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Lyu J, Yang M, Zhang C, Luo Y, Qin T, Su Z, Huang Z. DNA nanostructures directed by RNA clamps. NANOSCALE 2021; 13:19870-19874. [PMID: 34825903 DOI: 10.1039/d1nr03919a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA chains can be folded rationally by using DNA staples, and the programmed structures are of great potential in nanomaterial studies. However, due to the short DNA staples forming duplexes and displaying limitations in structural diversity and stability, the folded DNA nanostructures are usually generated with structural mis-formations, low yields and poor efficiencies, which can restrict their folding patterns and applications. To overcome these problems, we set out to use RNA as a clamp to form polygons, and herein demonstrated the ability to use a structural RNA-but not its corresponding DNA-to fold DNA chains into nanostructures with high efficiency (up to a 95.1% yield). Furthermore, we discovered that the 2'-methylated version of the RNA can, compared to the unmodified RNA, even more efficiently fold DNA chains (up to a 98.5% yield). Interestingly, the RNA clamp can fold DNA scaffolds with one, two or four folding units into the same square shape. Furthermore, the RNA can direct the DNA chains with three, four and five folding units into triangular, square and pentagonal nano-shapes, respectively. In addition, we confirmed their enlarged nano-shapes by performing electron microscopy (EM) imaging. These formed nanostructures revealed the potential cooperation between the DNA scaffold and RNA clamp. Moreover, our research demonstrated a novel strategy, involving using RNA clamps displaying structural diversity and duplex stability, for folding DNA into diverse nanostructures.
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Affiliation(s)
- Jiazhen Lyu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Mei Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Tong Qin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Zhen Huang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China.,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610000, Sichuan, P. R. China.
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Piro RM, Marsico A. Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations. Methods Mol Biol 2019; 1912:301-321. [PMID: 30635899 DOI: 10.1007/978-1-4939-8982-9_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery that a considerable portion of eukaryotic genomes is transcribed and gives rise to long noncoding RNAs (lncRNAs) provides an important new perspective on the transcriptome and raises questions about the centrality of these lncRNAs in gene-regulatory processes and diseases. The rapidly increasing number of mechanistically investigated lncRNAs has provided evidence for distinct functional classes, such as enhancer-like lncRNAs, which modulate gene expression via chromatin looping, and noncoding competing endogenous RNAs (ceRNAs), which act as microRNA decoys. Despite great progress in the last years, the majority of lncRNAs are functionally uncharacterized and their implication for disease biogenesis and progression is unknown. Here, we summarize recent developments in lncRNA function prediction in general and lncRNA-disease associations in particular, with emphasis on in silico methods based on network analysis and on ceRNA function prediction. We believe that such computational techniques provide a valuable aid to prioritize functional lncRNAs or disease-relevant lncRNAs for targeted, experimental follow-up studies.
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Affiliation(s)
- Rosario Michael Piro
- Institut für Informatik, Freie Universität Berlin, Berlin, Germany.,Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annalisa Marsico
- Institut für Informatik, Freie Universität Berlin, Berlin, Germany. .,Max-Planck-Institut für molekulare Genetik, Berlin, Germany.
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Leisegang MS. LET's sponge: How the lncRNA PFL promotes cardiac fibrosis. Theranostics 2018; 8:874-877. [PMID: 29463987 PMCID: PMC5817098 DOI: 10.7150/thno.23364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 10/26/2017] [Indexed: 12/22/2022] Open
Abstract
Compared to their protein-coding counterparts, almost nothing is known about the role of long noncoding RNAs (lncRNAs) in cardiac fibrosis. In the current report, Liang and Pan et al. characterized the pro-fibrotic lncRNA PFL in respect to cardiac fibrosis in mice. PFL was upregulated in the hearts of mice after myocardial infarction and in fibrotic cardiac fibroblasts. Moreover, PFL competitively sponged the cardio-protective miRNA let-7d in cardiac fibroblasts. Knockdown of platelet activating factor receptor (PTAFR) was shown to affect the pro-fibrotic collagen production mediated by PFL. PTAFR overexpression also led to collagen production and RNA abundance of PTAFR was also regulated by miRNA let-7d. Therefore, the PFL/PTAFR/let-7d-dependent gene regulatory mechanism proposed by the authors manifests the hypothesis of competing endogenous RNAs to cardiac fibrosis.
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Affiliation(s)
- Matthias S. Leisegang
- Goethe-University, Institute for Cardiovascular Physiology, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
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