Based on computational and experimental studies, we found that GLH-19 vesicles have better delivery characteristics than do GLH-20 vesicles in terms of stability, binding affinity, protection against nucleases, and transfection efficiency, while GLH-20 vesicles contribute to efficient release of the delivered siRNAs, which become available for silencing. Our studies with vesicles made from a mixture of the two bolas (GLH-19 and GLH-20) show that they were able to deliver siRNAs into cultured cancer cells, into a flank tumor and into the brain. The vesicles penetrate cell membranes and the blood-brain barrier (BBB) by endocytosis and transcytosis, respectively, mainly through the caveolae-dependent pathway. These results suggest that GLH-19 strengthens vesicle stability, provides protection against nucleases, and enhances transfection efficiency, while GLH-20 makes the siRNA available for gene silencing.
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Affiliation(s)
- Taejin Kim
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 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
| | - Kshitij Gupta
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Mary Popov
- Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | | | | | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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134
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Puri A, Viard M, Zakrevsky P, Zampino S, Chen A, Isemann C, Alvi S, Clogston J, Chitgupi U, Lovell JF, Shapiro BA. Photoactivation of sulfonated polyplexes enables localized gene silencing by DsiRNA in breast cancer cells. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2020; 26:102176. [PMID: 32151748 PMCID: PMC8117728 DOI: 10.1016/j.nano.2020.102176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/23/2020] [Accepted: 02/23/2020] [Indexed: 12/29/2022]
Abstract
Translation potential of RNA interference nanotherapeutics remains challenging due to in vivo off-target effects and poor endosomal escape. Here, we developed novel polyplexes for controlled intracellular delivery of dicer substrate siRNA, using a light activation approach. Sulfonated polyethylenimines covalently linked to pyropheophorbide-α for photoactivation and bearing modified amines (sulfo-pyro-PEI) for regulated endosomal escape were investigated. Gene knock-down by the polymer-complexed DsiRNA duplexes (siRNA-NPs) was monitored in breast cancer cells. Surprisingly, sulfo-pyro-PEI/siRNA-NPs failed to downregulate the PLK1 or eGFP proteins. However, photoactivation of these cell associated-polyplexes with a 661-nm laser clearly restored knock-down of both proteins. In contrast, protein down-regulation by non-sulfonated pyro-PEI/siRNA-NPs occurred without any laser treatments, indicating cytoplasmic disposition of DsiRNA followed a common intracellular release mechanism. Therefore, sulfonated pyro-PEI holds potential as a unique trap and release light-controlled delivery platform for on-demand gene silencing bearing minimal off target effects.
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Affiliation(s)
- Anu Puri
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA.
| | - Mathias Viard
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Paul Zakrevsky
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Serena Zampino
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Arabella Chen
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Camryn Isemann
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Sohaib Alvi
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Jeff Clogston
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA; Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Upendra Chitgupi
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jonathan F Lovell
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Bruce A Shapiro
- RNA Structure and Design Section, RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA.
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135
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Chen YT, Yang H, Chu JW. Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids. Chem Sci 2020; 11:4969-4979. [PMID: 34122953 PMCID: PMC8159235 DOI: 10.1039/d0sc00480d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals. The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.![]()
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China +886 3 5712121 ext. 56996
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136
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Yoon J, Shin M, Lim J, Kim DY, Lee T, Choi J. Nanobiohybrid Material‐Based Bioelectronic Devices. Biotechnol J 2020; 15:e1900347. [DOI: 10.1002/biot.201900347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/19/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Jinho Yoon
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Minkyu Shin
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Joungpyo Lim
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Dong Yeon Kim
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
| | - Taek Lee
- Department of Chemical EngineeringKwangwoon University Wolgye‐dong Nowon‐gu Seoul 01899 Republic of Korea
| | - Jeong‐Woo Choi
- Department of Chemical and Biomolecular EngineeringSogang University 35 Baekbeom‐Ro Mapo‐Gu Seoul 04107 Republic of Korea
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137
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Lv Z, Wang Y, Chen J, Wang J, Zhou Y, Han ST. Semiconductor Quantum Dots for Memories and Neuromorphic Computing Systems. Chem Rev 2020; 120:3941-4006. [DOI: 10.1021/acs.chemrev.9b00730] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ziyu Lv
- Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, P. R. China
| | - Yan Wang
- Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, P. R. China
| | - Jingrui Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, P. R. China
| | - Junjie Wang
- Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, P. R. China
| | - Ye Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, P. R. China
| | - Su-Ting Han
- Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, P. R. China
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138
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Badu S, Prabhakar S, Melnik R, Singh S. Atomistic to continuum model for studying mechanical properties of RNA nanotubes. Comput Methods Biomech Biomed Engin 2020; 23:396-407. [PMID: 32116031 DOI: 10.1080/10255842.2020.1733991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
With rapid advancements in the emerging field of RNA nanotechnology, its current and potential applications, new important problems arise in our quest to better understand properties of RNA nanocomplexes. In this paper, our focus is on the modeling of RNA nanotubes which are important for many biological processes. These RNA complexes are also important for human beings, with their theurapeutical and biomedical applications discussed vigorously in the literature over the recent years. Here, we develop a continuum model of RNA nanotubes, originally obtained from self assembly of RNA building blocks in the molecular dynamics simulation. Based on the finite element method, we calculate the elastic properties of these nanostructures and provide a relationship between stress and strain induced in the RNA nanotube. We also analyze the variations in the displacement vector along the assembly axis for RNA nanotubes of different sizes. In particular, we show that oscillations in the amplitudes of strains and displacements significantly differ for such RNA nanotubes. These findings are discussed in the context of atomistic simulations and experimental results in this field.
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Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Sanjay Prabhakar
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada.,BCAM - Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
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139
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Jiang Z, Thayumanavan S. Non-cationic Material Design for Nucleic Acid Delivery. ADVANCED THERAPEUTICS 2020; 3:1900206. [PMID: 34164572 PMCID: PMC8218910 DOI: 10.1002/adtp.201900206] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 12/16/2022]
Abstract
Nucleic acid delivery provides effective options to control intracellular gene expression and protein production. Efficient delivery of nucleic acid typically requires delivery vehicles to facilitate the entry of nucleic acid into cells. Among non-viral delivery vehicles, cationic materials are favored because of their high loading capacity of nucleic acids and prominent cellular uptake efficiency through electrostatic interaction. However, cationic moieties at high dosage tend to induce severe cytotoxicity due to the interference on cell membrane integrity. In contrast, non-cationic materials present alternative delivery approaches with less safety concerns than cationic materials. In this Progress Report, principles of non-cationic material design for nucleic acid delivery are discussed. Examples of such non-cationic platforms are highlighted, including complexation or conjugation with nucleic acids and self-assembled nucleic acid structures.
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Affiliation(s)
- Ziwen Jiang
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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140
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Mitchell C, Polanco JA, DeWald L, Kress D, Jaeger L, Grabow WW. Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch. Nucleic Acids Res 2020; 47:6439-6451. [PMID: 31045210 PMCID: PMC6614920 DOI: 10.1093/nar/gkz304] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/22/2019] [Accepted: 04/16/2019] [Indexed: 12/17/2022] Open
Abstract
Naturally occurring RNAs are known to exhibit a high degree of modularity, whereby specific structural modules (or motifs) can be mixed and matched to create new molecular architectures. The modular nature of RNA also affords researchers the ability to characterize individual structural elements in controlled synthetic contexts in order to gain new and critical insights into their particular structural features and overall performance. Here, we characterized the binding affinity of a unique loop–receptor interaction found in the tetrahydrofolate (THF) riboswitch using rationally designed self-assembling tectoRNAs. Our work suggests that the THF loop–receptor interaction has been fine-tuned for its particular role as a riboswitch component. We also demonstrate that the thermodynamic stability of this interaction can be modulated by the presence of folinic acid, which induces a local structural change at the level of the loop–receptor. This corroborates the existence of a THF binding site within this tertiary module and paves the way for its potential use as a THF responsive module for RNA nanotechnology and synthetic biology.
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Affiliation(s)
- Charles Mitchell
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Julio A Polanco
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Laura DeWald
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Dustin Kress
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA
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141
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Ultra-thermostable RNA nanoparticles for solubilizing and high-yield loading of paclitaxel for breast cancer therapy. Nat Commun 2020; 11:972. [PMID: 32080195 PMCID: PMC7033104 DOI: 10.1038/s41467-020-14780-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 01/24/2020] [Indexed: 11/17/2022] Open
Abstract
Paclitaxel is widely used in cancer treatments, but poor water-solubility and toxicity raise serious concerns. Here we report an RNA four-way junction nanoparticle with ultra-thermodynamic stability to solubilize and load paclitaxel for targeted cancer therapy. Each RNA nanoparticle covalently loads twenty-four paclitaxel molecules as a prodrug. The RNA-paclitaxel complex is structurally rigid and stable, demonstrated by the sub-nanometer resolution imaging of cryo-EM. Using RNA nanoparticles as carriers increases the water-solubility of paclitaxel by 32,000-fold. Intravenous injections of RNA-paclitaxel nanoparticles with specific cancer-targeting ligand dramatically inhibit breast cancer growth, with nearly undetectable toxicity and immune responses in mice. No fatalities are observed at a paclitaxel dose equal to the reported LD50. The use of ultra-thermostable RNA nanoparticles to deliver chemical prodrugs addresses issues with RNA unfolding and nanoparticle dissociation after high-density drug loading. This finding provides a stable nano-platform for chemo-drug delivery as well as an efficient method to solubilize hydrophobic drugs. Although paclitaxel is widely used as a chemotherapy, it suffers from poor solubility and toxicity issues. Here, the authors develop thermostable RNA nanoparticles and report the RNA-paclitaxel complex to display improved stability, drug loading capacity and solubility for improved targeted cancer therapy and reduced immune responses.
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142
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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143
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Lee T, Mohammadniaei M, Zhang H, Yoon J, Choi HK, Guo S, Guo P, Choi J. Single Functionalized pRNA/Gold Nanoparticle for Ultrasensitive MicroRNA Detection Using Electrochemical Surface-Enhanced Raman Spectroscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902477. [PMID: 32042566 PMCID: PMC7001639 DOI: 10.1002/advs.201902477] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/14/2019] [Indexed: 05/07/2023]
Abstract
Controlling the selective one-to-one conjugation of RNA with nanoparticles is vital for future applications of RNA nanotechnology. Here, the monofunctionalization of a gold nanoparticle (AuNP) with a single copy of RNA is developed for ultrasensitive microRNA-155 quantification using electrochemical surface-enhanced Raman spectroscopy (EC-SERS). A single AuNP is conjugated with one copy of the packaging RNA (pRNA) three-way junction (RNA 3WJ). pRNA 3WJ containing one strand of the 3WJ is connected to a Sephadex G100 aptamer and a biotin group at each arm (SEPapt/3WJ/Bio) which is then immobilized to the Sephadex G100 resin. The resulting complex is connected to streptavidin-coated AuNP (STV/AuNP). Next, the STV/AuNP-Bio/3WJa is purified and reassembled with another 3WJ to form a single-labeled 3WJ/AuNP. Later, the monoconjugate is immobilized onto the AuNP-electrodeposited indium tin oxide coated substrate for detecting microRNA-155 based on EC-SERS. Application of an optimum potential of +0.2 V results in extraordinary amplification (≈7 times) of methylene blue (reporter) SERS signal compared to the normal SERS signal. As a result, a highly sensitive detection of 60 × 10-18 m microRNA-155 in 1 h in serum based on monoconjugated AuNP/RNA is achieved. Thus, the monofunctionalization of RNA onto nanoparticle can provide a new methodology for biosensor construction and diverse RNA nanotechnology development.
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Affiliation(s)
- Taek Lee
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
- Department of Chemical EngineeringKwangwoon University20 Kwangwoon‐Ro, Nowon‐GuSeoul01897Republic of Korea
| | - Mohsen Mohammadniaei
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
| | - Hui Zhang
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
| | - Jinho Yoon
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
| | - Hye Kyu Choi
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
| | - Sijin Guo
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
| | - Peixuan Guo
- College of PharmacyCollege of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research InstituteOhio State UniversityColumbusOH43210USA
| | - Jeong‐Woo Choi
- Department of Chemical and Biomolecular EngineeringSogang University35 Baekbeom‐ro, Mapo‐guSeoul121‐742Republic of Korea
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144
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Datta LP, Manchineella S, Govindaraju T. Biomolecules-derived biomaterials. Biomaterials 2020; 230:119633. [DOI: 10.1016/j.biomaterials.2019.119633] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022]
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145
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Liu D, Geary CW, Chen G, Shao Y, Li M, Mao C, Andersen ES, Piccirilli JA, Rothemund PWK, Weizmann Y. Branched kissing loops for the construction of diverse RNA homooligomeric nanostructures. Nat Chem 2020; 12:249-259. [PMID: 31959958 DOI: 10.1038/s41557-019-0406-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 12/06/2019] [Indexed: 01/31/2023]
Abstract
In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy-homooligomerization-allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artificial nucleic acid structures. Here, we present a robust self-assembly system in which homooligomerizable tiles are formed from intramolecularly folded RNA single strands. Tiles are linked through an artificially designed branched kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bulged helix and a hairpin loop. By adjusting the tile geometry to gain control over the curvature, torsion and the number of helices, we have constructed 16 different linear and circular structures, including a finite-sized three-dimensional cage. We further demonstrate cotranscriptional self-assembly of tiles based on branched kissing loops, and show that tiles inserted into a transfer RNA scaffold can be overexpressed in bacterial cells.
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Affiliation(s)
- Di Liu
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Cody W Geary
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA
| | - Gang Chen
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Chemistry, University of Central Florida, Orlando, FL, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Mo Li
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Ebbe S Andersen
- Interdisciplinary Nanoscience Center and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Joseph A Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Paul W K Rothemund
- Departments of Bioengineering, Computational and Mathematical Sciences, and Computation and Neural Systems, California Institute of Technology, Pasadena, CA, USA.
| | - Yossi Weizmann
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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146
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Halman JR, Kim KT, Gwak SJ, Pace R, Johnson MB, Chandler MR, Rackley L, Viard M, Marriott I, Lee JS, Afonin KA. A cationic amphiphilic co-polymer as a carrier of nucleic acid nanoparticles (Nanps) for controlled gene silencing, immunostimulation, and biodistribution. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2020; 23:102094. [PMID: 31669854 PMCID: PMC6942546 DOI: 10.1016/j.nano.2019.102094] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022]
Abstract
Programmable nucleic acid nanoparticles (NANPs) provide controlled coordination of therapeutic nucleic acids (TNAs) and other biological functionalities. Beyond multivalence, recent reports demonstrate that NANP technology can also elicit a specific immune response, adding another layer of customizability to this innovative approach. While the delivery of nucleic acids remains a challenge, new carriers are introduced and tested continuously. Polymeric platforms have proven to be efficient in shielding nucleic acid cargos from nuclease degradation while promoting their delivery and intracellular release. Here, we venture beyond the delivery of conventional TNAs and combine the stable cationic poly-(lactide-co-glycolide)-graft-polyethylenimine with functionalized NANPs. Furthermore, we compare several representative NANPs to assess how their overall structures influence their delivery with the same carrier. An extensive study of various formulations both in vitro and in vivo reveals differences in their immunostimulatory activity, gene silencing efficiency, and biodistribution, with fibrous NANPs advancing for TNA delivery.
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Affiliation(s)
- Justin R Halman
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ki-Taek Kim
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - So-Jung Gwak
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Richard Pace
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - M Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, USA
| | - Morgan R Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Lauren Rackley
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Mathias Viard
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, USA
| | - Jeoung Soo Lee
- Drug Design, Development, and Delivery (4D) Laboratory, Department of Bioengineering, Clemson University, Clemson, SC, USA.
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
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147
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Engineering a Floxuridine-integrated RNA Prism as Precise Nanomedicine for Drug Delivery. Chem Res Chin Univ 2019. [DOI: 10.1007/s40242-019-0049-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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148
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Dobrovolskaia MA. Nucleic Acid Nanoparticles at a Crossroads of Vaccines and Immunotherapies. Molecules 2019; 24:molecules24244620. [PMID: 31861154 PMCID: PMC6943637 DOI: 10.3390/molecules24244620] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Vaccines and immunotherapies involve a variety of technologies and act through different mechanisms to achieve a common goal, which is to optimize the immune response against an antigen. The antigen could be a molecule expressed on a pathogen (e.g., a disease-causing bacterium, a virus or another microorganism), abnormal or damaged host cells (e.g., cancer cells), environmental agent (e.g., nicotine from a tobacco smoke), or an allergen (e.g., pollen or food protein). Immunogenic vaccines and therapies optimize the immune response to improve the eradication of the pathogen or damaged cells. In contrast, tolerogenic vaccines and therapies retrain or blunt the immune response to antigens, which are recognized by the immune system as harmful to the host. To optimize the immune response to either improve the immunogenicity or induce tolerance, researchers employ different routes of administration, antigen-delivery systems, and adjuvants. Nanocarriers and adjuvants are of particular interest to the fields of vaccines and immunotherapy as they allow for targeted delivery of the antigens and direct the immune response against these antigens in desirable direction (i.e., to either enhance immunogenicity or induce tolerance). Recently, nanoparticles gained particular attention as antigen carriers and adjuvants. This review focuses on a particular subclass of nanoparticles, which are made of nucleic acids, so-called nucleic acid nanoparticles or NANPs. Immunological properties of these novel materials and considerations for their clinical translation are discussed.
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Affiliation(s)
- Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
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149
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Nwokeoji AO, Kumar S, Kilby PM, Portwood DE, Hobbs JK, Dickman MJ. Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC. Analyst 2019; 144:4985-4994. [PMID: 31328735 DOI: 10.1039/c9an00954j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Long double-stranded (ds) RNA is emerging as a novel alternative to chemical and genetically-modified insect and fungal management strategies. The ability to produce large quantities of dsRNA in either bacterial systems, by in vitro transcription, in cell-free systems or in planta for RNA interference applications has generated significant demand for the development and application of analytical tools for analysis of dsRNA. We have utilised atomic force microscopy (AFM) in conjunction with ion-pair reverse-phase high performance liquid chromatography (IP-RP-HPLC) to provide novel insight into dsRNA for RNAi applications. The AFM analysis enabled direct structural characterisation of the A-form duplex dsRNA and accurate determination of the dsRNA duplex length. Moreover, further analysis under non-denaturing conditions revealed the presence of heterogeneous dsRNA species. IP-RP-HPLC fractionation and AFM analysis revealed that these alternative RNA species do not arise from different lengths of individual dsRNA molecules in the product, but represent misannealed RNA species that present as larger assemblies or multimeric forms of the RNA. These results for the first time provide direct structural insight into dsRNA produced both in vivo in bacterial systems and in vitro, highlighting the structural heterogeneity of RNA produced. These results are the first example of detailed characterisation of the different forms of dsRNA from two production systems and establish atomic force microscopy as an important tool for the characterisation of long dsRNA.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
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150
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Leonard M, Zhang X. Estrogen receptor coactivator Mediator Subunit 1 (MED1) as a tissue-specific therapeutic target in breast cancer. J Zhejiang Univ Sci B 2019; 20:381-390. [PMID: 31090264 DOI: 10.1631/jzus.b1900163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Breast cancer, one of the most frequent cancer types, is a leading cause of death in women worldwide. Estrogen receptor (ER) α is a nuclear hormone receptor that plays key roles in mammary gland development and breast cancer. About 75% of breast cancer cases are diagnosed as ER-positive; however, nearly half of these cancers are either intrinsically or inherently resistant to the current anti-estrogen therapies. Recent studies have identified an ER coactivator, Mediator Subunit 1 (MED1), as a unique, tissue-specific cofactor that mediates breast cancer metastasis and treatment resistance. MED1 is overexpressed in over 50% of human breast cancer cases and co-amplifies with another important breast cancer gene, receptor tyrosine kinase HER2. Clinically, MED1 expression highly correlates with poor disease-free survival of breast cancer patients, and recent studies have reported an increased frequency of MED1 mutations in the circulating tumor cells of patients after treatment. In this review, we discuss the biochemical characterization of MED1 and its associated MED1/Mediator complex, its crosstalk with HER2 in anti-estrogen resistance, breast cancer stem cell formation, and metastasis both in vitro and in vivo. Furthermore, we elaborate on the current advancements in targeting MED1 using state-of-the-art RNA nanotechnology and discuss the future perspectives as well.
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Affiliation(s)
- Marissa Leonard
- Department of Cancer Biology, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267, USA
| | - Xiaoting Zhang
- Department of Cancer Biology, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267, USA
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