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Mohammadinezhad R, Jalali SAH, Farahmand H. Evaluation of different direct and indirect SELEX monitoring methods and implementation of melt-curve analysis for rapid discrimination of variant aptamer sequences. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3823-3835. [PMID: 32676627 DOI: 10.1039/d0ay00491j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an iterative method for in vitro selection of aptamers from a random synthetic oligonucleotide library. Successful retrieving of aptamers by SELEX relies on optimization of various steps including target immobilization, aptamer partitioning, amplification, and ssDNA generation, which all require spending considerable effort and cost. Furthermore, due to the random nature of the initial library, SELEX may redirect toward the selection of low-affinity aptamers that are over-represented in the ssDNA population due to PCR bias. Thus, precise monitoring of the SELEX process is crucial to ensure the selection of target-specific aptamers. In the present study, we investigated the reliability and simplicity of different direct and indirect monitoring methods including UV-Vis spectroscopy, real-time PCR quantification and melt-curve analysis, electrophoretic mobility shift assay (EMSA) and enzyme-linked oligonucleotide assay (ELONA) for selection of DNA aptamers for a protein target. All the examined methods were capable of illustrating the gradual evolution of specific aptamers by the progression of SELEX and showed almost similar results regarding the identification of the enriched round of selection. Moreover, we describe the use of melt-curve analysis in the colony real-time PCR method as a simple, robust, and repeatable tool for pre-sequencing separation of distinct aptamer clones.
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Affiliation(s)
- Rezvan Mohammadinezhad
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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Lin CJ, Hu ZG, Yuan GD, Lei B, He SQ. Complements are involved in alcoholic fatty liver disease, hepatitis and fibrosis. World J Hepatol 2018; 10:662-669. [PMID: 30386459 PMCID: PMC6206158 DOI: 10.4254/wjh.v10.i10.662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 08/01/2018] [Indexed: 02/06/2023] Open
Abstract
The complement system is a key component of the body’s immune system. When abnormally activated, this system can induce inflammation and damage to normal tissues and participate in the development and progression of a variety of diseases. In the past, many scholars believed that alcoholic liver disease (ALD) is induced by the stress of ethanol on liver cells, including oxidative stress and dysfunction of mitochondria and protease bodies, causing hepatocyte injury and apoptosis. Recent studies have shown that complement activation is also involved in the genesis and development of ALD. This review focuses on the roles of complement activation in ALD and of therapeutic intervention in complement-activation pathways. We intend to provide new ideas on the diagnosis and treatment of ALD.
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Affiliation(s)
- Cheng-Jie Lin
- Department of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zhi-Gao Hu
- Department of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Guan-Dou Yuan
- Department of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Biao Lei
- Department of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Song-Qing He
- Department of Hepatopancreatobiliary Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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Mustoe AM, Busan S, Rice GM, Hajdin CE, Peterson BK, Ruda VM, Kubica N, Nutiu R, Baryza JL, Weeks KM. Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing. Cell 2018; 173:181-195.e18. [PMID: 29551268 DOI: 10.1016/j.cell.2018.02.034] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/02/2018] [Accepted: 02/15/2018] [Indexed: 11/25/2022]
Abstract
mRNAs can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited our understanding of the prevalence and functions of mRNA structure. We use SHAPE-MaP experiments in living E. coli cells to derive quantitative, nucleotide-resolution structure models for 194 endogenous transcripts encompassing approximately 400 genes. Individual mRNAs have exceptionally diverse architectures, and most contain well-defined structures. Active translation destabilizes mRNA structure in cells. Nevertheless, mRNA structure remains similar between in-cell and cell-free environments, indicating broad potential for structure-mediated gene regulation. We find that the translation efficiency of endogenous genes is regulated by unfolding kinetics of structures overlapping the ribosome binding site. We discover conserved structured elements in 35% of UTRs, several of which we validate as novel protein binding motifs. RNA structure regulates every gene studied here in a meaningful way, implying that most functional structures remain to be discovered.
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Affiliation(s)
- Anthony M Mustoe
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
| | - Steven Busan
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Greggory M Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA; Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | | | - Brant K Peterson
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Vera M Ruda
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Neil Kubica
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Razvan Nutiu
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Jeremy L Baryza
- Novartis Institutes for Biomedical Research, Inc., Cambridge, MA, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA.
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Development of aptamers against unpurified proteins. Biotechnol Bioeng 2017; 114:2706-2716. [DOI: 10.1002/bit.26389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/24/2017] [Accepted: 07/19/2017] [Indexed: 01/12/2023]
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Barfod A, Singh B, Johanson U, Riesbeck K, Kjellbom P. In vitro selection of RNA aptamers directed against protein E: a Haemophilus influenzae adhesin. Mol Biotechnol 2015; 56:714-25. [PMID: 24682699 DOI: 10.1007/s12033-014-9749-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein E (PE) of Haemophilus influenzae is a highly conserved ubiquitous surface protein involved in adhesion to and activation of epithelial cells. The host proteins-vitronectin, laminin, and plasminogen are major targets for PE-dependent interactions with the host. To identify novel inhibitory molecules of PE, we used an in vitro selection method based on systematic evolution of ligands by exponential enrichment known as SELEX in order to select 2'F-modified RNA aptamers that specifically bind to PE. Fourteen selection cycles were performed with decreasing concentrations of PE. Sequencing of clones from the 14th selection round revealed the presence of semiconserved sequence motifs in loop regions of the RNA aptamers. Among these, three aptamers showed the highest affinity to PE in electrophoretic mobility shift assays and in dot blots. These three aptamers also inhibited the interaction of PE with vitronectin as revealed by ELISA. Moreover, pre-treatment of H. influenzae with the aptamers significantly inhibited binding of vitronectin to the bacterial surface. Biacore experiments indicated that one of the aptamers had a higher binding affinity for PE as compared to the other aptamers. Our results show that it is possible to select RNA inhibitors against bacterial adhesins using SELEX in order to inhibit interactions with target proteins.
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Affiliation(s)
- Anders Barfod
- Department of Biochemistry and Structural Biology, CMPS, Lund University, Box 124, 221 00, Lund, Sweden,
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Lee SC, Gedi V, Ha NR, Cho JH, Park HC, Yoon MY. Development of receptor-based inhibitory RNA aptamers for anthrax toxin neutralization. Int J Biol Macromol 2015; 77:293-302. [PMID: 25841381 DOI: 10.1016/j.ijbiomac.2015.03.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/27/2015] [Accepted: 03/15/2015] [Indexed: 10/23/2022]
Abstract
Anthrax toxin excreted by Bacillus anthracis is the key causative agent of infectious anthrax disease. In the present study, we targeted the binding of PA to the ATR/TEM8 Von Willebrand factor type A (VWA) domain, which we cloned into Escherichia coli and purified to homogeneity under denaturing conditions. To develop an anthrax toxin inhibitor, we selected and identified short single strand RNA aptamers (approximately 30mer) consisting of different sequences of nucleic acids with a high binding affinity in the 100 nanomolar range against the recombinant ATR/TEM8 VWA domain using systematic evolution of ligands by exponential enrichment (SELEX). Five candidate aptamers were further characterized by several techniques including secondary structural analysis. The inhibitor efficiency (IC50) of one of the aptamers toward anthrax toxin was approximately 5μM in macrophage RAW 264.7 cells, as determined from cytotoxicity analysis by MTT assay. We believe that the candidate aptamers should be useful for blocking the binding of PA to its receptor in order to neutralize anthrax toxin.
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Affiliation(s)
- Sang-Choon Lee
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Vinayakumar Gedi
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Na-Reum Ha
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Jun-Haeng Cho
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Hae-Chul Park
- Veterinary Drugs & Biologics Division, Animal and Plant Quarantine Agency (QIA), Anyang 430-757, Republic of Korea
| | - Moon-Young Yoon
- Department of Chemistry and Research Institute of Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea.
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Maticzka D, Lange SJ, Costa F, Backofen R. GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol 2014; 15:R17. [PMID: 24451197 PMCID: PMC4053806 DOI: 10.1186/gb-2014-15-1-r17] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 01/22/2014] [Indexed: 12/01/2022] Open
Abstract
We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstrating that the modeled binding preferences conform to the literature, and showcase the biological relevance and two applications of GraphProt models. First, estimated binding affinities correlate with experimental measurements. Second, predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not. Computational binding models, such as those provided by GraphProt, are essential for predicting RBP binding sites and affinities in all tissues. GraphProt is freely available at http://www.bioinf.uni-freiburg.de/Software/GraphProt.
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Gopinath SCB. Mapping of RNA-protein interactions. Anal Chim Acta 2009; 636:117-28. [PMID: 19264161 DOI: 10.1016/j.aca.2009.01.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 01/26/2009] [Accepted: 01/26/2009] [Indexed: 12/19/2022]
Abstract
RNA-protein interactions are important biological events that perform multiple functions in all living organisms. The wide range of RNA interactions demands diverse conformations to provide contacts for the selective recognition of proteins. Various analytical procedures are presently available for quantitative analyses of RNA-protein complexes, but analytical-based mapping of these complexes is essential to probe specific interactions. In this overview, interactions of functional RNAs and RNA-aptamers with target proteins are discussed by means of mapping strategies.
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Affiliation(s)
- Subash Chandra Bose Gopinath
- Institute for Biological Resources and Functions & Center for Applied Near Field Optics Research (CAN-FOR), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba City 305-8562, Ibaraki, Japan
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Kim Y, Lee Y. Novel function of C5 protein as a metabolic stabilizer of M1 RNA. FEBS Lett 2008; 583:419-24. [PMID: 19114042 DOI: 10.1016/j.febslet.2008.12.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 12/04/2008] [Accepted: 12/17/2008] [Indexed: 11/26/2022]
Abstract
Escherichia coli RNase P is a ribonucleoprotein composed of a large RNA subunit (M1 RNA) and a small protein subunit (C5 protein). We examined if C5 protein plays a role in maintaining metabolic stability of M1 RNA. The sequestration of C5 protein available for M1 RNA binding reduced M1 RNA stability in vivo, and its reduced stability was recovered via overexpression of C5 protein. In addition, M1 RNA was rapidly degraded in a temperature-sensitive C5 protein mutant strain at non-permissive temperatures. Collectively, our results demonstrate that the C5 protein metabolically stabilizes M1 RNA in the cell.
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Affiliation(s)
- Yool Kim
- Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
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Kim HJ, Kwon M, Yu J. Elucidation of the RNA target of linezolid by using a linezolid-neomycin B heteroconjugate and genomic SELEX. Bioorg Med Chem 2007; 15:7688-95. [PMID: 17869523 DOI: 10.1016/j.bmc.2007.08.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 08/25/2007] [Accepted: 08/28/2007] [Indexed: 01/03/2023]
Abstract
A covalently modified heteroconjugate between linezolid and neomycin B leads to an enhanced and more specific binding affinity to hairpin RNA targets in comparison to neomycin B itself. This heteroconjugate was used as a lure to select linezolid-specific hairpin RNA from an Escherichia coli genome RNA. The selected RNA obtained after eight cycles not only has typical stem-loop structures but also includes known sequences of the linezolid binding site. The results of RNA footprinting show that the binding site of the heteroconjugate encompasses both stem and loop regions, suggesting that the possible binding site for linezolid is in the terminal loop. In addition, findings from application of a surface plasmon resonance assay clearly demonstrate that linezolid binds to selected hairpin RNA in a highly specific manner with a low millimolar affinity. The results suggest that heteroconjugates might represent a generally useful approach in studies aimed at uncovering loop-specific RNA binding ligands that would be otherwise difficult to identify owing to their weak affinities.
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Affiliation(s)
- Hyun Jin Kim
- Department of Chemistry and Education, Seoul National University, Seoul 151-742, Republic of Korea
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Expression of a Small Protein Encoded by the 3' Flanking Sequence of the Escherichia coli rnpB Gene. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.6.1010] [Citation(s) in RCA: 2] [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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Vaish NK, Kossen K, Andrews LE, Pasko C, Seiwert SD. Monitoring protein modification with allosteric ribozymes. Methods 2004; 32:428-36. [PMID: 15003605 DOI: 10.1016/j.ymeth.2003.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2003] [Indexed: 10/26/2022] Open
Abstract
An allosteric ribozyme is an RNA-based enzyme (ribozyme) whose catalytic activity is modulated by molecular recognition of a protein. The direct coupling of a detectable catalytic event to molecular recognition by an allosteric ribozyme enables simple assays for quantitative protein detection. Most significantly, the mode of development and molecular recognition characteristics of allosteric ribozymes are fundamentally different from antibodies, providing them with functional characteristics that complement those of antibodies. Allosteric ribozymes can be developed using native proteins and, therefore, are often sensitive to protein conformation. In contrast, antibodies tend to recognize a series of adjacent amino acids as a consequence of antigen presentation and typically are not sensitive to protein conformation. Unlike antibody development, the development of allosteric ribozymes is a completely in vitro process that allows the specificity of an allosteric ribozyme to be tightly controlled. These significant differences from antibodies allow the pre-programmed development of conformation-state-specific protein detection reagents that can be used to investigate the activation-state of signal transduction components.
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Affiliation(s)
- Narendra K Vaish
- Sirna Therapeutics, Inc, 2950 Wilderness Place, Boulder, CO 80301, USA.
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