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Ge P, Islam S, Zhong C, Zhang S. De novo discovery of structural motifs in RNA 3D structures through clustering. Nucleic Acids Res 2018; 46:4783-4793. [PMID: 29534235 PMCID: PMC5961109 DOI: 10.1093/nar/gky139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 02/09/2018] [Accepted: 02/16/2018] [Indexed: 11/16/2022] Open
Abstract
As functional components in three-dimensional (3D) conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline. Compared with other clustering approaches, our method has two benefits: first, the underlying alignment algorithm is tolerant to the variations in 3D structures. Second, sophisticated downstream analysis has been performed to ensure the clusters are valid and easily applied to further research. The final clustering results contain many interesting new variants of known motif families, such as GNAA tetraloop, kink-turn, sarcin-ricin and T-loop. We have also discovered potential novel functional motifs conserved in ribosomal RNA, sgRNA, SRP RNA, riboswitch and ribozyme.
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Affiliation(s)
- Ping Ge
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Shahidul Islam
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
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Abstract
As an indispensable process of cell life, apoptosis is essential for keeping homeostasis at cell level. Dysregulation of apoptosis is usually involved in the pathological processes of many complex diseases including cancer. With the properties such as high affinity and specificity to their targets, easy of synthesis and modification and good biocompatibility, aptamers have been attractive molecules applied in basic research, diagnostics and therapeutics. This review mainly focuses on the recent researches on application of aptamers in interference of cell apoptosis. Key targets along the intrinsic and extrinsic apoptosis pathways were respectively dissected using aptamers as a tool, providing an insight into the pathological processes, especially for cancer.
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Cho B. SELEX with Affinity Chromatography on RNA-RNA Interaction. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2015. [DOI: 10.5012/jkcs.2015.59.1.93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) protocol is a valuable technique to identify RNA aptamers interacting with RNA structural motifs. RNA aptamers are mainly resolved with affinity column chromatography and electrophoretic mobility shift assay (EMSA). Here, we describe the separation of the RNA aptamers binding to an RNA stem-loop target with affinity chromatography using the column attached the target RNA and nondenaturing polyacrylamide gel electrophoresis to obtain a single predominant RNA aptamer family.
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Affiliation(s)
- B Cho
- Department of Applied Chemistry, Cheongju University, 298 Daeseongro, Cheongju Chungbuk, 360-764, S. Korea,
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Bak G, Han K, Kim KS, Lee Y. Electrophoretic mobility shift assay of RNA-RNA complexes. Methods Mol Biol 2015; 1240:153-63. [PMID: 25352144 DOI: 10.1007/978-1-4939-1896-6_12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A simple, rapid, and sensitive electrophoretic mobility shift assay (EMSA) can be successfully used to analyze RNA-RNA interactions. The EMSA of RNA-RNA complexes can be further used to evaluate the specificity of interactions using competitor RNAs in combination with their mutated versions or nonspecific RNAs, such as yeast tRNA. RNA is simply prepared by in vitro transcription from PCR product templates. Detailed experimental descriptions for EMSA-based analysis of specific RNA-RNA interactions between Sib RNAs and ibs mRNAs as a representative example are presented.
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Affiliation(s)
- Geunu Bak
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
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Choi SY, Cho B. Identification of a Conserved Sequence Motif of an RNA Aptamer Binding to a G-rich Sequence RNA with Structural Probes. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.11.3471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Choi SY, Cho B. Secondary Structure Analysis of an RNA Interacting with Guanine-rich Sequence. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.12.4265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cho BR. Identification of Structural Motif of RNAs Interacting with the G-rich Sequence RNA. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.8.2796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cho BR. Secondary Structure Analysis of a G-rich Sequence Recognizing RNA Aptamer with Structure Specific Enzymes. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.6.2137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Identification of Structural Motifs of RNA Aptamers Interacting with the Stem-loop Sequence at the Gag-pol Junction of HIV-1 RNA. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.11.2227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Poole ES, Young DJ, Askarian-Amiri ME, Scarlett DJG, Tate WP. Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome. Cell Res 2007; 17:591-607. [PMID: 17621307 DOI: 10.1038/cr.2007.56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to span the decoding centre and the peptidyl transferase centre (PTC) of the ribosome. Structurally, it must fit into a site crafted for a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide, the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein that results in a critical conformational change allowing it to contact the PTC. A structural model of the bacterial termination complex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stop codon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix alpha5. The anticodon loop also makes contact with the base following the stop codon that is known to strongly influence termination efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the PTC. The mRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflect structural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiased SELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in its different binding conformations within the active centre of the ribosome.
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Affiliation(s)
- Elizabeth S Poole
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Kouvela EC, Gerbanas GV, Xaplanteri MA, Petropoulos AD, Dinos GP, Kalpaxis DL. Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine. Nucleic Acids Res 2007; 35:5108-19. [PMID: 17652323 PMCID: PMC1976436 DOI: 10.1093/nar/gkm546] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
5S rRNA is an integral component of the large ribosomal subunit in virtually all living organisms. Polyamine binding to 5S rRNA was investigated by cross-linking of N1-azidobenzamidino (ABA)-spermine to naked 5S rRNA or 50S ribosomal subunits and whole ribosomes from Escherichia coli cells. ABA-spermine cross-linking sites were kinetically measured and their positions in 5S rRNA were localized by primer extension analysis. Helices III and V, and loops A, C, D and E in naked 5S rRNA were found to be preferred polyamine binding sites. When 50S ribosomal subunits or poly(U)-programmed 70S ribosomes bearing tRNAPhe at the E-site and AcPhe-tRNA at the P-site were targeted, the susceptibility of 5S rRNA to ABA-spermine was greatly reduced. Regardless of 5S rRNA assembly status, binding of spermine induced significant changes in the 5S rRNA conformation; loop A adopted an apparent ‘loosening’ of its structure, while loops C, D, E and helices III and V achieved a more compact folding. Poly(U)-programmed 70S ribosomes possessing 5S rRNA cross-linked with spermine were more efficient than control ribosomes in tRNA binding, peptidyl transferase activity and translocation. Our results support the notion that 5S rRNA serves as a signal transducer between regions of 23S rRNA responsible for principal ribosomal functions.
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Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 933] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
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Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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Abstract
Complex traits are generally believed to be influenced by multiple loci. Identification of loci involved in complex traits is more difficult for interacting than for additive loci. Here we describe an extension of the program lm_twoqtl in the package MORGAN to handle two quantitative trait loci (QTLs) with gene-gene interaction. We investigate whether parametric linkage analysis that accounts for such epistasis improves prospects for linkage detection and accuracy of localization of QTLs. Through use of simulated data we show that analysis that accounts for epistasis provides higher lod scores and better localization than does analysis without epistasis. In addition, we demonstrate that the difference between lod scores in the presence vs. absence of use of an interaction model in analysis is greater in extended than in nuclear pedigrees.
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Affiliation(s)
- Yun Ju Sung
- Division of Medical Genetics, Department of Medicine, University of Washington, Washington, WA 98195-7720, USA
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Preparation of DNA Library and Affinity Column for the Analysis of RNA-RNA Interaction. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2006. [DOI: 10.5012/jkcs.2006.50.3.269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Szymański M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5 S rRNA: structure and interactions. Biochem J 2003; 371:641-51. [PMID: 12564956 PMCID: PMC1223345 DOI: 10.1042/bj20020872] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2002] [Revised: 01/28/2003] [Accepted: 02/04/2003] [Indexed: 11/17/2022]
Abstract
5 S rRNA is an integral component of the large ribosomal subunit in all known organisms. Despite many years of intensive study, the function of 5 S rRNA in the ribosome remains unknown. Advances in the analysis of ribosome structure that have revealed the crystal structures of large ribosomal subunits and of the complete ribosome from various organisms put the results of studies on 5 S rRNA in a new perspective. This paper summarizes recently published data on the structure and function of 5 S rRNA and its interactions in complexes with proteins, within and outside the ribosome.
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Affiliation(s)
- Maciej Szymański
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
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In vitro Selection of RNA Aptamers which Bind to Escherichia coli tRNA Val. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2002. [DOI: 10.5012/jkcs.2002.46.2.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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