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Sapkota K, Lucas JK, Faulkner JW, Lichte MF, Guo YL, Burke DH, Huang F. Post-transcriptional capping generates coenzyme A-linked RNA. RNA Biol 2024; 21:1-12. [PMID: 38032240 PMCID: PMC10761072 DOI: 10.1080/15476286.2023.2288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/01/2023] Open
Abstract
NAD can be inserted co-transcriptionally via non-canonical initiation to form NAD-RNA. However, that mechanism is unlikely for CoA-linked RNAs due to low intracellular concentration of the required initiator nucleotide, 3'-dephospho-CoA (dpCoA). We report here that phosphopantetheine adenylyltransferase (PPAT), an enzyme of CoA biosynthetic pathway, accepts RNA transcripts as its acceptor substrate and transfers 4'-phosphopantetheine to yield CoA-RNA post-transcriptionally. Synthetic natural (RNAI) and small artificial RNAs were used to identify the features of RNA that are needed for it to serve as PPAT substrate. RNAs with 4-10 unpaired nucleotides at the 5' terminus served as PPAT substrates, but RNAs having <4 unpaired nucleotides did not undergo capping. No capping was observed when the +1A was changed to G or when 5' triphosphate was removed by RNA pyrophosphohydrolase (RppH), suggesting the enzyme recognizes pppA-RNA as an ATP analog. PPAT binding affinities were equivalent for transcripts with +1A, +1 G, or 5'OH (+1A), indicating that productive enzymatic recognition is driven more by local positioning effects than by overall binding affinity. Capping rates were independent of the number of unpaired nucleotides in the range of 4-10 nucleotides. Capping was strongly inhibited by ATP, reducing CoA-RNA production ~70% when equimolar ATP and substrate RNA were present. Dual bacterial expression of candidate RNAs with different 5' structures followed by CoA-RNA CaptureSeq revealed 12-fold enrichment of the better PPAT substrate, consistent with in vivo CoA-capping of RNA transcripts by PPAT. These results suggest post-transcriptional RNA capping as a possible mechanism for the biogenesis of CoA-RNAs in bacteria.
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Affiliation(s)
- Krishna Sapkota
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Jordyn K. Lucas
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Jarrett W. Faulkner
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Matt F. Lichte
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Yan-Lin Guo
- Department of Cell and Molecular Biology, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Donald H. Burke
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO, USA
| | - Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
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2
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Feyrer H, Gurdap CO, Marušič M, Schlagnitweit J, Petzold K. Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR. PLoS One 2022; 17:e0264662. [PMID: 35802676 PMCID: PMC9269771 DOI: 10.1371/journal.pone.0264662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods represent an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.
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Affiliation(s)
- Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Cenk Onur Gurdap
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Maja Marušič
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Slovenian NMR Center, National Institute of Chemistry, Ljubljana, Slovenia
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- Centre de RMN à Très Hauts Champs de Lyon, UMR5082 CNRS/ENS-Lyon/Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
- * E-mail:
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3
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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4
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Xie Y, Fang Z, Yang W, He Z, Chen K, Heng P, Wang B, Zhou X. 6-Iodopurine as a Versatile Building Block for RNA Purine Architecture Modifications. Bioconjug Chem 2022; 33:353-362. [PMID: 35119264 DOI: 10.1021/acs.bioconjchem.1c00595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Natural modified bases in RNA were found to be indispensable for basic biological processes. In addition, artificial RNA modifications have been a versatile toolbox for the study of RNA interference, structure, and dynamics. Here, we present a chemical method for the facile synthesis of RNA containing C6-modified purine. 6-Iodopurine, as a postsynthetic building block with high reactivity, was used for metal-free construction of C-N, C-O, and C-S bonds under mild conditions and C-C bond formation by Suzuki-Miyaura cross-coupling. Our strategy provides a convenient approach for the synthesis of various RNA modifications, especially for oligonucleotides containing specific structures.
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Affiliation(s)
- Yalun Xie
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhentian Fang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Yang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiyong He
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Panpan Heng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Baoshan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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5
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Perzanowska O, Majewski M, Strenkowska M, Głowala P, Czarnocki-Cieciura M, Mazur M, Kowalska J, Jemielity J. Nucleotide-decorated AuNPs as probes for nucleotide-binding proteins. Sci Rep 2021; 11:15741. [PMID: 34344911 PMCID: PMC8333360 DOI: 10.1038/s41598-021-94983-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
Gold nanoparticles (AuNPs) decorated with biologically relevant molecules have variety of applications in optical sensing of bioanalytes. Coating AuNPs with small nucleotides produces particles with high stability in water, but functionality-compatible strategies are needed to uncover the full potential of this type of conjugates. Here, we demonstrate that lipoic acid-modified dinucleotides can be used to modify AuNPs surfaces in a controllable manner to produce conjugates that are stable in aqueous buffers and biological mixtures and capable of interacting with nucleotide-binding proteins. Using this strategy we obtained AuNPs decorated with 7-methylguanosine mRNA 5' cap analogs and showed that they bind cap-specific protein, eIF4E. AuNPs decorated with non-functional dinucleotides also interacted with eIF4E, albeit with lower affinity, suggesting that eIF4E binding to cap-decorated AuNPs is partially mediated by unspecific ionic interactions. This issue was overcome by applying lipoic-acid-Tris conjugate as a charge-neutral diluting molecule. Tris-Lipo-diluted cap-AuNPs conjugates interacted with eIF4E in fully specific manner, enabling design of functional tools. To demonstrate the potential of these conjugates in protein sensing, we designed a two-component eIF4E sensing system consisting of cap-AuNP and 4E-BP1-AuNP conjugates, wherein 4E-BP1 is a short peptide derived from 4E-BP protein that specifically binds eIF4E at a site different to that of the 5' cap. This system facilitated controlled aggregation, in which eIF4E plays the role of the agent that crosslinks two types of AuNP, thereby inducing a naked-eye visible absorbance redshift. The reported AuNPs-nucleotide conjugation method based on lipoic acid affinity for gold, can be harnessed to obtain other types of nucleotide-functionalized AuNPs, thereby paving the way to studying other nucleotide-binding proteins.
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Affiliation(s)
- Olga Perzanowska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland
| | - Maciej Majewski
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland
| | - Malwina Strenkowska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland
| | - Paulina Głowala
- Faculty of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Mariusz Czarnocki-Cieciura
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Księcia Trojdena 4, 02-109, Warsaw, Poland
| | - Maciej Mazur
- Faculty of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093, Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 02-097, Warsaw, Poland.
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6
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A Novel NAD-RNA Decapping Pathway Discovered by Synthetic Light-Up NAD-RNAs. Biomolecules 2020; 10:biom10040513. [PMID: 32231086 PMCID: PMC7226252 DOI: 10.3390/biom10040513] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/20/2022] Open
Abstract
The complexity of the transcriptome is governed by the intricate interplay of transcription, RNA processing, translocation, and decay. In eukaryotes, the removal of the 5’-RNA cap is essential for the initiation of RNA degradation. In addition to the canonical 5’-N7-methyl guanosine cap in eukaryotes, the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD) was identified as a new 5’-RNA cap structure in prokaryotic and eukaryotic organisms. So far, two classes of NAD-RNA decapping enzymes have been identified, namely Nudix enzymes that liberate nicotinamide mononucleotide (NMN) and DXO-enzymes that remove the entire NAD cap. Herein, we introduce 8-(furan-2-yl)-substituted NAD-capped-RNA (FurNAD-RNA) as a new research tool for the identification and characterization of novel NAD-RNA decapping enzymes. These compounds are found to be suitable for various enzymatic reactions that result in the release of a fluorescence quencher, either nicotinamide (NAM) or nicotinamide mononucleotide (NMN), from the RNA which causes a fluorescence turn-on. FurNAD-RNAs allow for real-time quantification of decapping activity, parallelization, high-throughput screening and identification of novel decapping enzymes in vitro. Using FurNAD-RNAs, we discovered that the eukaryotic glycohydrolase CD38 processes NAD-capped RNA in vitro into ADP-ribose-modified-RNA and nicotinamide and therefore might act as a decapping enzyme in vivo. The existence of multiple pathways suggests that the decapping of NAD-RNA is an important and regulated process in eukaryotes.
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7
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Guo S, Piao X, Li H, Guo P. Methods for construction and characterization of simple or special multifunctional RNA nanoparticles based on the 3WJ of phi29 DNA packaging motor. Methods 2018. [PMID: 29530505 DOI: 10.1016/j.ymeth.2018.02.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The field of RNA nanotechnology has developed rapidly over the last decade, as more elaborate RNA nanoarchitectures and therapeutic RNA nanoparticles have been constructed, and their applications have been extensively explored. Now it is time to offer different levels of RNA construction methods for both the beginners and the experienced researchers or enterprisers. The first and second parts of this article will provide instructions on basic and simple methods for the assembly and characterization of RNA nanoparticles, mainly based on the pRNA three-way junction (pRNA-3WJ) of phi29 DNA packaging motor. The third part of this article will focus on specific methods for the construction of more sophisticated multivalent RNA nanoparticles for therapeutic applications. In these parts, some simple protocols are provided to facilitate the initiation of the RNA nanoparticle construction in labs new to the field of RNA nanotechnology. This article is intended to serve as a general reference aimed at both apprentices and senior scientists for their future design, construction and characterization of RNA nanoparticles based on the pRNA-3WJ of phi29 DNA packaging motor.
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Affiliation(s)
- Sijin Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Xijun Piao
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH 43210, USA; College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry, The Ohio State University, Columbus, OH 43210, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA; James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
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8
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Valdés FZ, Luna VZ, Arévalo BR, Brown NV, Gutiérrez MC. Adenosine: Synthetic Methods of Its Derivatives and Antitumor Activity. Mini Rev Med Chem 2018; 18:1684-1701. [PMID: 29769005 PMCID: PMC6327119 DOI: 10.2174/1389557518666180516163539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/23/2017] [Accepted: 11/27/2017] [Indexed: 01/13/2023]
Abstract
Since 1929, several researchers have conducted studies in relation to the nucleoside of adenosine (1) mainly distribution identifying, characterizing their biological importance and synthetic chemistry to which this type of molecule has been subjected to obtain multiple of its derivatives. The receptors that interact with adenosine and its derivatives, called purinergic receptors, are classified as A1, A2A, A2B and A3. In the presence of agonists and antagonists, these receptors are involved in various physiological processes and diseases. This review describes and compares some of the synthetic methods that have been developed over the last 30 years for obtaining some adenosine derivatives, classified according to substitution processes, complexation, mating and conjugation. Finally, we mention that although the concentrations of these nucleosides are low in normal tissues, they can increase rapidly in pathophysiological conditions such as hypoxia, ischemia, inflammation, trauma and cancer. In particular, the evaluation of adenosine derivatives as adjunctive therapy promises to have a significant impact on the treatment of certain cancers, although the transfer of these results to clinical practice requires a deeper understanding of how adenosine regulates the process of tumorigenesis.
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Affiliation(s)
- Francisco Z. Valdés
- Laboratory of Synthesis and Biological Activity, Institute of Chemistry of Naturals Resources, University of Talca, Talca, Chile
| | - Víctor Z. Luna
- Center for Bioinformatics and Molecular Simulation, University of Talca, Talca, Chile
| | - Bárbara R. Arévalo
- Laboratory of Synthesis and Biological Activity, Institute of Chemistry of Naturals Resources, University of Talca, Talca, Chile
| | - Nelson V. Brown
- Center for Medical Research, University of Talca School of Medicine, Talca, Chile
- Programa de Investigación Asociativa en cáncer gástrico (PIA-CG)
| | - Margarita C. Gutiérrez
- Laboratory of Synthesis and Biological Activity, Institute of Chemistry of Naturals Resources, University of Talca, Talca, Chile
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9
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Sun G, Riggs AD. A Simple and Cost-Effective Approach for In Vitro Production of Sliced siRNAs as Potent Triggers for RNAi. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 8:345-355. [PMID: 28918034 PMCID: PMC5537206 DOI: 10.1016/j.omtn.2017.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 07/08/2017] [Accepted: 07/09/2017] [Indexed: 12/25/2022]
Abstract
We have studied the molecular properties of in-vitro-transcribed sliced small interfering RNAs (tsli-siRNAs) as an alternative RNAi agent for chemically synthesized siRNA. We describe here a simple and cost-effective procedure for high-purity production of tsli-siRNA using bacteriophage T7 RNA polymerases. tsli-siRNAs exhibit potent gene knockdown effects, with efficacy comparable with that of chemically synthesized sli-siRNAs and classical siRNAs. Furthermore, we found that it is very easy to prepare potent tsli-siRNAs with modified bases, such as 2′-fluorine- or biotin-16-modified tsli-siRNAs. tsli-siRNAs can cause a mild innate immune response, which can be easily eliminated by alkaline phosphatase treatment. On the other hand, this feature, which can be useful as a trigger of the innate immune response, can be enhanced by polynucleotide kinase treatment. Because of the simplicity of preparation and purification, the procedure presented here could be useful for the production of RNAi or immunostimulatory reagents.
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Affiliation(s)
- Guihua Sun
- Department of Diabetes Complications & Metabolism, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
| | - Arthur D Riggs
- Department of Diabetes Complications & Metabolism, Diabetes & Metabolism Research Institute, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA.
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10
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Holstein JM, Rentmeister A. Current covalent modification methods for detecting RNA in fixed and living cells. Methods 2015; 98:18-25. [PMID: 26615954 DOI: 10.1016/j.ymeth.2015.11.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/20/2015] [Accepted: 11/22/2015] [Indexed: 12/13/2022] Open
Abstract
Labeling RNAs is of particular interest for elucidating localization, transport, and regulation of specific transcripts, ideally in living cells. Numerous methods have been developed ranging from hybridizing probes to genetically encoded reporters and chemo-enzymatic approaches. This review focuses on covalent labeling approaches that rely on the introduction of a small reactive group into the nascent or completed transcript followed by bioorthogonal click chemistry. State of the approaches for labeling RNA in fixed and living cells will be presented and emerging strategies with great potential for application in the complex cellular environment will be discussed.
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Affiliation(s)
- Josephin M Holstein
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, 48149 Muenster, Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Muenster, 48149 Muenster, Germany.
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11
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Krasnov VP, Gruzdev DA, Chulakov EN, Vigorov AY, Musiyak VV, Matveeva TV, Tumashov AA, Levit GL, Charushin VN. Synthesis of novel purin-6-yl conjugates with heterocyclic amines linked via 6-aminohexanoyl fragment. MENDELEEV COMMUNICATIONS 2015. [DOI: 10.1016/j.mencom.2015.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Ameta S, Becker J, Jäschke A. RNA-peptide conjugate synthesis by inverse-electron demand Diels-Alder reaction. Org Biomol Chem 2015; 12:4701-7. [PMID: 24871687 DOI: 10.1039/c4ob00076e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Here we report an efficient method for the synthesis of RNA-peptide conjugates by inverse-electron demand Diels-Alder reaction. Various dienophiles were enzymatically incorporated into RNA and reacted with a chemically synthesized diene-modified peptide. The Diels-Alder reaction proceeds with near-quantitative yields in aqueous solution with stoichiometric amounts of reactants, even at low micromolar concentrations.
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Affiliation(s)
- Sandeep Ameta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
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13
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Advances in methods for native expression and purification of RNA for structural studies. Curr Opin Struct Biol 2014; 26:1-8. [PMID: 24607442 DOI: 10.1016/j.sbi.2014.01.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 11/23/2022]
Abstract
Many RNAs present unique challenges in obtaining material suitable for structural or biophysical characterization. These issues include synthesis of chemically and conformationally homogeneous RNAs, refolding RNA purified using denaturing preparation techniques, and avoiding chemical damage. To address these challenges, new methodologies in RNA expression and purification have been developed seeking to emulate those commonly used for proteins. In this review, recent developments in the preparation of high-quality RNA for structural biology and biophysical applications are discussed, with an emphasis on native methods.
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14
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Zhang H, Guo P. Single molecule photobleaching (SMPB) technology for counting of RNA, DNA, protein and other molecules in nanoparticles and biological complexes by TIRF instrumentation. Methods 2014; 67:169-76. [PMID: 24440482 DOI: 10.1016/j.ymeth.2014.01.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 12/28/2013] [Accepted: 01/08/2014] [Indexed: 11/25/2022] Open
Abstract
Direct counting of biomolecules within biological complexes or nanomachines is demanding. Single molecule counting using optical microscopy is challenging due to the diffraction limit. The single molecule photobleaching (SMPB) technology for direct counting developed by our team (Shu et al., 2007 [18]; Zhang et al., 2007 [19]) offers a simple and straightforward method to determine the stoichiometry of molecules or subunits within biocomplexes or nanomachines at nanometer scales. Stoichiometry is determined by real-time observation of the number of descending steps resulted from the photobleaching of individual fluorophore. This technology has now been used extensively for single molecule counting of protein, RNA, and other macromolecules in a variety of complexes or nanostructures. Here, we elucidate the SMPB technology, using the counting of RNA molecules within a bacteriophage phi29 DNA-packaging biomotor as an example. The method described here can be applied to the single molecule counting of other molecules in other systems. The construction of a concise, simple and economical single molecule total internal reflection fluorescence (TIRF) microscope combining prism-type and objective-type TIRF is described. The imaging system contains a deep-cooled sensitive EMCCD camera with single fluorophore detection sensitivity, a laser combiner for simultaneous dual-color excitation, and a Dual-View™ imager to split the multiple outcome signals to different detector channels based on their wavelengths. Methodology of the single molecule photobleaching assay used to elucidate the stoichiometry of RNA on phi29 DNA packaging motor and the mechanism of protein/RNA interaction are described. Different methods for single fluorophore labeling of RNA molecules are reviewed. The process of statistical modeling to reveal the true copy number of the biomolecules based on binomial distribution is also described.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA.
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15
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Jemielity J, Lukaszewicz M, Kowalska J, Czarnecki J, Zuberek J, Darzynkiewicz E. Synthesis of biotin labelled cap analogue--incorporable into mRNA transcripts and promoting cap-dependent translation. Org Biomol Chem 2013; 10:8570-4. [PMID: 22832840 DOI: 10.1039/c2ob26060c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analogues of the eukaryotic messenger RNA 5' end (m(7)G cap) are useful tools for studying mRNA fate and serve as reagents for in vitro preparation of 5' capped mRNAs. We designed a biotin-labeled dinucleotide cap analogue that can be incorporated into transcripts to produce 5'-capped and biotinylated mRNAs which retain their biological functionality and may be employed for biotin-(strept)avidin technologies.
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Affiliation(s)
- Jacek Jemielity
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.
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16
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Guo P, Shu Y, Binzel D, Cinier M. Synthesis, conjugation, and labeling of multifunctional pRNA nanoparticles for specific delivery of siRNA, drugs, and other therapeutics to target cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 928:197-219. [PMID: 22956144 DOI: 10.1007/978-1-62703-008-3_16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
RNA is unique in nanoscale fabrication due to its amazing diversity of function and structure. RNA nanoparticles can be fabricated with a level of simplicity characteristic of DNA while possessing versatile tertiary structure and catalytic function similar to that of proteins. A large variety of single stranded loops are suitable for inter- and intramolecular interactions, serving as mounting dovetails in self-assembly without the need for external linking dowels. Novel properties of RNA nanoparticles have been explored for treatment and detection of diseases and various other realms. The higher thermodynamic stability, holding of noncanonical base pairing, stronger folding due to base stacking properties, and distinctive in vivo attributes make RNA unique in comparison to DNA. Indeed, the potential application of RNA nanotechnology in therapeutics is an exciting area of research. The use of RNAi in biomedical research has opened up new possibilities to silence or regulate the biological function of individual genes. Small interfering RNA (siRNA) has been extensively explored to genetically manipulate the expression in vitro and in vivo of particular genes identified to play a key role in cancerous or viral diseases. However, the efficient silencing of the desired gene depends upon efficient delivery of siRNA to targeted cells, as well as in vivo stability. In this chapter, we use the bacteriophage phi29 motor pRNA-derived nanocarrier as a polyvalent targeted delivery system, introduce the potential of RNA-based therapeutics using nanobiotechnology or nanotechnology methods with the fabrication and modification of pRNA nanoparticles, and highlight its potential to become a valuable research tool and viable clinical approach for gene therapy.
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Affiliation(s)
- Peixuan Guo
- Nanobiomedical Center, University of Cincinnati, Cincinnati, OH, USA
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17
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Szczepaniak SA, Zuberek J, Darzynkiewicz E, Kufel J, Jemielity J. Affinity resins containing enzymatically resistant mRNA cap analogs--a new tool for the analysis of cap-binding proteins. RNA (NEW YORK, N.Y.) 2012; 18:1421-32. [PMID: 22589334 PMCID: PMC3383972 DOI: 10.1261/rna.032078.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/12/2012] [Indexed: 05/21/2023]
Abstract
Cap-binding proteins have been routinely isolated using m⁷GTP-Sepharose; however, this resin is inefficient for proteins such as DcpS (scavenger decapping enzyme), which interacts not only with the 7-methylguanosine, but also with the second cap base. In addition, DcpS purification may be hindered by the reduced resin capacity due to the ability of DcpS to hydrolyze m⁷GTP. Here, we report the synthesis of new affinity resins, m⁷GpCH₂pp- and m⁷GpCH₂ppA-Sepharoses, with attached cap analogs resistant to hydrolysis by DcpS. Biochemical tests showed that these matrices, as well as a hydrolyzable m⁷GpppA-Sepharose, bind recombinant mouse eIF4E²⁸⁻²¹⁷ specifically and at high capacity. In addition, purification of cap-binding proteins from yeast extracts confirmed the presence of all expected cap-binding proteins, including DcpS in the case of m⁷GpCH₂pp- and m⁷GpCH₂ppA-Sepharoses. In contrast, binding studies in vitro demonstrated that recombinant human DcpS efficiently bound only m⁷GpCH₂ppA-Sepharose. Our data prove the applicability of these novel resins, especially m⁷GpCH₂ppA-Sepharose, in biochemical studies such as the isolation and identification of cap-binding proteins from different organisms.
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Affiliation(s)
- Sylwia Anna Szczepaniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Jacek Jemielity
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
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18
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PCR amplification and transcription for site-specific labeling of large RNA molecules by a two-unnatural-base-pair system. J Nucleic Acids 2012; 2012:230943. [PMID: 22792445 PMCID: PMC3390107 DOI: 10.1155/2012/230943] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 04/16/2012] [Indexed: 01/04/2023] Open
Abstract
For the site-specific labeling and modification of RNA by genetic alphabet expansion, we developed a PCR and transcription system using two hydrophobic unnatural base pairs: 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) as a third pair for PCR amplification and Ds and pyrrole-2-carbaldehyde (Pa) for the incorporation of functional components as modified Pa bases into RNA by T7 transcription. To prepare Ds-containing DNA templates with long chains, the Ds-Px pair was utilized in a fusion PCR method, by which we demonstrated the synthesis of 282-bp DNA templates containing Ds at specific positions. Using these Ds-containing DNA templates and a biotin-linked Pa substrate (Biotin-PaTP) as a modified Pa base, 260-mer RNA transcripts containing Biotin-Pa at a specific position were generated by T7 RNA polymerase. This two-unnatural-base-pair system, combining the Ds-Px and Ds-Pa pairs with modified Pa substrates, provides a powerful tool for the site-specific labeling and modification of desired positions in large RNA molecules.
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19
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Huang F, Shi Y. Synthesis of photolabile transcription initiators and preparation of photocleavable functional RNA by transcription. Bioorg Med Chem Lett 2012; 22:4254-8. [PMID: 22677315 DOI: 10.1016/j.bmcl.2012.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/03/2012] [Accepted: 05/08/2012] [Indexed: 12/20/2022]
Abstract
Two new photolabile adenosine-containing transcription initiators with terminal thiol and amino functionalities are chemically synthesized. Transcription in the presence of the transcription initiators under the T7 phi2.5 promoter produces 5' thiol- and amino-functionalized RNA conjugated by a photocleavable (PC) linker. Further RNA functionalization with biotin may be achieved through acyl transfer reactions from either biotinyl AMP to the RNA thiol group or biotin NHS to the RNA amino group. Photocleavage of the PC linker displays relatively fast kinetics with a half-life of 4-5 min. The availability of these transcription initiators makes new photolabile RNA accessible for affinity purification of RNA, in vitro selection of functional RNAs, and functional RNA caging.
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Affiliation(s)
- Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
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20
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Jani B, Fuchs R. In vitro transcription and capping of Gaussia luciferase mRNA followed by HeLa cell transfection. J Vis Exp 2012:3702. [PMID: 22473375 DOI: 10.3791/3702] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg(2+) ions. Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing(1), RNAi experiments in mammalian cells(2), antisense RNA amplification by the "Eberwine method"(3), microarray analysis(4) and for RNA vaccine studies(5). The technique can also be used for producing radiolabeled and dye labeled probes(6). Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA(7). The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 μg RNA per 20 μl reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed. Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability(8), efficient translation(9), nuclear transport(10) and splicing(11). The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme(12,13). The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications(14) such as generating viral genomic RNA for reverse-genetic systems(15) and crystallographic studies of cap binding proteins such as eIF4E(16). In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.
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21
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Wahl F, Jäschke A. PEG-tethered guanosine acetal conjugates for the enzymatic synthesis of modified RNA. Biochem Biophys Res Commun 2012; 417:1224-6. [PMID: 22230383 DOI: 10.1016/j.bbrc.2011.12.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 12/23/2011] [Indexed: 01/18/2023]
Abstract
A short and efficient synthetic route to guanosine monophosphate conjugates connected to a protected aldehyde group via a flexible polydisperse polyethylene glycol linker is described. These conjugates are enzymatically incorporated into RNA transcripts with 52% yield. The resulting aldehyde-modified RNA gave full conversion in the reaction with biotin hydrazide, demonstrating the utility of the method.
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Affiliation(s)
- Florentine Wahl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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22
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Ishizuka T, Kimoto M, Sato A, Hirao I. Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry. Chem Commun (Camb) 2012; 48:10835-7. [DOI: 10.1039/c2cc36293g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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23
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Hirao I, Kimoto M. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2012; 88:345-67. [PMID: 22850726 PMCID: PMC3422687 DOI: 10.2183/pjab.88.345] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/01/2012] [Indexed: 05/30/2023]
Abstract
Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.
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Affiliation(s)
- Ichiro Hirao
- RIKEN Systems and Structural Biology Center (SSBC), Yokohama, Japan.
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24
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Tanpure AA, Srivatsan SG. A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site. Chemistry 2011; 17:12820-7. [PMID: 21956450 DOI: 10.1002/chem.201101194] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/18/2011] [Indexed: 11/10/2022]
Abstract
Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pashan, Pune, India
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25
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Laing BM, Guo P, Bergstrom DE. Optimized method for the synthesis and purification of adenosine--folic acid conjugates for use as transcription initiators in the preparation of modified RNA. Methods 2011; 54:260-6. [PMID: 21163352 PMCID: PMC3090705 DOI: 10.1016/j.ymeth.2010.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 11/15/2022] Open
Abstract
We present an optimized synthetic strategy for the attachment of molecules to 5'-adenosine monophosphate (AMP), which can then be used to label the 5'-end of RNA by T7 RNA polymerase mediated in vitro transcription. Through the use of a boronate affinity gel, we have developed an efficient route to the preparation of folate conjugated AMP with high yields and purity. Affi-Gel boronate is an affinity resin that selectively binds nucleoside and nucleoside derivatives at pH>7.5 and releases them at pH<6.5. This resin is used to efficiently bind and purify ribonucleotides such as AMP. This allows for the addition of a large excess of reactants and reagents in order to drive the reaction to completion and then allow easy purification without HPLC. The synthesis can be successfully scaled up to produce large quantities of AMP conjugates.
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Affiliation(s)
- Brian M. Laing
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907
| | - Peixuan Guo
- Department of Biomedical Engineering College of Engineering/College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Donald E. Bergstrom
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907
- Walther Cancer Institute, Indianapolis, IN 46208
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26
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Shu Y, Cinier M, Shu D, Guo P. Assembly of multifunctional phi29 pRNA nanoparticles for specific delivery of siRNA and other therapeutics to targeted cells. Methods 2011; 54:204-14. [PMID: 21320601 DOI: 10.1016/j.ymeth.2011.01.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/06/2011] [Accepted: 01/20/2011] [Indexed: 01/31/2023] Open
Abstract
Recent advances in RNA nanotechnology have led to the emergence of a new field and brought vitality to the area of therapeutics [P. Guo, The emerging field of RNA nanotechnology, Nat. Nanotechnol., 2010]. Due to the complementary nature of the four nucleotides and its special catalytic activity, RNA can be manipulated with simplicity characteristic of DNA, while possessing versatile structure and diverse function similar to proteins. Loops and tertiary architecture serve as mounting dovetails or wedges to eliminate external linking dowels. Unique features in transcription, termination, self-assembly, self-processing, and acid-resistance enable in vivo production of nanoparticles harboring aptamer, siRNA, ribozyme, riboswitch, or other regulators for therapy, detection, regulation, and intracellular computation. The unique property of noncanonical base-pairing and stacking enables RNA to fold into well-defined structures for constructing nanoparticles with special functionalities. Bacteriophage phi29 DNA packaging motor is geared by a ring consisting of six packaging RNA (pRNA) molecules. pRNA is able to form a multimeric complex via the interaction of two reengineered interlocking loops. This unique feature makes it an ideal polyvalent vehicle for nanomachine fabrication, pathogen detection, and delivery of siRNA or other therapeutics. This review describes methods in using pRNA as a building block for the construction of RNA dimers, trimers, and hexamers as nanoparticles in medical applications. Methods for industrial-scale production of large and stable RNA nanoparticles will be introduced. The unique favorable PK (pharmacokinetics) profile with a half life (T(1/2)) of 5-10h comparing to 0.25 of conventional 2'-F siRNA, and advantageous in vivo features such as non-toxicity, non-induction of interferons or non-stimulating of cytokine response in animals will also be reviewed.
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Affiliation(s)
- Yi Shu
- Nanobiomedical Center, University of Cincinnati, Cincinnati, OH 45267, USA
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27
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Pawar MG, Srivatsan SG. Synthesis, photophysical characterization, and enzymatic incorporation of a microenvironment-sensitive fluorescent uridine analog. Org Lett 2011; 13:1114-7. [PMID: 21275418 DOI: 10.1021/ol103147t] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The synthesis of a microenvironment-sensitive base-modified fluorescent ribonucleoside analog based on a 5-(benzo[b]thiophen-2-yl)pyrimidine core, enzymatic incorporation of its corresponding triphosphate into RNA oligonucleotides, and photophysical characterization of fluorescently modified oligoribonucleotides are described.
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Affiliation(s)
- Maroti G Pawar
- Indian Institute of Science Education and Research, Pashan, Pune, India
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28
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Yang S, Froeyen M, Lescrinier E, Marlière P, Herdewijn P. 3-Phosphono-l-alanine as pyrophosphate mimic for DNA synthesis using HIV-1 reverse transcriptase. Org Biomol Chem 2011; 9:111-9. [DOI: 10.1039/c0ob00554a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Huang F, Shi Y. Synthesis of symmetrical thiol-adenosine conjugate and 5′ thiol-RNA preparation by efficient one-step transcription. Bioorg Med Chem Lett 2010; 20:6254-7. [DOI: 10.1016/j.bmcl.2010.08.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/19/2010] [Indexed: 12/20/2022]
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30
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Zhang HM, Su Y, Guo S, Yuan J, Lim T, Liu J, Guo P, Yang D. Targeted delivery of anti-coxsackievirus siRNAs using ligand-conjugated packaging RNAs. Antiviral Res 2009; 83:307-16. [PMID: 19616030 PMCID: PMC3909712 DOI: 10.1016/j.antiviral.2009.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/02/2009] [Accepted: 07/08/2009] [Indexed: 11/22/2022]
Abstract
Coxsackievirus B3 (CVB3) is a common pathogen of myocarditis. We previously synthesized a siRNA targeting the CVB3 protease 2A (siRNA/2A) gene and achieved reduction of CVB3 replication by 92% in vitro. However, like other drugs under development, CVB3 siRNA faces a major challenge of targeted delivery. In this study, we investigated a novel approach to deliver CVB3 siRNAs to a specific cell population (e.g. HeLa cells containing folate receptor) using receptor ligand (folate)-linked packaging RNA (pRNA) from bacterial phage phi29. pRNA monomers can spontaneously form dimers and multimers under optimal conditions by base-pairing between their stem loops. By covalently linking a fluorescence-tag to folate, we delivered the conjugate specifically to HeLa cells without the need of transfection. We further demonstrated that pRNA covalently conjugated to siRNA/2A achieved an equivalent antiviral effect to that of the siRNA/2A alone. Finally, the drug targeted delivery was further evaluated by using pRNA monomers or dimers, which carried both the siRNA/2A and folate ligand and demonstrated that both of them strongly inhibited CVB3 replication. These data indicate that pRNA as a siRNA carrier can specifically deliver the drug to target cells via its ligand and specific receptor interaction and inhibit virus replication effectively.
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Affiliation(s)
- Huifang M Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
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31
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Li N, Ebright JN, Stovall GM, Chen X, Nguyen HH, Singh A, Syrett A, Ellington AD. Technical and biological issues relevant to cell typing with aptamers. J Proteome Res 2009; 8:2438-48. [PMID: 19271740 DOI: 10.1021/pr801048z] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A number of aptamers have been selected against cell surface biomarkers or against eukaryotic tissue culture cells themselves. To determine the general utility of aptamers for assessing the cell surface proteome, we developed a standardized flow cytometry assay and carried out a comprehensive study with 7 different aptamers and 14 different cell lines. By examining how aptamers performed with a variety of cell lines, we identified difficulties in using aptamers for cell typing. While there are some aptamers that show excellent correlation between cell surface binding and the expression of a biomarker on the cell surface, other aptamers showed nonspecific binding by flow cytometry. For example, it has recently been claimed that an anti-PTK7 (protein tyrosine kinase 7) aptamer identified a new biomarker for leukemia cells, but data with the additional cell lines shows that it is possible that the aptamer instead identifies a propensity for adherence. Better understanding and controlling for the role of background and nonspecific binding to cells should open the way to using arrays of aptamers for describing and quantifying the cell surface proteome.
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Affiliation(s)
- Na Li
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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32
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Shu Y, Shu D, Diao Z, Shen G, Guo P. Fabrication of Polyvalent Therapeutic RNA Nanoparticles for Specific Delivery of siRNA, Ribozyme and Drugs to Targeted Cells for Cancer Therapy. IEEE/NIH LIFE SCIENCE SYSTEMS AND APPLICATIONS WORKSHOP. IEEE/NIH LIFE SCIENCE SYSTEMS AND APPLICATIONS WORKSHOP 2009; 2009:9-12. [PMID: 21243099 DOI: 10.1109/lissa.2009.4906696] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacteriophage phi29 DNA packaging motor is geared by a six-pRNA ring. pRNA is able to form a multimeric complex and patterned superstructures via the interaction of two reengineered interlocking loops. This unique feature makes it an ideal polyvalent vehicle for nanomachine fabrication, pathogen detection, and the delivery of therapeutics. This report describes novel approaches for the fabrication of polyvalent therapeutic pRNA nanoparticles, especially tetramers for specific siRNA delivery to cancer cells and for the silencing of targeted genes. RNA 3-D design, circular permutation, folding energy alteration, and nucleotide modification were applied to generate stable RNA nanoparticles with low toxicity. Animal trials demonstrated the high efficiency of the polyvalent RNA nanoparticles in the prevention and treatment of cancer. Using such protein-free nanoparticles as therapeutic reagents would allow for long-term administration to avoid the induction of antibody due to repeated treatment for chronic diseases.
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Affiliation(s)
- Yi Shu
- Department of Biomedical Engineering, College of Medicine/College of Engineering, University of Cincinnati, 3125 Eden Ave., Cincinnati, OH, USA
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33
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Abstract
The enzymatic incorporation of a series of emissive pyrimidine analogues into RNA oligonucleotides is explored. T7 RNA polymerase is challenged with accepting three non-natural, yet related, triphosphates as substrates and incorporating them into diverse RNA transcripts. The three ribonucleoside triphosphates differ only in the modification of their uracil nucleus and include a thieno[3,2-d]pyrimidine nucleoside, a thieno[3,4-d]pyrimidine derivative, and a uridine containing a thiophene ring conjugated at its 5-position. All thiophene-containing uridine triphosphates (UTPs) get incorporated into RNA oligonucleotides at positions that are remote to the promoter, although the yields of the transcripts vary compared with the transcript obtained with only native triphosphates. Among the three derivatives, the 5-modified UTP is found to be the most "polymerase-friendly" and is well accommodated by T7 RNA polymerase. Although the fused thiophene analogues cannot be incorporated next to the promoter region, the 5-modified non-natural UTP gets incorporated near the promoter (albeit in relatively low yields) and even in multiple copies. Labeling experiments shed light on the mediocre incorporation of the fused analogues, suggesting the enzyme frequently pauses at the incorporation position. When incorporation does take place, the enzyme fails to elongate the modified oligonucleotide and yields aborted transcripts. Taken together, these results highlight the versatility and robustness, as well as the scope and limitation, of T7 RNA polymerase in accepting and incorporating reporter nucleotides into modified RNA transcripts.
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Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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34
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Synthesis of biotin-AMP conjugate for 5' biotin labeling of RNA through one-step in vitro transcription. Nat Protoc 2009; 3:1848-61. [PMID: 18989262 DOI: 10.1038/nprot.2008.185] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Biotin-labeled RNA has found broad applications in chemistry, biology and biomedicine. In this protocol, we describe a simple procedure for 5' RNA biotin labeling by one-step in vitro transcription. A biotin-AMP (adenosine 5'-monophosphate) conjugate, biotin-HDAAMP (adenosine 5'-(6-aminohexyl) phosphoramide; where HDA is 1,6-hexanediamine), is chemically synthesized. Transcription initiation by biotin-HDAAMP under the T7 phi 2.5 promoter produces 5' biotin-labeled RNA with high labeling efficiency. The procedure is especially useful for biotin labeling of RNA that is larger than 60 nucleotides. In addition, the protocol provides an attractive alternative to chemical synthesis of biotin-labeled small RNA of less than 60 nucleotides, particularly when the desired quantity of RNA is low. The whole procedure, from chemical syntheses to isolated biotin-labeled RNA, can be completed within 2 weeks.
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35
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Li N, Wang Y, Pothukuchy A, Syrett A, Husain N, Gopalakrisha S, Kosaraju P, Ellington AD. Aptamers that recognize drug-resistant HIV-1 reverse transcriptase. Nucleic Acids Res 2008; 36:6739-51. [PMID: 18948292 PMCID: PMC2588506 DOI: 10.1093/nar/gkn775] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Drug-resistant variants of HIV-1 reverse transcriptase (RT) are also known to be resistant to anti-RT RNA aptamers. In order to be able to develop diagnostics and therapies that can focus on otherwise drug-resistant viruses, we have isolated two aptamers against a well-known, drug-resistant HIV-1 RT, Mutant 3 (M3) from the multidrug-resistant HIV-1 RT panel. One aptamer, M302, bound M3 but showed no significant affinity for wild-type (WT) HIV-1 RT, while another aptamer, 12.01, bound to both M3 and WT HIV-1 RTs. In contrast to all previously selected anti-RT aptamers, neither of these aptamers showed observable inhibition of either polymerase or RNase H activities. Aptamers M302 and 12.01 competed with one another for binding to M3, but they did not compete with a pseudoknot aptamer for binding to the template/primer cleft of WT HIV-1 RT. These results represent the surprising identification of an additional RNA-binding epitope on the surface of HIV-1 RT. M3 and WT HIV-1 RTs could be distinguished using an aptamer-based microarray. By probing protein conformation as a correlate to drug resistance we introduce an additional and useful measure for determining HIV-1 drug resistance.
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Affiliation(s)
- Na Li
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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36
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Xiao F, Zhang H, Guo P. Novel mechanism of hexamer ring assembly in protein/RNA interactions revealed by single molecule imaging. Nucleic Acids Res 2008; 36:6620-32. [PMID: 18940870 PMCID: PMC2582624 DOI: 10.1093/nar/gkn669] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Many nucleic acid-binding proteins and the AAA+ family form hexameric rings, but the mechanism of hexamer assembly is unclear. It is generally believed that the specificity in protein/RNA interaction relies on molecular contact through a surface charge or 3D structure matching via conformational capture or induced fit. The pRNA of bacteriophage phi29 DNA-packaging motor also forms a ring, but whether the pRNA ring is a hexamer or a pentamer is under debate. Here, single molecule studies elucidated a mechanism suggesting the specificity and affinity in protein/RNA interaction relies on pRNA static ring formation. A combined pRNA ring-forming group was very specific for motor binding, but the isolated individual members of the ring-forming group bind to the motor nonspecifically. pRNA did not form a ring prior to motor binding. Only those RNAs that formed a static ring, via the interlocking loops, stayed on the motor. Single interlocking loop interruption resulted in pRNA detachment. Extension or reduction of the ring circumference failed in motor binding. This new mechanism was tested by redesigning two artificial RNAs that formed hexamer and packaged DNA. The results confirmed the stoichiometry of pRNA on the motor was the common multiple of two and three, thus, a hexamer.
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Affiliation(s)
- Feng Xiao
- Department of Biomedical Engineering, College of Engineering/College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA
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37
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Hocek M, Fojta M. Cross-coupling reactions of nucleoside triphosphates followed by polymerase incorporation. Construction and applications of base-functionalized nucleic acids. Org Biomol Chem 2008; 6:2233-41. [PMID: 18563253 DOI: 10.1039/b803664k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Construction of functionalized nucleic acids (DNA or RNA) via polymerase incorporation of modified nucleoside triphosphates is reviewed and selected applications of the modified nucleic acids are highlighted. The classical multistep approach for the synthesis of modified NTPs by triphosphorylation of modified nucleosides is compared to the novel approach consisting of direct aqueous cross-coupling reactions of unprotected halogenated nucleoside triphosphates. The combination of cross-coupling of NTPs with polymerase incorporation gives an efficient and straightforward two-step synthesis of modified nucleic acids. Primer extension using biotinylated templates followed by separation using streptavidine-coated magnetic beads and DNA duplex denaturation is used for preparation of modified single stranded oligonucleotides. Examples of using this approach for electrochemical DNA labelling and bioanalytical applications are given.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.
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38
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Wolf J, Dombos V, Appel B, Müller S. Synthesis of guanosine 5'-conjugates and their use as initiator molecules for transcription priming. Org Biomol Chem 2008; 6:899-907. [PMID: 18292882 DOI: 10.1039/b716151d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have synthesised two guanosine derivatives that are linked to biotinylated adenosine moieties by using two different strategies, one that includes synthetic steps on the solid phase and another one that is performed entirely in solution. The synthesised derivatives were shown to function as initiator molecules in transcription priming experiments. The incorporation efficiency was determined to be approximately 2%. Even though this value is rather low, the use of either molecule in selection experiments seems reasonable. Basically, RNA libraries with sequence complexities of 10(15) to 10(16) can be generated. Labelling of such a library with our initiator molecule would still produce 10(13) to 10(14) labelled/functionalised sequences, and thus sufficient sequence space for selection.
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Affiliation(s)
- Jörn Wolf
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Biochemie, Bioorganische Chemie, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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39
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Zhang H, Shu D, Huang F, Guo P. Instrumentation and metrology for single RNA counting in biological complexes or nanoparticles by a single-molecule dual-view system. RNA (NEW YORK, N.Y.) 2007; 13:1793-802. [PMID: 17698643 PMCID: PMC1986819 DOI: 10.1261/rna.587607] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Limited by the spatial resolution of optical microscopy, direct detection or counting of single components in biological complexes or nanoparticles is challenging, especially for RNA, which is conformationally versatile and structurally flexible. We report here the assembly of a customized single-molecule dual-viewing total internal reflection fluorescence imaging system for direct counting of RNA building blocks. The RNA molecules were labeled with a single fluorophore by in vitro transcription in the presence of a fluorescent AMP. Precise calculation of identical or mixed pRNA building blocks of one, two, three, or six copies within the bacteriophage phi29 DNA packaging motor or other complexes was demonstrated by applying a photobleaching assay and evaluated by binomial distribution. The dual-viewing system for excitation and recording at different wavelengths simultaneously will enable the differentiation of different complexes with different labels or relative motion of each labeled component in motion machines.
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Affiliation(s)
- Hui Zhang
- Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana 47907, USA
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40
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Guo S, Huang F, Guo P. Construction of folate-conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells. Gene Ther 2006; 13:814-20. [PMID: 16482206 PMCID: PMC2840388 DOI: 10.1038/sj.gt.3302716] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nasopharyngeal carcinoma is a poorly differentiated upper respiratory tract cancer that highly expresses human folate receptors (hFR). Binding of folate to hFR triggers endocytosis. The folate was conjugated into adenosine 5'-monophosphate (AMP) by 1,6-hexanediamine linkages. After reverse HPLC to reach 93% purity, the folate-AMP, which can only be used for transcription initiation but not for chain extension, was incorporated into the 5'-end of bacteriophage phi29 motor pRNA. A 16:1 ratio of folate-AMP to ATP in transcription resulted in more than 60% of the pRNA containing folate. A pRNA with a 5'-overhang is needed to enhance the accessibility of the 5' folate for specific receptor binding. Utilizing the engineered left/right interlocking loops, polyvalent dimeric pRNA nanoparticles were constructed using RNA nanotechnology to carry folate, a detection marker, and siRNA targeting at an antiapoptosis factor. The chimeric pRNAs were processed into ds-siRNA by Dicer. Incubation of nasopharyngeal epidermal carcinoma (KB) cells with the dimer resulted in its entry into cancer cells, and the subsequent silencing of the target gene. Such a protein-free RNA nanoparticle with undetectable antigenicity has a potential for repeated long-term administration for nasopharyngeal carcinoma as the effectiveness and specificity were confirmed by ex vivo delivery in the animal trial.
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Affiliation(s)
- S Guo
- Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - F Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - P Guo
- Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
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41
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Hirao I. Placing extra components into RNA by specific transcription using unnatural base pair systems. Biotechniques 2006; 40:711, 713, 715 passim. [PMID: 16774113 DOI: 10.2144/000112187] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Ichiro Hirao
- Protein Research Group, RIKEN Genomic Sciences Center, Kanagawa, Japan
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42
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Schlatterer JC, Jäschke A. Universal initiator nucleotides for the enzymatic synthesis of 5'-amino- and 5'-thiol-modified RNA. Biochem Biophys Res Commun 2006; 344:887-92. [PMID: 16631608 DOI: 10.1016/j.bbrc.2006.03.218] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 03/31/2006] [Indexed: 11/21/2022]
Abstract
We report the chemical synthesis of 5'-amino- and 5'-thiol-hexaethylene glycol guanosine nucleotides and their enzymatic incorporation into RNA, followed by chemical modifications at their nucleophilic ends. By using two similar routes, the conjugates of guanosine-5'-monophosphate and hexaethylene glycol with attached reactive groups (SH or NH(2)) were synthesized using phosphoramidite chemistry, and characterized by MALDI TOF mass spectrometry. These initiator molecules were efficiently incorporated into RNA at the 5'-end by run-off transcription using T7 RNA polymerase. The potential of these RNA conjugates for a broad reaction range with electrophiles is shown here, thereby enabling their use for diverse biochemical applications.
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Affiliation(s)
- Jörg C Schlatterer
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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43
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Harris D, Zhang Z, Chaubey B, Pandey VN. Identification of cellular factors associated with the 3'-nontranslated region of the hepatitis C virus genome. Mol Cell Proteomics 2006; 5:1006-18. [PMID: 16500930 DOI: 10.1074/mcp.m500429-mcp200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chronic infection by hepatitis C virus (HCV) is the leading cause of severe hepatitis that often develops into liver cirrhosis and hepatocellular carcinoma. The molecular mechanisms underlying HCV replication and pathogenesis are poorly understood. Similarly, the role(s) of host factors in the replication of HCV remains largely undefined. Based on our knowledge of other RNA viruses, it is likely that a number of cellular factors may be involved in facilitating HCV replication. It has been demonstrated that elements within the 3'-nontranslated region (3'-NTR) of the (+) strand HCV genome are essential for initiation of (-) strand synthesis. The RNA signals within the highly conserved 3'-NTR may be the site for recruiting cellular factors that mediate virus replication/pathogenesis. However, the identities of putative cellular factors interacting with these RNA signals remain unknown. In this report, we demonstrate that an RNA affinity capture system developed in our laboratory used in conjunction with LC/MS/MS allowed us to positively identify more than 70 cellular proteins that interact with the 3'-NTR (+) of HCV. Binding of these cellular proteins was not competed out by a 10-fold excess of nonspecific competitor RNA. With few exceptions, all of the identified cellular proteins are RNA-binding proteins whose reported cellular functions provide unique insights into host cell-virus interactions and possible mechanisms influencing HCV replication and HCV-associated pathogenesis. Small interfering RNA-mediated silencing of selected 3'-NTR-binding proteins in an HCV replicon cell line reduced replicon RNA to undetectable levels, suggesting important roles for these cellular factors in HCV replication.
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Affiliation(s)
- Dylan Harris
- Department of Biochemistry and Molecular Biology and Centre for the Study of Emerging and Re-emerging Pathogens, University of Medicine and Dentistry of New Jersey--New Jersey Medical School, Newark, New Jersey 07103, USA
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44
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Collett JR, Cho EJ, Ellington AD. Production and processing of aptamer microarrays. Methods 2005; 37:4-15. [PMID: 16199170 DOI: 10.1016/j.ymeth.2005.05.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2005] [Accepted: 05/01/2005] [Indexed: 11/24/2022] Open
Abstract
Aptamers are nucleic acid species that are selected in vitro for their specific binding properties. We describe methods for the production and processing of aptamer microarrays, including detailed procedures for the high-throughput, enzymatic synthesis of 5' RNA biotinylated aptamers and for arraying them onto streptavidin-coated glass slides. Also presented are methods for processing the aptamer microarrays, including blocking, washing, drying, and scanning. Examples are shown for the specific capture of fluorescently labeled target proteins either alone in binding buffer or in competition with labeled intracellular proteins from cell lysates. Consideration is given to the challenges involved in producing multiplex aptamer chips composed of aptamers taken from disparate literature sources, and to the development of standardized methods for characterizing the performance of capture reagents used in biosensors.
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Affiliation(s)
- James R Collett
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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45
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Moriyama K, Kimoto M, Mitsui T, Yokoyama S, Hirao I. Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs. Nucleic Acids Res 2005; 33:e129. [PMID: 16113238 PMCID: PMC1188086 DOI: 10.1093/nar/gni128] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Direct site-specific biotinylation of RNA molecules was achieved by specific transcription mediated by unnatural base pairs. Unnatural base pairs between 2-amino-6-(2-thienyl)purine (denoted by s) and 2-oxo(1H)pyridine (denoted by y), or 2-amino-6-(2-thiazolyl)purine (denoted as v) and y specifically function in T7 transcription. Using these unnatural base pairs, the substrate of biotinylated-y (Bio-yTP) was selectively incorporated into RNA, opposite s or v in the DNA templates, by T7 RNA polymerase. This method was applied to the immobilization of an RNA aptamer on sensor chips, and the aptamer accurately recognized its target protein. This direct site-specific biotinylation will provide a tool for RNA-based biotechnologies.
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Affiliation(s)
- Kei Moriyama
- Research Center for Advanced Science and Technology, The University of Tokyo4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Michiko Kimoto
- Protein Research Group, RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tsuneo Mitsui
- Research Center for Advanced Science and Technology, The University of Tokyo4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shigeyuki Yokoyama
- Protein Research Group, RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Harima Institute at SPring-81-1-1 Kohto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan
| | - Ichiro Hirao
- Research Center for Advanced Science and Technology, The University of Tokyo4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Protein Research Group, RIKEN Genomic Sciences Center1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- To whom correspondence should be addressed at Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan. Tel: +81 3 5452 5442; Fax: +81 3 5452 5442;
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46
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Pratico ED, Wang Y, Silverman SK. A deoxyribozyme that synthesizes 2',5'-branched RNA with any branch-site nucleotide. Nucleic Acids Res 2005; 33:3503-12. [PMID: 15967808 PMCID: PMC1153712 DOI: 10.1093/nar/gki656] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 05/26/2005] [Accepted: 05/26/2005] [Indexed: 11/14/2022] Open
Abstract
RNA molecules with internal 2',5'-branches are intermediates in RNA splicing, and branched RNAs have recently been proposed as retrotransposition intermediates. A broadly applicable in vitro synthetic route to branched RNA that does not require self-splicing introns or spliceosomes would substantially improve our ability to study biochemical processes that involve branched RNA. We recently described 7S11, a deoxyribozyme that was identified by in vitro selection and has general RNA branch-forming ability. However, an important restriction for 7S11 is that the branch-site RNA nucleotide must be a purine (A or G), because a pyrimidine (U or C) is not tolerated. Here, we describe the compact 6CE8 deoxyribozyme (selected using a 20 nt random region) that synthesizes 2',5'-branched RNA with any nucleotide at the branch site. The Mn2+-dependent branch-forming ligation reaction is between an internal branch-site 2'-hydroxyl nucleophile on one RNA substrate with a 5'-triphosphate on another RNA substrate. The preference for the branch-site nucleotide is U > C congruent with A > G, although all four nucleotides are tolerated with useful ligation rates. Nearly all other nucleotides elsewhere in both RNA substrates allow ligation activity, except that the sequence requirement for the RNA strand with the 5'-triphosphate is 5'-pppGA, with 5'-pppGAR (R = purine) preferred. These characteristics permit 6CE8 to prepare branched RNAs of immediate practical interest, such as the proposed branched intermediate of Ty1 retrotransposition. Because this branched RNA has two strands with identical sequence that emerge from the branch site, we developed strategies to control which of the two strands bind with the deoxyribozyme during the branch-forming reaction. The ability to synthesize the proposed branched RNA of Ty1 retrotransposition will allow us to explore this important biochemical pathway in greater detail.
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Affiliation(s)
- Elizabeth D. Pratico
- Department of Biochemistry, University of Illinois at Urbana-Champaign600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Yangming Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Scott K. Silverman
- To whom correspondence should be addressed. Tel: +1 217 244 4489; Fax: +1 217 244 8024;
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47
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Li N, Yu C, Huang F. Novel cyanine-AMP conjugates for efficient 5' RNA fluorescent labeling by one-step transcription and replacement of [gamma-32P]ATP in RNA structural investigation. Nucleic Acids Res 2005; 33:e37. [PMID: 15731330 PMCID: PMC549576 DOI: 10.1093/nar/gni036] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 φ2.5 promoter. Efficient fluorophore labeling of 5′ RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current work makes fluorescently labeled RNA readily available for broad applications in biochemistry, molecular biology, structural biology and biomedicine. In particular, site-specifically fluorophore-labeled large RNAs prepared by the current method may be used to investigate RNA structure, folding and mechanism by various fluorescence techniques. In addition, F550/570 and F650/670 may replace [γ-32P]ATP to prepare 5′ labeled RNA for RNA structural and functional investigation, thereby eliminating the need for the unstable and radio-hazardous [γ-32P]ATP.
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Affiliation(s)
| | - Changjun Yu
- AdeGenix, Inc.870 S. Myrtle Avenue, Monrovia, CA 91016, USA
| | - Faqing Huang
- To whom correspondence should be addressed. Tel: +1 601 266 4371; Fax: +1 601 266 6075;
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48
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Coleman TM, Wang G, Huang F. Superior 5' homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter. Nucleic Acids Res 2004; 32:e14. [PMID: 14744982 PMCID: PMC373309 DOI: 10.1093/nar/gnh007] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcription from the commonly used GTP- initiating T7 class III promoter phi6.5 frequently produces heterogeneous RNA at both 3' and 5' ends. We demonstrate here that RNA transcripts from the T7 class II promoter phi2.5 have superior 5' homogeneity over those from the phi6.5 promoter, with comparable total RNA yields. The overall homogeneity of RNA transcripts is improved to different degrees depending on RNA sequences, although transcription under phi2.5 does not affect the 3' heterogeneity of RNA. In combination with 3' RNA trimming by DNAzymes or ribozymes, this ATP- initiated transcription system based on the T7 phi2.5 promoter can provide excellent quality of RNA for applications requiring a high degree of RNA size homogeneity.
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Affiliation(s)
- Tricia M Coleman
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA
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