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Laguía O, Bosso G, Martínez-Torrecuadrada J, Míguez-Amil S, Fernández-Leiro R, Blasco MA. Protocol for the generation and purification of high-molecular-weight covalent RNA-DNA hybrids with T4 RNA ligase. STAR Protoc 2024; 5:102930. [PMID: 38430520 PMCID: PMC10914518 DOI: 10.1016/j.xpro.2024.102930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 03/04/2024] Open
Abstract
RNA-DNA covalent hybrids (RDHs) are widely employed in biology. Although RDHs can be manufactured, the synthesis of molecules longer than 120 nucleotides is challenging. Here, we present a protocol for the generation and purification of high-grade purified high-molecular-weight 5'-RNA-DNA-3' hybrids. We describe steps for preparing oligos and buffers, ligation reaction, and high-performance liquid chromatography-based RDH purification. This protocol is executable in standard molecular biology laboratories.
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Affiliation(s)
- Oscar Laguía
- Telomeres and Telomerase Group, Molecular Oncology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Giuseppe Bosso
- Telomeres and Telomerase Group, Molecular Oncology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | | | - Samuel Míguez-Amil
- Genome Integrity and Structural Biology Group, Structural Biology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Rafael Fernández-Leiro
- Genome Integrity and Structural Biology Group, Structural Biology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
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Fu W, Ma L, Ju Y, Xu J, Li H, Shi S, Zhang T, Zhou R, Zhu J, Xu R, You C, Lin Y. Therapeutic siCCR2 Loaded by Tetrahedral Framework DNA Nanorobotics in Therapy for Intracranial Hemorrhage. ADVANCED FUNCTIONAL MATERIALS 2021. [DOI: 10.1002/adfm.202101435] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Wei Fu
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Lu Ma
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Yan Ju
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Jianguo Xu
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Hao Li
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
| | - Ronghui Zhou
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
| | - Jianwei Zhu
- Department of Neurosurgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu 610072 China
| | - Ruxiang Xu
- Department of Neurosurgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu 610072 China
| | - Chao You
- Department of Neurosurgery West China Hospital of Sichuan University Chengdu 610041 P. R. China
- Department of Neurosurgery West China Hospital of Sichuan University China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases West China Hospital of Stomatology Sichuan University Chengdu 610041 P. R. China
- Department of Neurosurgery Sichuan Provincial People's Hospital University of Electronic Science and Technology of China Chengdu 610072 China
- College of Biomedical Engineering Sichuan University Chengdu Sichuan 610041 China
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Borgheti-Cardoso LN, Viegas JSR, Silvestrini AVP, Caron AL, Praça FG, Kravicz M, Bentley MVLB. Nanotechnology approaches in the current therapy of skin cancer. Adv Drug Deliv Rev 2020; 153:109-136. [PMID: 32113956 DOI: 10.1016/j.addr.2020.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/16/2019] [Accepted: 02/26/2020] [Indexed: 02/07/2023]
Abstract
Skin cancer is a high burden disease with a high impact on global health. Conventional therapies have several drawbacks; thus, the development of effective therapies is required. In this context, nanotechnology approaches are an attractive strategy for cancer therapy because they enable the efficient delivery of drugs and other bioactive molecules to target tissues with low toxic effects. In this review, nanotechnological tools for skin cancer will be summarized and discussed. First, pathology and conventional therapies will be presented, followed by the challenges of skin cancer therapy. Then, the main features of developing efficient nanosystems will be discussed, and next, the most commonly used nanoparticles (NPs) described in the literature for skin cancer therapy will be presented. Subsequently, the use of NPs to deliver chemotherapeutics, immune and vaccine molecules and nucleic acids will be reviewed and discussed as will the combination of physical methods and NPs. Finally, multifunctional delivery systems to codeliver anticancer therapeutic agents containing or not surface functionalization will be summarized.
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Yu J, Li J, Zhai S, Lin L, Wang K, Tang B, Meng H, Tian L. Enzymatically Synthesized DNA Polymer as Co-carrier for Enhanced RNA Interference. ACS APPLIED BIO MATERIALS 2019; 2:5204-5215. [DOI: 10.1021/acsabm.9b00862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P. R. China
- School of Advanced Materials, Peking University Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Kui Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Bin Tang
- Department of Biomedical Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Shenzhen, Guangdong 518055, P. R. China
| | - Hong Meng
- School of Advanced Materials, Peking University Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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Abstract
As synthetic small interfering RNA (siRNA) against antitumoral gene targets show promise for cancer treatment, different siRNA delivery systems have sparkled intense investigations. To develop tumor-specific carriers for cytosolic and systemic siRNA delivery, our laboratory has recently generated folate-conjugated targeted combinatorial siRNA polyplexes based on sequence-defined oligomer platform compatible with solid-phase-supported synthesis. These polyplexes presented efficient siRNA-mediated gene silencing in folate receptor-expressing tumors in vitro and in vivo. In this chapter, we provide a brief background on the formulation design and detailed protocols to evaluate polyplex formation, gene silencing efficiency, and receptor-directed cell killing in cancer cells using targeted combinatorial siRNA polyplexes.
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Affiliation(s)
- Dian-Jang Lee
- Department of Pharmacy, Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
- Nanosystems Initiative Munich (NIM), Munich, Germany
| | - Ernst Wagner
- Department of Pharmacy, Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany.
- Nanosystems Initiative Munich (NIM), Munich, Germany.
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Abstract
Gene therapy is an important therapeutic strategy in the treatment of a wide range of genetic disorders. Polymers forming stable complexes with nucleic acids (NAs) are non-viral gene carriers. The self-assembly of polymers and nucleic acids is typically a complex process that involves many types of interaction at different scales. Electrostatic interaction, hydrophobic interaction, and hydrogen bonds are three important and prevalent interactions in the polymer/nucleic acid system. Electrostatic interactions and hydrogen bonds are the main driving forces for the condensation of nucleic acids, while hydrophobic interactions play a significant role in the cellular uptake and endosomal escape of polymer-nucleic acid complexes. To design high-efficiency polymer candidates for the DNA and siRNA delivery, it is necessary to have a detailed understanding of the interactions between them in solution. In this chapter, we survey the roles of the three important interactions between polymers and nucleic acids during the formation of polyplexes and summarize recent understandings of the linear polyelectrolyte-NA interactions and dendrimer-NA interactions. We also review recent progress optimizing the gene delivery system by tuning these interactions.
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Lee DJ, He D, Kessel E, Padari K, Kempter S, Lächelt U, Rädler JO, Pooga M, Wagner E. Tumoral gene silencing by receptor-targeted combinatorial siRNA polyplexes. J Control Release 2016; 244:280-291. [DOI: 10.1016/j.jconrel.2016.06.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 02/06/2023]
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Reinhard S, Wagner E. How to Tackle the Challenge of siRNA Delivery with Sequence-Defined Oligoamino Amides. Macromol Biosci 2016; 17. [PMID: 27328447 DOI: 10.1002/mabi.201600152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 05/24/2016] [Indexed: 12/31/2022]
Abstract
RNA interference (RNAi) as a mechanism of gene regulation provides exciting opportunities for medical applications. Synthetic small interfering RNA (siRNA) triggers the knockdown of complementary mRNA sequences in a catalytic fashion and has to be delivered into the cytosol of the targeted cells. The design of adequate carrier systems to overcome multiple extracellular and intracellular roadblocks within the delivery process has utmost importance. Cationic polymers form polyplexes through electrostatic interaction with negatively charged nucleic acids and present a promising class of carriers. Issues of polycations regarding toxicity, heterogeneity, and polydispersity can be overcome by solid-phase-assisted synthesis of sequence-defined cationic oligomers. These medium-sized highly versatile nucleic acid carriers display low cytotoxicity and can be modified and tailored in multiple ways to meet specific requirements of nucleic acid binding, polyplex size, shielding, targeting, and intracellular release of the cargo. In this way, sequence-defined cationic oligomers can mimic the dynamic and bioresponsive behavior of viruses.
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Affiliation(s)
- Sören Reinhard
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig Maximilians University, 81377, Munich, Germany
| | - Ernst Wagner
- Pharmaceutical Biotechnology, Department of Pharmacy, Ludwig Maximilians University, 81377, Munich, Germany.,Nanosystems Initiative Munich (NIM), 80799, Munich, Germany
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