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Cardador CM, Muehlmann LA, Coelho CM, Silva LP, Garay AV, Carvalho AMDS, Bastos IMD, Longo JPF. Nucleotides Entrapped in Liposome Nanovesicles as Tools for Therapeutic and Diagnostic Use in Biomedical Applications. Pharmaceutics 2023; 15:873. [PMID: 36986734 PMCID: PMC10056227 DOI: 10.3390/pharmaceutics15030873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The use of nucleotides for biomedical applications is an old desire in the scientific community. As we will present here, there are references published over the past 40 years with this intended use. The main problem is that, as unstable molecules, nucleotides require some additional protection to extend their shelf life in the biological environment. Among the different nucleotide carriers, the nano-sized liposomes proved to be an effective strategic tool to overcome all these drawbacks related to the nucleotide high instability. Moreover, due to their low immunogenicity and easy preparation, the liposomes were selected as the main strategy for delivery of the mRNA developed for COVID-19 immunization. For sure this is the most important and relevant example of nucleotide application for human biomedical conditions. In addition, the use of mRNA vaccines for COVID-19 has increased interest in the application of this type of technology to other health conditions. For this review article, we will present some of these examples, especially focused on the use of liposomes to protect and deliver nucleotides for cancer therapy, immunostimulatory activities, enzymatic diagnostic applications, some examples for veterinarian use, and the treatment of neglected tropical disease.
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Affiliation(s)
- Camila Magalhães Cardador
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
| | | | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
| | - Luciano Paulino Silva
- Laboratório de Nanobiotecnologia (LNANO), Embrapa Recursos Genéticos e Biotecnologia, Brasilia 70770-917, DF, Brazil
| | - Aisel Valle Garay
- Molecular Biophysics Laboratory, Department of Cell Biology, Institute of Biological Science, University of Brasília (UnB), Brasília 70910-900, DF, Brazil
| | | | - Izabela Marques Dourado Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia (UnB), Brasilia 70910-900, DF, Brazil
| | - João Paulo Figueiró Longo
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília (UnB), Brasilia 70910-900, DF, Brazil
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Rahman MS, Gulshan MA, Matsumura S, Ikawa Y. Polyethylene glycol molecular crowders enhance the catalytic ability of bimolecular bacterial RNase P ribozymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:715-729. [PMID: 32039645 DOI: 10.1080/15257770.2019.1687909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The modular structure of bacterial ribonuclease P (RNase P) ribozymes, which recognize tertiary structures of precursor tRNAs (pre-tRNAs) to cleave their 5' leader sequence, can be dissected physically into the two structured domain RNAs (S-domain and C-domain). Separately prepared S-domain RNA and C-domain RNA assemble to form bimolecular forms of RNase P ribozymes. We analyzed the effects of polyethylene glycols (PEGs) on pre-tRNA cleavage catalyzed by bimolecular RNase P ribozymes to examine the effects of molecular crowding on the reaction. PEG molecular crowders significantly enhanced the activities of bimolecular RNase P ribozymes, some of which were hardly active without PEGs.
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Affiliation(s)
- Md Sohanur Rahman
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Mst Ara Gulshan
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
| | - Yoshiya Ikawa
- Department of Chemistry, Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama, Japan.,Graduate School of Innovative Life Science, University of Toyama, Gofuku 3190, Toyama, Japan
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Tsuruga R, Uehara N, Suzuki Y, Furuta H, Sugiyama H, Endo M, Matsumura S, Ikawa Y. Oligomerization of a modular ribozyme assembly of which is controlled by a programmable RNA–RNA interface between two structural modules. J Biosci Bioeng 2019; 128:410-415. [DOI: 10.1016/j.jbiosc.2019.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
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Rahman MM, Matsumura S, Ikawa Y. Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site. J Mol Evol 2018; 86:431-442. [DOI: 10.1007/s00239-018-9862-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022]
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Blythe AJ, Fox AH, Bond CS. The ins and outs of lncRNA structure: How, why and what comes next? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:46-58. [PMID: 26325022 DOI: 10.1016/j.bbagrm.2015.08.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/07/2015] [Accepted: 08/27/2015] [Indexed: 12/20/2022]
Abstract
The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Amanda J Blythe
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Archa H Fox
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia 6009, Australia.
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Cantara WA, Olson ED, Musier-Forsyth K. Progress and outlook in structural biology of large viral RNAs. Virus Res 2014; 193:24-38. [PMID: 24956407 PMCID: PMC4252365 DOI: 10.1016/j.virusres.2014.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
Abstract
The field of viral molecular biology has reached a precipice for which pioneering studies on the structure of viral RNAs are beginning to bridge the gap. It has become clear that viral genomic RNAs are not simply carriers of hereditary information, but rather are active players in many critical stages during replication. Indeed, functions such as cap-independent translation initiation mechanisms are, in some cases, primarily driven by RNA structural determinants. Other stages including reverse transcription initiation in retroviruses, nuclear export and viral packaging are specifically dependent on the proper 3-dimensional folding of multiple RNA domains to recruit necessary viral and host factors required for activity. Furthermore, a large-scale conformational change within the 5'-untranslated region of HIV-1 has been proposed to regulate the temporal switch between viral protein synthesis and packaging. These RNA-dependent functions are necessary for replication of many human disease-causing viruses such as severe acute respiratory syndrome (SARS)-associated coronavirus, West Nile virus, and HIV-1. The potential for antiviral development is currently hindered by a poor understanding of RNA-driven molecular mechanisms, resulting from a lack of structural information on large RNAs and ribonucleoprotein complexes. Herein, we describe the recent progress that has been made on characterizing these large RNAs and provide brief descriptions of the techniques that will be at the forefront of future advances. Ongoing and future work will contribute to a more complete understanding of the lifecycles of retroviruses and RNA viruses and potentially lead to novel antiviral strategies.
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Affiliation(s)
| | | | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
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Ishikawa J, Furuta H, Ikawa Y. RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:651-64. [PMID: 23836522 DOI: 10.1002/wrna.1185] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/30/2013] [Accepted: 06/04/2013] [Indexed: 12/24/2022]
Abstract
RNA molecules are versatile biomaterials that act not only as DNA-like genetic materials but also have diverse functions in regulation of cellular biosystems. RNA is capable of regulating gene expression by sequence-specific hybridization. This feature allows the design of RNA-based artificial gene regulators (riboregulators). RNA can also build complex two-dimensional (2D) and 3D nanostructures, which afford protein-like functions and make RNA an attractive material for nanobiotechnology. RNA tectonics is a methodology in RNA nanobiotechnology for the design and construction of RNA nanostructures/nanoobjects through controlled self-assembly of modular RNA units (tectoRNAs). RNA nanostructures designed according to the concept of RNA tectonics are also attractive as tools in synthetic biology, but in vivo RNA tectonics is still in the early stages. This review presents a summary of the achievements of RNA tectonics and its related researches in vitro, and also introduces recent developments that facilitated the use of RNA nanostructures in bacterial cells.
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Affiliation(s)
- Junya Ishikawa
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
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Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M. Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs. BMC Genomics 2012; 13 Suppl 7:S13. [PMID: 23282220 PMCID: PMC3521395 DOI: 10.1186/1471-2164-13-s7-s13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also have similar functions for Burkholderia pseudomallei, a soil bacterium that can adapt to diverse environmental conditions, which causes the disease melioidosis and is also able to infect a wide variety of hosts. RESULTS By integrating several proven sRNA prediction programs into a computational pipeline, available Burkholderia spp. genomes were screened to identify sRNA gene candidates. Orthologous sRNA candidates were then identified via comparative analysis. From the total prediction, 21 candidates were found to have Rfam homologs. RT-PCR and sequencing of candidate sRNA genes of unknown functions revealed six putative sRNAs which were highly conserved in Burkholderia spp. and two that were unique to B. pseudomallei present in a normal culture conditions transcriptome. The validated sRNAs include potential cis-acting elements associated with the modulation of methionine metabolism and one B. pseudomallei-specific sRNA that is expected to bind to the Hfq protein. CONCLUSIONS The use of the pipeline developed in this study and subsequent comparative analysis have successfully aided in the discovery and shortlisting of sRNA gene candidates for validation. This integrated approach identified 29 B. pseudomallei sRNA genes - of which 21 have Rfam homologs and 8 are novel.
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Affiliation(s)
- Jia-Shiun Khoo
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
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Nguyen P, Qin PZ. RNA dynamics: perspectives from spin labels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:62-72. [PMID: 21882345 DOI: 10.1002/wrna.104] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dynamics are important and indispensible physical attributes that play essential roles in RNA function. RNA dynamics are complex, spanning vast timescales, and encompassing a large number of physical modes. The technique of site-directed spin labeling (SDSL), which derives information on local structural and dynamic features of a macromolecule by monitoring a chemically stable nitroxide radical using electron paramagnetic resonance spectroscopy, has been applied to monitor intrinsic dynamics at defined structural states as well as to probe conformational transition dynamics of RNAs. The current state of SDSL studies of RNA dynamics is summarized here. Further development and application of SDSL promise to open up many more opportunities for probing RNA dynamics and connecting dynamics to structure and function.
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Affiliation(s)
- Phuong Nguyen
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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Lönnberg T. Understanding Catalysis of Phosphate‐Transfer Reactions by the Large Ribozymes. Chemistry 2011; 17:7140-53. [DOI: 10.1002/chem.201100009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20140 Turku (Finland), Fax: (+358) 2‐333‐6700
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The Recent Progress of Non-coding RNA and RNomics. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2010.00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Research frontiers highlighted in Science China Life Sciences in 2009. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-4229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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