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Pe KBA, Yatsuzuka K, Hakariya H, Kida T, Katsuda Y, Fukuda M, Sato SI. RNA-based cooperative protein labeling that permits direct monitoring of the intracellular concentration change of an endogenous protein. Nucleic Acids Res 2021; 49:e132. [PMID: 34581825 PMCID: PMC8682759 DOI: 10.1093/nar/gkab839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Imaging the dynamics of proteins in living cells is a powerful means for understanding cellular functions at a deeper level. Here, we report a versatile method for spatiotemporal imaging of specific endogenous proteins in living mammalian cells. The method employs a bifunctional aptamer capable of selective protein recognition and fluorescent probe-binding, which is induced only when the aptamer specifically binds to its target protein. An aptamer for β-actin protein preferentially recognizes its monomer forms over filamentous forms, resulting in selective G-actin staining in both fixed and living cells. Through actin-drug treatment, the method permitted direct monitoring of the intracellular concentration change of endogenous G-actin. This protein-labeling method, which is highly selective and non-covalent, provides rich insights into the study of spatiotemporal protein dynamics in living cells.
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Affiliation(s)
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hayase Hakariya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masatora Fukuda
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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2
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Ning Y, Hu J, Lu F. Aptamers used for biosensors and targeted therapy. Biomed Pharmacother 2020; 132:110902. [PMID: 33096353 PMCID: PMC7574901 DOI: 10.1016/j.biopha.2020.110902] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/07/2023] Open
Abstract
Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.
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Affiliation(s)
- Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Jue Hu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China.
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Komarova N, Kuznetsov A. Inside the Black Box: What Makes SELEX Better? Molecules 2019; 24:E3598. [PMID: 31591283 PMCID: PMC6804172 DOI: 10.3390/molecules24193598] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.
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Affiliation(s)
- Natalia Komarova
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
| | - Alexander Kuznetsov
- Scientific-Manufacturing Complex Technological Centre, 1-7 Shokin Square, Zelenograd, Moscow 124498, Russia.
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4
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Yang Y, Zhao L, Zhang S, Xu Z, Hao L, Cui Z, Bi K, Zhang Y, Liu Z. Structural optimization and anti-allergic activity of nucleotide aptamers target to Cε3-Cε4. Biochem Pharmacol 2019; 161:121-135. [PMID: 30653949 DOI: 10.1016/j.bcp.2019.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/09/2019] [Indexed: 12/27/2022]
Abstract
Nucleic acid aptamers have shown a broad application prospect in basic research, clinical diagnosis and treatment, new drug development and various other fields. We have screened the DNA aptamer A1 and A2 target at Cε3-Cε4 with high affinity and specificity, another aptamer A8, no affinity with Cε3-Cε4 protein, was as a negative control in this study. The structures of aptamer A1 and A2 were optimized using the deletion method, complementary sequence method, and point mutation method, to make them perform biological functions better, improve the pertinence of the subsequent modification and study the mechanism of action of aptamers coupled Cε3-Cε4. Additionally, the affinity was detected using competitive ELISA, then the most optimal and minimalist aptamer G39-A1-29C was obtained. The results indicated that the G39-A1-29C can significantly inhibit the IgE-dependent cell degranulation, but no effect in IgE-independent manner, and have a notable therapeutic effect with dose-dependent on PCA experiments in vivo. Moreover, it is found that the aptamer maintains the secondary structure through the fixed sequence, consecutive four GC pairings can significantly increase the binding affinity, and the G base on the loop region of A1 may be the key sites for binding to the domain of the target protein Cε3-Cε4. Therefore, the stem-loop structure of A1 is the structural basis of its binding, too short sequence cannot maintain the secondary structure, so that its affinity is significantly reduced. The results facilitated the modification and chemical synthesis of aptamers in next work, which provided the foundation for the development of new drugs for the treatment of allergy diseases.
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Affiliation(s)
- Yanlei Yang
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Lijian Zhao
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Su Zhang
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Zhenzhen Xu
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Lifang Hao
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Zhe Cui
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Kewei Bi
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China
| | - Yanfen Zhang
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China; Offices of Science and Technology, Hebei University, Baoding 071002, China.
| | - Zhongcheng Liu
- College of Pharmaceutical Sciences, Hebei University, Baoding 071002, China; Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Baoding 071002, China.
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Taiwe GS, Montnach J, Nicolas S, De Waard S, Fiore E, Peyrin E, El-Aziz TMA, Amar M, Molgó J, Ronjat M, Servent D, Ravelet C, De Waard M. Aptamer Efficacies for In Vitro and In Vivo Modulation of αC-Conotoxin PrXA Pharmacology. Molecules 2019; 24:molecules24020229. [PMID: 30634526 PMCID: PMC6359527 DOI: 10.3390/molecules24020229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/02/2019] [Accepted: 01/07/2019] [Indexed: 01/03/2023] Open
Abstract
The medical staff is often powerless to treat patients affected by drug abuse or misuse and poisoning. In the case of envenomation, the treatment of choice remains horse sera administration that poses a wealth of other medical conditions and threats. Previously, we have demonstrated that DNA-based aptamers represent powerful neutralizing tools for lethal animal toxins of venomous origin. Herein, we further pursued our investigations in order to understand whether all toxin-interacting aptamers possessed equivalent potencies to neutralize αC-conotoxin PrXA in vitro and in vivo. We confirmed the high lethality in mice produced by αC-conotoxin PrXA regardless of the mode of injection and further characterized myoclonus produced by the toxin. We used high-throughput patch-clamp technology to assess the effect of αC-conotoxin PrXA on ACh-mediated responses in TE671 cells, responses that are carried by muscle-type nicotinic receptors. We show that 2 out of 4 aptamers reduce the affinity of the toxin for its receptor, most likely by interfering with the pharmacophore. In vivo, more complex responses on myoclonus and mice lethality are observed depending on the type of aptamer and mode of administration (concomitant or differed). Concomitant administration always works better than differed administration indicating the stability of the complex in vivo. The most remarkable conclusion is that an aptamer that has no or a limited efficacy in vitro may nevertheless be functional in vivo probably owing to an impact on the biodistribution or pharmacokinetics of the toxin in vivo. Overall, the results highlight that a blind selection of aptamers against toxins leads to efficient neutralizing compounds in vivo regardless of the mode of action. This opens the door to the use of aptamer mixtures as substitutes to horse sera for the neutralization of life-threatening animal venoms, an important WHO concern in tropical areas.
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Affiliation(s)
- Germain Sotoing Taiwe
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
- Department of Zoology and Animal Physiology, Faculty of Sciences, University of Buea, P.O. Box 63, Buea, Cameroon.
| | - Jérôme Montnach
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Sébastien Nicolas
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Stéphan De Waard
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Emmanuelle Fiore
- CNRS, DPM UMR 5063, University Grenoble Alpes, 38041 Grenoble, France.
| | - Eric Peyrin
- CNRS, DPM UMR 5063, University Grenoble Alpes, 38041 Grenoble, France.
| | | | - Muriel Amar
- Service d'Ingénierie Moléculaire des Protéines, Institut des Sciences du Vivant Frédéric Joliot, Commissariat à l'Energie Atomique, Université Paris-Saclay, F-91191 Gif sur Yvette, France.
| | - Jordi Molgó
- Service d'Ingénierie Moléculaire des Protéines, Institut des Sciences du Vivant Frédéric Joliot, Commissariat à l'Energie Atomique, Université Paris-Saclay, F-91191 Gif sur Yvette, France.
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS/Université Paris-Sud, 91198 Gif sur Yvette, France.
| | - Michel Ronjat
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
| | - Denis Servent
- Service d'Ingénierie Moléculaire des Protéines, Institut des Sciences du Vivant Frédéric Joliot, Commissariat à l'Energie Atomique, Université Paris-Saclay, F-91191 Gif sur Yvette, France.
| | - Corinne Ravelet
- CNRS, DPM UMR 5063, University Grenoble Alpes, 38041 Grenoble, France.
| | - Michel De Waard
- INSERM UMR 1087/CNRS UMR 6291, Institut du Thorax, Nouvelle Université à Nantes, LabEx Ion Channels, Science and Therapeutics, 8 Quai Moncousu, BP 70721 Nantes CEDEX 1, France.
- Smartox Biotechnology, 6 rue des Platanes, 38120 Saint Egrève, France.
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6
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Chaves EJF, Padilha IQM, Araújo DAM, Rocha GB. Determining the Relative Binding Affinity of Ricin Toxin A Inhibitors by Using Molecular Docking and Nonequilibrium Work. J Chem Inf Model 2018; 58:1205-1213. [PMID: 29750861 DOI: 10.1021/acs.jcim.8b00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ricin is a ribosome-inactivating protein (RIP type 2) consisting of two subunits, ricin toxin A (RTA) and ricin toxin B (RTB). Because of its cytotoxicity, ricin has worried world authorities for its potential use as a chemical weapon; therefore, its inhibition is of great biotechnological interest. RTA is the target for inhibitor synthesis, and pterin derivatives are promising candidates to inhibit it. In this study, we used a combination of the molecular docking approach and fast steered molecular dynamics (SMD) to assess the correlation between nonequilibrium work, ⟨ W⟩, and the IC50 for six RTA inhibitors. The results showed that molecular docking is a powerful tool to predict good bioactive poses of RTA inhibitors, and ⟨ W⟩ presented a strong correlation with IC50 ( R2 = 0.961). Such a profile ranked the RTA inhibitors better than the molecular docking approach. Therefore, the combination of docking and fast SMD simulation was shown to be a promising tool to distinguish RTA-active inhibitors from inactive ones and could be used as postdocking filtering approach.
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Affiliation(s)
- Elton J F Chaves
- Department of Biotechnology , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| | - Itácio Q M Padilha
- Department of Biotechnology , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| | - Demétrius A M Araújo
- Department of Biotechnology , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
| | - Gerd B Rocha
- Department of Chemistry , Federal University of Paraíba , 58051-900 João Pessoa - PB , Brazil
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7
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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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8
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Gupta N, Noël R, Goudet A, Hinsinger K, Michau A, Pons V, Abdelkafi H, Secher T, Shima A, Shtanko O, Sakurai Y, Cojean S, Pomel S, Liévin-Le Moal V, Leignel V, Herweg JA, Fischer A, Johannes L, Harrison K, Beard PM, Clayette P, Le Grand R, Rayner JO, Rudel T, Vacus J, Loiseau PM, Davey RA, Oswald E, Cintrat JC, Barbier J, Gillet D. Inhibitors of retrograde trafficking active against ricin and Shiga toxins also protect cells from several viruses, Leishmania and Chlamydiales. Chem Biol Interact 2016; 267:96-103. [PMID: 27712998 DOI: 10.1016/j.cbi.2016.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 08/09/2016] [Accepted: 10/03/2016] [Indexed: 11/25/2022]
Abstract
Medical countermeasures to treat biothreat agent infections require broad-spectrum therapeutics that do not induce agent resistance. A cell-based high-throughput screen (HTS) against ricin toxin combined with hit optimization allowed selection of a family of compounds that meet these requirements. The hit compound Retro-2 and its derivatives have been demonstrated to be safe in vivo in mice even at high doses. Moreover, Retro-2 is an inhibitor of retrograde transport that affects syntaxin-5-dependent toxins and pathogens. As a consequence, it has a broad-spectrum activity that has been demonstrated both in vitro and in vivo against ricin, Shiga toxin-producing O104:H4 entero-hemorrhagic E. coli and Leishmania sp. and in vitro against Ebola, Marburg and poxviruses and Chlamydiales. An effect is anticipated on other toxins or pathogens that use retrograde trafficking and syntaxin-5. Since Retro-2 targets cell components of the host and not directly the pathogen, no selection of resistant pathogens is expected. These lead compounds need now to be developed as drugs for human use.
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Affiliation(s)
- Neetu Gupta
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Romain Noël
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Amélie Goudet
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Karen Hinsinger
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Aurélien Michau
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Valérie Pons
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Hajer Abdelkafi
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | | | | | - Olena Shtanko
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Sandrine Cojean
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Sébastien Pomel
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Vanessa Liévin-Le Moal
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Véronique Leignel
- DRUGABILIS (French Research Performer SME), F-92290, Chatenay-Malabry, France
| | - Jo-Ana Herweg
- University of Würzburg, Biocenter, Chair of Microbiology, Am Hubland, D-97074, Würzburg, Germany
| | - Annette Fischer
- University of Würzburg, Biocenter, Chair of Microbiology, Am Hubland, D-97074, Würzburg, Germany
| | - Ludger Johannes
- Institut Curie, PSL Research University, Endocytic Trafficking and Therapeutic Delivery Group, 26 rue d'Ulm, F-75248, Paris Cedex 05, France; CNRS, UMR3666, F-75005, Paris, France; INSERM, U1143, F-75005, Paris, France
| | - Kate Harrison
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9RG, United Kingdom
| | - Philippa M Beard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9RG, United Kingdom; The Pirbright Institute, Ash Rd, Pirbright, Surrey GH24 0NF, United Kingdom
| | - Pascal Clayette
- ImmunoPharmacology and Biosafety Laboratory, BERTIN Pharma, CEA, F-92265, Fontenay-aux-Roses, France
| | - Roger Le Grand
- Institute of Emerging Diseases and Innovative Therapies, CEA, U1184, Immunology of Viral Infections and Autoimmune Diseases, Infectious Disease Models and Innovative Therapies Infrastructure, F-92265, Fontenay-aux-Roses, France; INSERM, U1184, F-94276, Le Kremlin-Bicêtre, France; University of Paris South, U1184, F-92265, Fontenay-aux-Roses, France; Vaccine Research Institute, Henri Mondor Hospital, F-94010, Créteil, France
| | - Jonathan O Rayner
- Infectious Disease Research, Southern Research, 2000 Ninth Avenue South, Birmingham, AL 35205, USA
| | - Thomas Rudel
- University of Würzburg, Biocenter, Chair of Microbiology, Am Hubland, D-97074, Würzburg, Germany
| | - Joël Vacus
- DRUGABILIS (French Research Performer SME), F-92290, Chatenay-Malabry, France
| | - Philippe M Loiseau
- Antiparasitic Chemotherapy, UMR 8076, CNRS BioCIS, LabEx LERMIT, Université Paris-Sud, Université Paris-Saclay, F-92290, Chatenay-Malabry, France
| | - Robert A Davey
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Jean-Christophe Cintrat
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Julien Barbier
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France
| | - Daniel Gillet
- Institute of Biology and Technology of Saclay (IBITECS), CEA, LabEx LERMIT, Université Paris-Saclay, F-91191, Gif Sur Yvette, France.
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9
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Yuan H, Stratton CF, Schramm VL. Transition State Structure of RNA Depurination by Saporin L3. ACS Chem Biol 2016; 11:1383-90. [PMID: 26886255 DOI: 10.1021/acschembio.5b01069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Saporin L3 from the leaves of the common soapwort is a catalyst for hydrolytic depurination of adenine from RNA. Saporin L3 is a type 1 ribosome inactivating protein (RIP) composed only of a catalytic domain. Other RIPs have been used in immunotoxin cancer therapy, but off-target effects have limited their development. In the current study, we use transition state theory to understand the chemical mechanism and transition state structure of saporin L3. In favorable cases, transition state structures guide the design of transition state analogues as inhibitors. Kinetic isotope effects (KIEs) were determined for an A14C mutant of saporin L3. To permit KIE measurements, small stem-loop RNAs that contain an AGGG tetraloop structure were enzymatically synthesized with the single adenylate bearing specific isotopic substitutions. KIEs were measured and corrected for forward commitment to obtain intrinsic values. A model of the transition state structure for depurination of stem-loop RNA (5'-GGGAGGGCCC-3') by saporin L3 was determined by matching KIE values predicted via quantum chemical calculations to a family of intrinsic KIEs. This model indicates saporin L3 displays a late transition state with the N-ribosidic bond to the adenine nearly cleaved, and the attacking water nucleophile weakly bonded to the ribosyl anomeric carbon. The transition state retains partial ribocation character, a feature common to most N-ribosyl transferases. However, the transition state geometry for saporin L3 is distinct from ricin A-chain, the only other RIP whose transition state is known.
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Affiliation(s)
- Hongling Yuan
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Christopher F. Stratton
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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10
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Du Y, Zhen SJ, Li B, Byrom M, Jiang YS, Ellington AD. Engineering Signaling Aptamers That Rely on Kinetic Rather Than Equilibrium Competition. Anal Chem 2016; 88:2250-7. [PMID: 26750592 DOI: 10.1021/acs.analchem.5b03930] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During the past decade, aptasensors have largely been designed on the basis of the notion that ligand-modulated equilibration between aptamer conformations could be exploited for sensing. One implementation of this strategy has been to denature the aptamer with an antisense oligonucleotide, wait for dissociation of the antisense oligonucleotide, and stabilize the folded, signaling conformer with a ligand. However, there is a large kinetic barrier associated with releasing the oligonucleotide from the aptamer to again obtain an active, binding conformation. If the length of the antisense oligonucleotide is decreased to make dissociation from the aptamer more favorable, higher background signals are observed. To improve the general methodology for developing aptasensors, we have developed a novel and robust strategy for aptasensor design in which an oligonucleotide kinetically competes with the ligand for binding rather than having to be released from a stable duplex. While the oligonucleotide can induce conformational change, it initially chooses between the aptamer and a molecular beacon (MB), a process that does not require a lengthy pre-equilibration. Using an anti-ricin aptamer as a starting point, we developed a "competitive" aptasensor with a measured limit of detection (LOD) of 30 nM with an optical readout and as low as 3 nM for ricin toxin A-chain (RTA) detection on an electrochemical platform.
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Affiliation(s)
- Yan Du
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Shu Jun Zhen
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States.,Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , 400715, Chongqing, P.R. China
| | - Bingling Li
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michelle Byrom
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu Sherry Jiang
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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11
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Abstract
RNAs have highly complex and dynamic cellular localization patterns. Technologies for imaging RNA in living cells are important for uncovering their function and regulatory pathways. One approach for imaging RNA involves genetically encoding fluorescent RNAs using RNA mimics of green fluorescent protein (GFP). These mimics are RNA aptamers that bind fluorophores resembling those naturally found in GFP and activate their fluorescence. These RNA-fluorophore complexes, including Spinach, Spinach2, and Broccoli, can be used to tag RNAs and to image their localization in living cells. In this article, we describe the generation and optimization of these aptamers, along with strategies for expanding the spectral properties of their associated RNA-fluorophore complexes. We also discuss the structural basis for the fluorescence and photophysical properties of Spinach, and we describe future prospects for designing enhanced RNA-fluorophore complexes with enhanced photostability and increased sensitivity.
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Affiliation(s)
- Mingxu You
- Department of Pharmacology, Weill Medical College, Cornell University, New York, New York 10065; ,
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12
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Fetter L, Richards J, Daniel J, Roon L, Rowland TJ, Bonham AJ. Electrochemical aptamer scaffold biosensors for detection of botulism and ricin toxins. Chem Commun (Camb) 2015; 51:15137-40. [PMID: 26323568 DOI: 10.1039/c5cc05933j] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein toxins present considerable health risks, but detection often requires laborious analysis. Here, we developed electrochemical aptamer biosensors for ricin and botulinum neurotoxins, which display robust and specific signal at nanomolar concentrations and function in dilute serum. These biosensors may aid future efforts for the rapid diagnosis of toxins.
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Affiliation(s)
- Lisa Fetter
- Department of Chemistry, Metropolitan State University of Denver, Denver, CO 80204, USA.
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13
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Szilágyi A, Kun Á, Szathmáry E. Local neutral networks help maintain inaccurately replicating ribozymes. PLoS One 2014; 9:e109987. [PMID: 25299454 PMCID: PMC4192543 DOI: 10.1371/journal.pone.0109987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/05/2014] [Indexed: 12/03/2022] Open
Abstract
The error threshold of replication limits the selectively maintainable genome size against recurrent deleterious mutations for most fitness landscapes. In the context of RNA replication a distinction between the genotypic and the phenotypic error threshold has been made; where the latter concerns the maintenance of secondary structure rather than sequence. RNA secondary structure is treated as a proxy for function. The phenotypic error threshold allows higher per digit mutation rates than its genotypic counterpart, and is known to increase with the frequency of neutral mutations in sequence space. Here we show that the degree of neutrality, i.e. the frequency of nearest-neighbour (one-step) neutral mutants is a remarkably accurate proxy for the overall frequency of such mutants in an experimentally verifiable formula for the phenotypic error threshold; this we achieve by the full numerical solution for the concentration of all sequences in mutation-selection balance up to length 16. We reinforce our previous result that currently known ribozymes could be selectively maintained by the accuracy known from the best available polymerase ribozymes. Furthermore, we show that in silico stabilizing selection can increase the mutational robustness of ribozymes due to the fact that they were produced by artificial directional selection in the first place. Our finding offers a better understanding of the error threshold and provides further insight into the plausibility of an ancient RNA world.
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Affiliation(s)
- András Szilágyi
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary
| | - Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany
- MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
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14
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Characterization and epitope mapping of the polyclonal antibody repertoire elicited by ricin holotoxin-based vaccination. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2014; 21:1534-40. [PMID: 25209559 DOI: 10.1128/cvi.00510-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ricin, one of the most potent and lethal toxins known, is classified by the Centers for Disease Control and Prevention (CDC) as a select agent. Currently, there is no available antidote against ricin exposure, and the most promising therapy is based on neutralizing antibodies elicited by active vaccination or that are given passively. The aim of this study was to characterize the repertoire of anti-ricin antibodies generated in rabbits immunized with ricin toxoid. These anti-ricin antibodies exhibit an exceptionally high avidity (thiocyanate-based avidity index, 9 M) toward ricin and an apparent affinity of 1 nM. Utilizing a novel tissue culture-based assay that enables the determination of ricin activity within a short time period, we found that the anti-ricin antibodies also possess a very high neutralizing titer. In line with these findings, these antibodies conferred mice with full protection against pulmonary ricinosis when administered as a passive vaccination. Epitope mapping analysis using phage display random peptide libraries revealed that the polyclonal serum contains four immunodominant epitopes, three of which are located on the A subunit and one on the B subunit of ricin. Only two of the four epitopes were found to have a significant role in ricin neutralization. To the best of our knowledge, this is the first work that characterizes these immunological aspects of the polyclonal response to ricin holotoxin-based vaccination. These findings provide useful information and a possible strategy for the development and design of an improved ricin holotoxin-based vaccine.
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15
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Ye F, Zheng Y, Wang X, Tan X, Zhang T, Xin W, Wang J, Huang Y, Fan Q, Wang J. Recognition of Bungarus multicinctus venom by a DNA aptamer against β-bungarotoxin. PLoS One 2014; 9:e105404. [PMID: 25144237 PMCID: PMC4140777 DOI: 10.1371/journal.pone.0105404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/21/2014] [Indexed: 01/03/2023] Open
Abstract
Antibody-based technology is the main method for diagnosis and treatment of snake bite envenoming currently. However, the development of an antibody, polyclonal or monoclonal, is a complicated and costly procedure. Aptamers are single stranded oligonucleotides that recognize specific targets such as proteins and have shown great potential over the years as diagnostic and therapeutic agents. In contrast to antibodies, aptamers can be selected in vitro without immunization of animals, and synthesized chemically with extreme accuracy, low cost and high degree of purity. In this study we firstly report on the identification of DNA aptamers that bind to β-bungarotoxin (β-BuTx), a neurotoxin from the venom of Bungarus multicinctus. A plate-SELEX method was used for the selection of β-BuTx specific aptamers. After 10 rounds of selection, four aptamer candidates were obtained, with the dissociation constant ranged from 65.9 nM to 995 nM measured by fluorescence spectroscopy. Competitive binding assays using both the fluorescently labeled and unlabeled aptamers revealed that the four aptamers bound to the same binding site of β-BuTx. The best binder, βB-1, bound specifically to β-BuTx, but not to BSA, casein or α-Bungarotoxin. Moreover, electrophoretic mobility shift assay and enzyme-linked aptamer assay demonstrated that βB-1 could discriminate B. multicinctus venom from other snake venoms tested. The results suggest that aptamer βB-1 can serve as a useful tool for the design and development of drugs and diagnostic tests for β-BuTx poisoning and B. multicinctus bites.
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Affiliation(s)
- Fengping Ye
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Ying Zheng
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Xi Wang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Xiaolong Tan
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Tao Zhang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
| | - Jie Wang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Yong Huang
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Quanshui Fan
- Institute of Military Medicine, Chengdu Military Region's Center for Disease Control & Prevention, Kunming, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
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16
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Nucleic acid aptamers: research tools in disease diagnostics and therapeutics. BIOMED RESEARCH INTERNATIONAL 2014; 2014:540451. [PMID: 25050359 PMCID: PMC4090538 DOI: 10.1155/2014/540451] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022]
Abstract
Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.
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Bagaria S, Ponnalagu D, Bisht S, Karande AA. Mechanistic insights into the neutralization of cytotoxic abrin by the monoclonal antibody D6F10. PLoS One 2013; 8:e70273. [PMID: 23922965 PMCID: PMC3726390 DOI: 10.1371/journal.pone.0070273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 06/14/2013] [Indexed: 01/06/2023] Open
Abstract
Abrin, an A/B toxin obtained from the Abrus precatorius plant is extremely toxic and a potential bio-warfare agent. Till date there is no antidote or vaccine available against this toxin. The only known neutralizing monoclonal antibody against abrin, namely D6F10, has been shown to rescue the toxicity of abrin in cells as well as in mice. The present study focuses on mapping the epitopic region to understand the mechanism of neutralization of abrin by the antibody D6F10. Truncation and mutational analysis of abrin A chain revealed that the amino acids 74-123 of abrin A chain contain the core epitope and the residues Thr112, Gly114 and Arg118 are crucial for binding of the antibody. In silico analysis of the position of the mapped epitope indicated that it is present close to the active site cleft of abrin A chain. Thus, binding of the antibody near the active site blocks the enzymatic activity of abrin A chain, thereby rescuing inhibition of protein synthesis by the toxin in vitro. At 1∶10 molar concentration of abrin:antibody, the antibody D6F10 rescued cells from abrin-mediated inhibition of protein synthesis but did not prevent cell attachment of abrin. Further, internalization of the antibody bound to abrin was observed in cells by confocal microscopy. This is a novel finding which suggests that the antibody might function intracellularly and possibly explains the rescue of abrin's toxicity by the antibody in whole cells and animals. To our knowledge, this study is the first report on a neutralizing epitope for abrin and provides mechanistic insights into the poorly understood mode of action of anti-A chain antibodies against several toxins including ricin.
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Affiliation(s)
- Shradha Bagaria
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
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18
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Yang J, Bowser MT. Capillary electrophoresis-SELEX selection of catalytic DNA aptamers for a small-molecule porphyrin target. Anal Chem 2013; 85:1525-30. [PMID: 23234289 DOI: 10.1021/ac302721j] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has previously been used to select aptamers for large-molecule targets such as proteins, lipopolysaccharides, and peptides. For the first time, we have performed CE-SELEX selection for a small-molecule target, N-methyl mesoporphyrin (NMM), with a molecular weight of only 580 g/mol. DNA aptamers with high-nanomolar to low-micromolar dissociation constants were achieved after only three rounds of selection. This corresponds to an >50-fold improvement in affinity over the random library. Two out of eight randomly chosen aptamers were found to catalyze the metal insertion reaction of mesoporphyrin with 1.7- and 2.0-fold rate enhancements, respectively.
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Affiliation(s)
- Jing Yang
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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19
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Lauridsen LH, Veedu RN. Nucleic acid aptamers against biotoxins: a new paradigm toward the treatment and diagnostic approach. Nucleic Acid Ther 2012; 22:371-9. [PMID: 23113767 DOI: 10.1089/nat.2012.0377] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with very high affinity and specificity, and are generally selected by a process referred to as systematic evolution of ligands by exponential enrichment. Conventional antibody-based therapeutic and diagnostic approach currently employed against biotoxins pose major limitations such as the requirement of a live animal for the in vivo enrichment of the antibody species, decreased stability, high production cost, and side effects. Aptamer technology is a viable alternative that can be used to combat these problems. Fully sequestered in vitro, aptamers eliminate the need for a living host. Furthermore, one of the key advantages of using aptamers instead of antibodies is that they can be selected against very weakly immunogenic and cytotoxic substances. In this review, we focus on nucleic acid aptamers developed against various biotoxins of plant, microorganism, or animal origin and show how these can be used in diagnostics (e.g., biosensors) and therapy.
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Affiliation(s)
- Lasse Holm Lauridsen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
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20
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Wang B, Guo C, Zhang M, Park B, Xu B. High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction. J Phys Chem B 2012; 116:5316-22. [PMID: 22489938 DOI: 10.1021/jp301765n] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the molecular details of DNA aptamer-ricin interactions. The toxic protein ricin molecules were immobilized on a Au(111) surface using a N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in situ using the AFM tip modified with an antiricin aptamer. Computer simulation was used to illustrate the protein and aptamer structures, the single-molecule ricin images on a Au(111) surface, and the binding conformations of ricin-aptamer and ricin-antibody complexes. The various ricin conformations on a Au(111) surface were caused by the different lysine residues reacting with the NHS ester. It was also observed that most of the binding sites for aptamer and antibody on the A chains of ricin molecules were not interfered by the immobilization reaction. The different locations of the ricin binding sites to aptamer and antibody were also distinguished by AFM recognition images and interpreted by simulations.
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Affiliation(s)
- Bin Wang
- Single Molecule Study Laboratory, Faculty of Engineering and Nanoscale Science and Engineering Center, University of Georgia, Athens, Georgia 30602, United States
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21
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Properties of an LNA-modified ricin RNA aptamer. Biochem Biophys Res Commun 2012; 419:60-5. [PMID: 22326915 DOI: 10.1016/j.bbrc.2012.01.127] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/26/2012] [Indexed: 11/21/2022]
Abstract
'Locked nucleic acids' (LNAs) are sugar modified nucleic acids containing the 2'-O-4'C-methylene-β-D-ribofuranoses. The substitution of RNAs with LNAs leads to an enhanced thermostability. Aptamers are nucleic acids, which are selected for specific target binding from a large library pool by the 'SELEX' method. Introduction of modified nucleic acids into aptamers can improve their stability. The stem region of a ricin A chain RNA aptamer was substituted by locked nucleic acids. Different constructs of the LNA-substituted aptamers were examined for their thermostability, binding activity, folding and RNase sensitivity as compared to the natural RNA counterpart. The LNA-modified aptamers were active in target binding, while the loop regions and the adjacent stem nucleotides remained unsubstituted. The thermostability and RNase resistance of LNA substituted aptamers were enhanced as compared to the native RNA aptamer. This study supports the approach to substitute the aptamer stem region by LNAs and to leave the loop region unmodified, which is responsible for ligand binding. Thus, LNAs possess an encouraging potential for the development of new stabilized nucleic acids and will promote future diagnostic and therapeutic applications.
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Inhibitors of the cellular trafficking of ricin. Toxins (Basel) 2012; 4:15-27. [PMID: 22347620 PMCID: PMC3277095 DOI: 10.3390/toxins4010015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/22/2011] [Accepted: 12/23/2011] [Indexed: 12/26/2022] Open
Abstract
Throughout the last decade, efforts to identify and develop effective inhibitors of the ricin toxin have focused on targeting its N-glycosidase activity. Alternatively, molecules disrupting intracellular trafficking have been shown to block ricin toxicity. Several research teams have recently developed high-throughput phenotypic screens for small molecules acting on the intracellular targets required for entry of ricin into cells. These screens have identified inhibitory compounds that can protect cells, and sometimes even animals against ricin. We review these newly discovered cellular inhibitors of ricin intoxication, discuss the advantages and drawbacks of chemical-genetics approaches, and address the issues to be resolved so that the therapeutic development of these small-molecule compounds can progress.
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23
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Zhu G, Lübbecke M, Walter JG, Stahl F, Scheper T. Characterization of Optimal Aptamer-Microarray Binding Chemistry and Spacer Design. Chem Eng Technol 2011. [DOI: 10.1002/ceat.201000551] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Worbs S, Köhler K, Pauly D, Avondet MA, Schaer M, Dorner MB, Dorner BG. Ricinus communis intoxications in human and veterinary medicine-a summary of real cases. Toxins (Basel) 2011; 3:1332-72. [PMID: 22069699 PMCID: PMC3210461 DOI: 10.3390/toxins3101332] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 09/26/2011] [Accepted: 09/30/2011] [Indexed: 12/11/2022] Open
Abstract
Accidental and intended Ricinus communis intoxications in humans and animals have been known for centuries but the causative agent remained elusive until 1888 when Stillmark attributed the toxicity to the lectin ricin. Ricinus communis is grown worldwide on an industrial scale for the production of castor oil. As by-product in castor oil production ricin is mass produced above 1 million tons per year. On the basis of its availability, toxicity, ease of preparation and the current lack of medical countermeasures, ricin has gained attention as potential biological warfare agent. The seeds also contain the less toxic, but highly homologous Ricinus communis agglutinin and the alkaloid ricinine, and especially the latter can be used to track intoxications. After oil extraction and detoxification, the defatted press cake is used as organic fertilizer and as low-value feed. In this context there have been sporadic reports from different countries describing animal intoxications after uptake of obviously insufficiently detoxified fertilizer. Observations in Germany over several years, however, have led us to speculate that the detoxification process is not always performed thoroughly and controlled, calling for international regulations which clearly state a ricin threshold in fertilizer. In this review we summarize knowledge on intended and unintended poisoning with ricin or castor seeds both in humans and animals, with a particular emphasis on intoxications due to improperly detoxified castor bean meal and forensic analysis.
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Affiliation(s)
- Sylvia Worbs
- Centre for Biological Security, Microbial Toxins (ZBS3), Robert Koch-Institut, Nordufer 20, Berlin 13353, Germany; (S.W.); (D.P.); (M.B.D.)
| | - Kernt Köhler
- Institute of Veterinary Pathology, Justus Liebig University Giessen, Frankfurter Street 96, Giessen 35392, Germany;
| | - Diana Pauly
- Centre for Biological Security, Microbial Toxins (ZBS3), Robert Koch-Institut, Nordufer 20, Berlin 13353, Germany; (S.W.); (D.P.); (M.B.D.)
| | - Marc-André Avondet
- Biology and Chemistry Section, Federal Department of Defence, Civil Protection and Sports DDPS SPIEZ LABORATORY, Austrasse 1, Spiez CH-3700, Switzerland; (M.-A.A.); (M.S.)
| | - Martin Schaer
- Biology and Chemistry Section, Federal Department of Defence, Civil Protection and Sports DDPS SPIEZ LABORATORY, Austrasse 1, Spiez CH-3700, Switzerland; (M.-A.A.); (M.S.)
| | - Martin B. Dorner
- Centre for Biological Security, Microbial Toxins (ZBS3), Robert Koch-Institut, Nordufer 20, Berlin 13353, Germany; (S.W.); (D.P.); (M.B.D.)
| | - Brigitte G. Dorner
- Centre for Biological Security, Microbial Toxins (ZBS3), Robert Koch-Institut, Nordufer 20, Berlin 13353, Germany; (S.W.); (D.P.); (M.B.D.)
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25
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Kärkkäinen RM, Drasbek MR, McDowall I, Smith CJ, Young NW, Bonwick GA. Aptamers for safety and quality assurance in the food industry: detection of pathogens. Int J Food Sci Technol 2011. [DOI: 10.1111/j.1365-2621.2010.02470.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Ramasamy S, Liu CQ, Tran H, Gubala A, Gauci P, McAllister J, Vo T. Principles of antidote pharmacology: an update on prophylaxis, post-exposure treatment recommendations and research initiatives for biological agents. Br J Pharmacol 2010; 161:721-48. [PMID: 20860656 DOI: 10.1111/j.1476-5381.2010.00939.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The use of biological agents has generally been confined to military-led conflicts. However, there has been an increase in non-state-based terrorism, including the use of asymmetric warfare, such as biological agents in the past few decades. Thus, it is becoming increasingly important to consider strategies for preventing and preparing for attacks by insurgents, such as the development of pre- and post-exposure medical countermeasures. There are a wide range of prophylactics and treatments being investigated to combat the effects of biological agents. These include antibiotics (for both conventional and unconventional use), antibodies, anti-virals, immunomodulators, nucleic acids (analogues, antisense, ribozymes and DNAzymes), bacteriophage therapy and micro-encapsulation. While vaccines are commercially available for the prevention of anthrax, cholera, plague, Q fever and smallpox, there are no licensed vaccines available for use in the case of botulinum toxins, viral encephalitis, melioidosis or ricin. Antibiotics are still recommended as the mainstay treatment following exposure to anthrax, plague, Q fever and melioidosis. Anti-toxin therapy and anti-virals may be used in the case of botulinum toxins or smallpox respectively. However, supportive care is the only, or mainstay, post-exposure treatment for cholera, viral encephalitis and ricin - a recommendation that has not changed in decades. Indeed, with the difficulty that antibiotic resistance poses, the development and further evaluation of techniques and atypical pharmaceuticals are fundamental to the development of prophylaxis and post-exposure treatment options. The aim of this review is to present an update on prophylaxis and post-exposure treatment recommendations and research initiatives for biological agents in the open literature from 2007 to 2009.
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Affiliation(s)
- S Ramasamy
- Defence Science & Technology Organisation, Human Protection and Performance Division, Fishermans Bend, Vic., Australia.
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27
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Gu LQ, Ding S, Gao C. Aptamer-encoded nanopore for ultrasensitive detection of bioterrorist agent ricin at single-molecule resolution. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:6699-702. [PMID: 19964179 DOI: 10.1109/iembs.2009.5333281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The molecular-scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Here we will review our recent discoveries with a lab-in-hand glass nanopore: single-molecule discrimination of chiral enantiomers with a trapped cyclodextrin, and sensing of bioterrorist agent ricin.
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Affiliation(s)
- Li-Qun Gu
- Dalton Cardiovascular Research Center and Department of Biological Engineering, University of Missouri, Columbia, MO 65211, USA.
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Weiss TC, Zhai GG, Romaniuk PJ. An RNA aptamer with high affinity and high specificity for the 5S RNA binding zinc finger proteins TFIIIA and p43. Biochemistry 2010; 49:1755-65. [PMID: 20095591 DOI: 10.1021/bi901664h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Xenopus zinc finger proteins TFIIIA and p43 bind to 5S RNA in immature oocytes to form 7S and 42S ribonucleoprotein storage particles. To probe the similarities and differences in the RNA binding domains of these two proteins, a library of random RNA molecules was enriched using TFIIIA as the bait protein. One of the abundant aptamers isolated, RNA22, bound to both TFIIIA and p43 derived zinc finger peptides with high affinity and specificity even though the predicted secondary structure of the RNA was unrelated to that of 5S RNA. The interactions of TFIIIA and p43 peptides with RNA22 were compared to their interactions with 5S RNA by characterizing the effects of assay conditions, mutations in RNA22, and mutations in the zinc finger proteins. The similarities and differences in the mechanisms by which these two zinc finger proteins interact with 5S RNA compared to RNA22 suggest they share a common platform for RNA binding with enough flexibility to form specific interactions with both RNAs.
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Affiliation(s)
- Tristen C Weiss
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, Victoria, British Columbia V8W 3P6, Canada
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Abstract
This method describes a microarray-based platform to perform nucleic acid selections. Chemical ligands to which a nucleic acid binder is desired are immobilized onto an agarose microarray surface; the array is then incubated with an RNA library. Bound RNA library members are harvested directly from the array surface via gel excision at the position on the array where a ligand was immobilized. The RNA is then amplified via RT-PCR, cloned, and sequenced. This method has the following advantages over traditional resin-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX): (1) multiple selections can be completed in parallel on a single microarray surface; (2) kinetic biases in the selections are mitigated since all RNA binders are harvested from an array via gel excision; (3) the amount of chemical ligand needed to perform a selection is minimized; (4) selections do not require expensive resins or equipment; and (5) the matrix used for selections is inexpensive and easy to prepare. Although this protocol was demonstrated for RNA selections, it should be applicable for any nucleic acid selection.
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Lombardi A, Marshall RS, Savino C, Fabbrini MS, Ceriotti A. Type I Ribosome-Inactivating Proteins from Saponaria officinalis. TOXIC PLANT PROTEINS 2010. [DOI: 10.1007/978-3-642-12176-0_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, Ellington AD. Design, Synthesis, and Amplification of DNA Pools for In Vitro Selection. ACTA ACUST UNITED AC 2009; Chapter 9:Unit 9.2. [DOI: 10.1002/0471142700.nc0902s39] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, University of Texas Austin Texas
| | | | - Pooja Satya
- Freshman Research Initiative, University of Texas Austin Texas
| | - Krystal Ogle
- Freshman Research Initiative, University of Texas Austin Texas
| | - Jack Pollard
- 3rd Millennium Corporation Cambridge Massachusetts
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Hall B, Micheletti JM, Satya P, Ogle K, Pollard J, Ellington AD. Design, synthesis, and amplification of DNA pools for in vitro selection. ACTA ACUST UNITED AC 2009; Chapter 24:Unit 24.2. [PMID: 19816932 DOI: 10.1002/0471142727.mb2402s88] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Preparation of a random-sequence DNA pool is presented. The degree of randomization and the length of the random sequence are discussed, as is synthesis of the pool using a DNA synthesizer or via commercial synthesis companies. Purification of a single-stranded pool and conversion to a double-stranded pool are presented as step-by-step protocols. Support protocols describe determination of the complexity and skewing of the pool, and optimization of amplification conditions.
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Affiliation(s)
- Bradley Hall
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas, USA
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Gnanam AJ, Hall B, Shen X, Piasecki S, Vernados A, Galyov EE, Smither SJ, Kitto GB, Titball RW, Ellington AD, Brown KA. Development of aptamers specific for potential diagnostic targets in Burkholderia pseudomallei. Trans R Soc Trop Med Hyg 2009; 102 Suppl 1:S55-7. [PMID: 19121689 DOI: 10.1016/s0035-9203(08)70015-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Improved diagnostic reagents would be of considerable benefit in enhancing the specificity and sensitivity of rapid assays for Burkholderia pseudomallei, the causative agent of melioidosis. The purpose of this work is to develop aptamers, high affinity RNA-based molecular recognition molecules, which could be used as reagents for identification of the whole organism in assays of biological samples. Data are presented demonstrating the purification of recombinant B. pseudomallei secreted or surface-exposed macromolecules, which have been expressed in Escherichia coli, and the initial stages of aptamer generation using these recombinant proteins. Future studies will focus upon the expansion of this methodology to include other target macromolecules located on or near the outer membrane of this organism.
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Affiliation(s)
- Annie J Gnanam
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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Förster C, Oberthuer D, Gao J, Eichert A, Quast FG, Betzel C, Nitsche A, Erdmann VA, Fürste JP. Crystallization and preliminary X-ray diffraction data of an LNA 7-mer duplex derived from a ricin aptamer. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:881-5. [PMID: 19724123 PMCID: PMC2795591 DOI: 10.1107/s1744309109029145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 07/22/2009] [Indexed: 12/28/2022]
Abstract
Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as beta-D-2'-O,4'-C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The beta-D-2'-O,4'-C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, which makes them of interest for stabilizing the structure of different nucleic acids. Aptamers, which are DNAs or RNAs targeted against specific ligands, are candidates for substitution with LNAs in order to increase their stability. A 7-mer helix derived from the terminal part of an aptamer that was targeted against ricin was chosen. The ricin aptamer originally consisted of natural RNA building blocks and showed high affinity in ricin binding. For future stabilization of the aptamer, the terminal helix has been constructed as an ;all-locked' LNA and was successfully crystallized in order to investigate its structural properties. Optimization of crystal growth succeeded by the use of different metal salts as additives, such as CuCl(2), MgCl(2), MnCl(2), CaCl(2), CoCl(2) and ZnSO(4). Preliminary X-ray diffraction data were collected and processed to 2.8 A resolution. The LNA crystallized in space group P6(5), with unit-cell parameters a = 50.11, b = 50.11, c = 40.72 A. The crystals contained one LNA helix per asymmetric unit with a Matthews coefficient of 3.17 A(3) Da(-1), which implies a solvent content of 70.15%.
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Affiliation(s)
- Charlotte Förster
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Dominik Oberthuer
- Institute of Biochemistry and Food Chemistry, University of Hamburg, Notkestrasse 85, Building 22a, c/o DESY, 22603 Hamburg, Germany
| | - Jiang Gao
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - André Eichert
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Frederick G. Quast
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Betzel
- Institute of Biochemistry and Food Chemistry, University of Hamburg, Notkestrasse 85, Building 22a, c/o DESY, 22603 Hamburg, Germany
| | - Andreas Nitsche
- Robert Koch-Institut, Zentrum für Biologische Sicherheit 1, Nordufer 20, 13353 Berlin, Germany
| | - Volker A. Erdmann
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jens P. Fürste
- Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
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Ding S, Gao C, Gu LQ. Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore. Anal Chem 2009; 81:6649-55. [PMID: 19627120 PMCID: PMC3009471 DOI: 10.1021/ac9006705] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nanopore-based single-molecule biosensors have been extensively studied. Protein pores that have receptors attached to them are target-selective, but their real-time applications are limited by the fragility of the lipid membrane into which the protein pores are embedded. Synthetic nanopores are more stable and provide flexible pore sizes, but the selectivity is low when detecting in the translocation mode. In spite of modifications with probing molecules, such as antibodies, to potentiate specific targeting, these nanopores fail to bind individual target molecules. Distinguishing between binding and translocation blocks remains unsolved. Here, we propose an aptamer-encoded nanopore that overcomes these challenges. Aptamers are well-known probing oligonucleotides that have high sensitivity and selectivity. In contrast to antibodies, aptamers are much smaller than their targets, rendering target blockades in the nanopore much more distinguishable. We used aptamer-encoded nanopores to detect single molecules of immunoglobulin E and the bioterrorist agent ricin, sequentially captured by the immobilized aptamer in the sensing zone of the pore. The functional nanopore also probed sequence-dependent aptamer-protein interactions. These findings will facilitate the development of a universal nanopore for multitarget detection.
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Affiliation(s)
- Shu Ding
- Department of Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri – Columbia, MO 65211, USA
| | - Changlu Gao
- Department of Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri – Columbia, MO 65211, USA
| | - Li-Qun Gu
- Department of Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri – Columbia, MO 65211, USA
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Bai Y, Monzingo AF, Robertus JD. The X-ray structure of ricin A chain with a novel inhibitor. Arch Biochem Biophys 2008; 483:23-8. [PMID: 19138659 DOI: 10.1016/j.abb.2008.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/18/2008] [Accepted: 12/20/2008] [Indexed: 11/17/2022]
Abstract
Ricin is a potent heterodimeric cytotoxin; the B chain binds eucaryotic cell surfaces aiding uptake and the A chain, RTA, reaches the cytoplasm where it enzymatically depurinates a key ribosomal adenine, inhibiting protein synthesis. Ricin is known to be an agent in bioterrorist repertoires and there is great interest in finding, or creating, efficacious inhibitors of the toxin as potential antidotes. We have previously identified two families of bicyclic RTA inhibitors, pterins and purines. Both classes have poor solubility which impairs inhibitor development. Here we report the use of 2-amino-4,6-dihydroxy-pyrimidines as RTA inhibitors. Unlike previously observed single ring inhibitor platforms, these displace Tyr 80 and bind deep in the RTA specificity pocket. These compounds are at least 10 times more soluble than pterin-based inhibitors and appear to be useful new class of ricin inhibitors.
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Affiliation(s)
- Yan Bai
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas, Austin, 78712, USA
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37
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Abstract
Aptamers are oligonucleotides (typically 10-60 bases in length) capable of binding target ligands with affinities similar to antibodies. The generation of high density multiplexed aptamer arrays for molecular diagnostics was first proposed nearly ten years ago for the quantification of the thousands of proteins within biological samples, including blood and urine. The tagless aptameric detection of small molecular compounds extends the application of such arrays to bioanalyses at the metabolite level. We present here a minireview on some existing technologies and highlight recent innovations that are being applied to this field, which may facilitate the vision of highly multi-parallelized arrays for the quantitative analysis of biological systems.
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Affiliation(s)
- William Rowe
- Manchester Interdisciplinary Biocentre, The University of Manchester, UK
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38
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Fan S, Wu F, Martiniuk F, Hale ML, Ellington AD, Tchou-Wong KM. Protective effects of anti-ricin A-chain RNA aptamer against ricin toxicity. World J Gastroenterol 2008; 14:6360-5. [PMID: 19009652 PMCID: PMC2766118 DOI: 10.3748/wjg.14.6360] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the therapeutic potential of an RNA ligand (aptamer) specific for the catalytic ricin A-chain (RTA), the protective effects of a 31-nucleotide RNA aptamer (31RA), which formed a high affinity complex with RTA, against ricin-induced toxicity in cell-based luciferase translation and cell cytotoxicity assays were evaluated.
METHODS: To test the therapeutic potential of anti-RTA aptamers in Chinese hamster ovary (CHO) AA8 cells stably transfected with a tetracycline regulatable promoter, ricin ribotoxicity was measured using luciferase and ricin-induced cytotoxicity was ascertained by MTS cell proliferation assay with tetrazolium compound [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium].
RESULTS: Inhibition of protein synthesis by ricin in CHO AA8 cells resulted in diminished luciferase activity and treatment with polyclonal antibody against deglycosylated RTA (dgA) neutralized the inhibitory effects of ricin on luciferase activity and protected against ricin-induced cytotoxicity as measured by MTS assay. The 31RA anti-RTA aptamer inhibited the translation of luciferase mRNA in cell-free reticulocyte translation assay. 31RA aptamer also partially neutralized the inhibitory effects of ricin on luciferase activity and partially protected against ricin-induced cytotoxicity in CHO AA8 cells.
CONCLUSION: We have shown that anti-RTA RNA aptamer can protect against ricin ribotoxicity in cell-based luciferase and cell cytotoxicity assays. Hence, RNA aptamer that inhibits RTA enzymatic activity represents a novel class of nucleic acid inhibitor that has the potential to be developed as a therapeutic agent for the treatment of ricin intoxication.
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Mok W, Li Y. Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays. SENSORS 2008; 8:7050-7084. [PMID: 27873915 PMCID: PMC3787431 DOI: 10.3390/s8117050] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/25/2008] [Accepted: 10/30/2008] [Indexed: 02/03/2023]
Abstract
As the key constituents of the genetic code, the importance of nucleic acids to life has long been appreciated. Despite being composed of only four structurally similar nucleotides, single-stranded nucleic acids, as in single-stranded DNAs and RNAs, can fold into distinct three-dimensional shapes due to specific intramolecular interactions and carry out functions beyond serving as templates for protein synthesis. These functional nucleic acids (FNAs) can catalyze chemical reactions, regulate gene expression, and recognize target molecules. Aptamers, whose name is derived from the Latin word aptus meaning “to fit”, are oligonucleotides that can bind their target ligands with high affinity and specificity. Since aptamers exist in nature but can also be artificially isolated from pools of random nucleic acids through a process called in vitro selection, they can potentially bind a diverse array of compounds. In this review, we will discuss the research that is being done to develop aptamers against various biomolecules, the progress in engineering biosensors by coupling aptamers to signal transducers, and the prospect of employing these sensors for a range of chemical and biological applications. Advances in aptamer technology emphasizes that nucleic acids are not only the fundamental molecules of life, they can also serve as research tools to enhance our understanding of life. The possibility of using aptamer-based tools in drug discovery and the identification of infectious agents can ultimately augment our quality of life.
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Affiliation(s)
- Wendy Mok
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada.
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main Street West, Hamilton, Ontario, L8N 3Z5, Canada.
- Department of Chemistry, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4M1, Canada.
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Yunusov D, So M, Shayan S, Okhonin V, Musheev MU, Berezovski MV, Krylov SN. Kinetic capillary electrophoresis-based affinity screening of aptamer clones. Anal Chim Acta 2008; 631:102-7. [PMID: 19046686 DOI: 10.1016/j.aca.2008.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 10/02/2008] [Accepted: 10/07/2008] [Indexed: 02/07/2023]
Abstract
DNA aptamers are single stranded DNA (ssDNA) molecules artificially selected from random-sequence DNA libraries for their specific binding to a certain target. DNA aptamers have a number of advantages over antibodies and promise to replace them in both diagnostic and therapeutic applications. The development of DNA aptamers involves three major stages: library enrichment, obtaining individual DNA clones, and the affinity screening of the clones. The purpose of the screening is to obtain the nucleotide sequences of aptamers and the binding parameters of their interaction with the target. Highly efficient approaches have been recently developed for the first two stages, while the third stage remained the rate-limiting one. Here, we introduce a new method for affinity screening of individual DNA aptamer clones. The proposed method amalgamates: (i) aptamer amplification by asymmetric PCR (PCR with a primer ratio different from unity), (ii) analysis of aptamer-target interaction, combining in-capillary mixing of reactants by transverse diffusion of laminar flow profiles (TDLFP) and affinity analysis using kinetic capillary electrophoresis (KCE), and (iii) sequencing of only aptamers with satisfying binding parameters. For the first time we showed that aptamer clones can be directly used in TDLFP/KCE-based affinity analysis without an additional purification step after asymmetric PCR amplification. We also demonstrated that mathematical modeling of TDLFP-based mixing allows for the determination of K(d) values for the in-capillary reaction of an aptamer and a target and that the obtained K(d) values can be used for the accurate affinity ranking of aptamers. The proposed method does not require the knowledge of aptamer sequences before screening, avoids lengthy (3-5 h) purification steps of aptamer clones, and minimizes reagent consumption to nanoliters.
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Affiliation(s)
- Diana Yunusov
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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41
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Lee MS, Olson MA. Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model. J Phys Chem B 2008; 112:13411-7. [PMID: 18821791 DOI: 10.1021/jp802460p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A comparative analysis is provided of the effect of different solvent models on the calculation of a potential of mean force (PMF) for determining the absolute binding affinity of the small molecule inhibitor pteroic acid bound to ricin toxin A-chain (RTA). Solvent models include the distance-dependent dielectric constant, several different generalized Born (GB) approximations, and a hybrid explicit/GB-based implicit solvent model. We found that the simpler approximation of dielectric screening and a GB model, with Born radii fitted to a switching-window dielectric-boundary surface Poisson solvent model, severely overpredicted the binding affinity as compared to the experimental value, estimated to range from -4.4 to -6.0 kcal/mol. In contrast, GB models that are parametrized to fit the Lee-Richards molecular surface performed much better, predicting binding free energy within 1-3 kcal/mol of experimental estimates. However, the predicted free-energy profiles of these GB models displayed alternative binding modes not observed in the crystal structure. Finally, the most rigorous and computationally costly approach in this work, which used a hybrid explicit/implicit solvent model, correctly determined a binding funnel in the PMF near the crystallographic bound state and predicted an absolute binding affinity that was 2 kcal/mol more favorable than the estimated experimental binding affinity.
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Affiliation(s)
- Michael S Lee
- Computational Sciences and Engineering Branch, U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA.
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42
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Warsinke A. Electrochemical biochips for protein analysis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 109:155-93. [PMID: 17928973 DOI: 10.1007/10_2007_079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Proteins bear important functions for most life processes. It is estimated that the human proteome comprises more than 250,000 proteins. Over the last years, highly sophisticated and powerful instruments have been developed that allow their detection and characterization with great precision and sensitivity. However, these instruments need well-equipped laboratories and a well-trained staff. For the determination of proteins in a hospital, in a doctor's office, or at home, low-budget protein analysis methods are needed that are easy to perform. In addition, for a proteomic approach, highly parallel measurements with small sample sizes are required. Biochips are considered as promising tools for such applications. The following chapter describes electrochemical biochips for protein analysis that use antibodies or aptamers as recognition elements.
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Affiliation(s)
- Axel Warsinke
- University of Potsdam, Institute of Biochemistry and Biology, iPOC Research Group, Karl-Liebknecht-Strasse 24-25, D-14476 Golm, Germany.
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Boese BJ, Breaker RR. In vitro selection and characterization of cellulose-binding DNA aptamers. Nucleic Acids Res 2007; 35:6378-88. [PMID: 17881365 PMCID: PMC2095800 DOI: 10.1093/nar/gkm708] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 08/24/2007] [Accepted: 08/24/2007] [Indexed: 01/09/2023] Open
Abstract
Many nucleic acid enzymes and aptamers have modular architectures that allow them to retain their functions when combined with other nucleotide sequences. This modular function facilitates the engineering of RNAs and DNAs that have more complex functions. We sought to create new DNA aptamers that bind cellulose to provide a module for immobilizing DNAs. Cellulose has been used in a variety of applications ranging from coatings and films to pharmaceutical preparations, and therefore DNA aptamers that bind cellulose might enable new applications. We used in vitro selection to isolate aptamers from a pool of random-sequence DNAs and subjected two distinct clones to additional rounds of mutagenesis and selection. One aptamer (CELAPT 14) was chosen for sequence minimization and more detailed biochemical analysis. CELAPT 14 aptamer variants exhibit robust binding both to cellulose powder and paper. Also, an allosteric aptamer construct was engineered that exhibits ATP-mediated cellulose binding during paper chromatography.
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Affiliation(s)
- Benjamin J. Boese
- Department of Chemical Engineering, Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
| | - Ronald R. Breaker
- Department of Chemical Engineering, Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8103, USA
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Famulok M, Hartig JS, Mayer G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 2007; 107:3715-43. [PMID: 17715981 DOI: 10.1021/cr0306743] [Citation(s) in RCA: 666] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael Famulok
- LIMES Institute, Program Unit Chemical Biology and Medicinal Chemistry, c/o Kekulé-Institut für Organische Chemie und Biochemie, Gerhard Domagk-Strasse 1, 53121 Bonn, Germany.
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Nitsche A, Kurth A, Dunkhorst A, Pänke O, Sielaff H, Junge W, Muth D, Scheller F, Stöcklein W, Dahmen C, Pauli G, Kage A. One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX. BMC Biotechnol 2007; 7:48. [PMID: 17697378 PMCID: PMC1994675 DOI: 10.1186/1472-6750-7-48] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 08/15/2007] [Indexed: 11/15/2022] Open
Abstract
Background As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX) to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Results The selection against complete Vaccinia virus particles resulted in a 64-base DNA aptamer specifically binding to orthopoxviruses as validated by dot blot analysis, Surface Plasmon Resonance, Fluorescence Correlation Spectroscopy and real-time PCR, following an aptamer blotting assay. The same oligonucleotide showed the ability to inhibit in vitro infection of Vaccinia virus and other orthopoxviruses in a concentration-dependent manner. Conclusion The MonoLEX method is a straightforward procedure as demonstrated here for the identification of a high-affinity DNA aptamer binding Vaccinia virus. MonoLEX comprises a single affinity chromatography step, followed by subsequent physical segmentation of the affinity resin and a single final PCR amplification step of bound aptamers. Therefore, this procedure improves the selection of high affinity aptamers by reducing the competition between aptamers of different affinities during the PCR step, indicating an advantage for the single-round MonoLEX method.
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Affiliation(s)
- Andreas Nitsche
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Andreas Kurth
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Anna Dunkhorst
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Oliver Pänke
- Department of Biology/Chemistry, Division of Biophysics, University of Osnabrueck, 49069 Osnabrueck, Germany
- Biosystems Technology, University of Applied Sciences Wildau, Bahnhofstr. 1, 15747 Wildau, Germany
| | - Hendrik Sielaff
- Department of Biology/Chemistry, Division of Biophysics, University of Osnabrueck, 49069 Osnabrueck, Germany
| | - Wolfgang Junge
- Department of Biology/Chemistry, Division of Biophysics, University of Osnabrueck, 49069 Osnabrueck, Germany
| | - Doreen Muth
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Frieder Scheller
- Institute of Biochemistry and Biology, Department of Analytical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Golm, Germany
| | - Walter Stöcklein
- Institute of Biochemistry and Biology, Department of Analytical Biochemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Golm, Germany
| | - Claudia Dahmen
- AptaRes AG, Im Biotechnologiepark TGZ I, 14943 Luckenwalde, Germany
| | - Georg Pauli
- Centre for Biological Safety 1, Robert Koch-Institut, Nordufer 20, 13353 Berlin, Germany
| | - Andreas Kage
- Institute of Laboratory Medicine and Pathobiochemistry, Charité Universitätsmedizin Berlin, Westend Haus 31, Spandauer Damm 130, 14050 Berlin, Germany
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Stoltenburg R, Reinemann C, Strehlitz B. SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. ACTA ACUST UNITED AC 2007; 24:381-403. [PMID: 17627883 DOI: 10.1016/j.bioeng.2007.06.001] [Citation(s) in RCA: 934] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 02/07/2023]
Abstract
SELEX stands for systematic evolution of ligands by exponential enrichment. This method, described primarily in 1990 [Ellington, A.D., Szostak, J.W., 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822; Tuerk, C., Gold, L., 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510] aims at the development of aptamers, which are oligonucleotides (RNA or ssDNA) binding to their target with high selectivity and sensitivity because of their three-dimensional shape. Aptamers are all new ligands with a high affinity for considerably differing molecules ranging from large targets as proteins over peptides, complex molecules to drugs and organic small molecules or even metal ions. Aptamers are widely used, including medical and pharmaceutical basic research, drug development, diagnosis, and therapy. Analytical and separation tools bearing aptamers as molecular recognition and binding elements are another big field of application. Moreover, aptamers are used for the investigation of binding phenomena in proteomics. The SELEX method was modified over the years in different ways to become more efficient and less time consuming, to reach higher affinities of the aptamers selected and for automation of the process. This review is focused on the development of aptamers by use of SELEX and gives an overview about technologies, advantages, limitations, and applications of aptamers.
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Affiliation(s)
- Regina Stoltenburg
- UFZ, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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Fischer NO, Tarasow TM, Tok JBH. Aptasensors for biosecurity applications. Curr Opin Chem Biol 2007; 11:316-28. [PMID: 17548236 DOI: 10.1016/j.cbpa.2007.05.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
Nucleic acid (aptasensors) have found steadily increased utility and application over the past decade. In particular, aptamers have been touted as a valuable complement to and, in some cases, replacement for antibodies owing to their structural and functional robustness as well as their ease in generation and synthesis. They are thus attractive for biosecurity applications (e.g. pathogen detection) and are especially well suited because their in vitro generation process does not require infection of any host systems. Herein we provide a brief overview of the aptamers generated against pathogens and toxins over the past few years. In addition, a few recently described detection platforms using aptamers and potentially suitable applications for biosecurity will be discussed.
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Affiliation(s)
- Nicholas O Fischer
- BioSecurity and NanoSciences Laboratory, Chemistry, Materials & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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48
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Haes AJ, Giordano BC, Collins GE. Aptamer-based detection and quantitative analysis of ricin using affinity probe capillary electrophoresis. Anal Chem 2007; 78:3758-64. [PMID: 16737234 DOI: 10.1021/ac060021x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to detect sub-nanomolar concentrations of ricin using fluorescently tagged RNA aptamers is demonstrated. Aptamers rival the specificity of antibodies and have the power to simplify immunoassays using capillary electrophoresis. Under nonequilibrium conditions, a dissociation constant, Kd, of 134 nM has been monitored between the RNA aptamer and ricin A-chain. With use of this free-solution assay, the detection of 500 pM (approximately 14 ng/mL) or 7.1 amol of ricin is demonstrated. The presence of interfering proteins such as bovine serum albumin and casein do not inhibit this interaction at sub-nanomolar concentrations. When spiked with RNAse A, ricin can still be detected down to 1 nM concentrations despite severe aptamer degradation. This approach offers a promising method for the rapid, selective, and sensitive detection of biowarfare agents.
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Affiliation(s)
- Amanda J Haes
- Naval Research Laboratory, 4555 Overlook Avenue, SW, Chemistry Division, Code 6112, Washington, DC 20375-5342, USA
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Abstract
Kinetic capillary electrophoresis (KCE) is defined as capillary electrophoresis of species that interact during electrophoresis. KCE can serve as a conceptual platform for development of homogeneous kinetic affinity methods for affinity measurements (measurements of binding parameters and quantitative measurements) and affinity purification (purification of known molecules and search of unknown molecules). A number of different KCE methods can be designed by varying initial and boundary conditions - the way interacting species enter and exit the capillary. KCE methods will find multiple practical applications in the designing of biomedical diagnostics and the development of drug candidates. Here, the concept of KCE, its up-to-date applications, and future prospective are reviewed.
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Affiliation(s)
- Sergey N Krylov
- Department of Chemistry, York University, Toronto, Ontario, Canada.
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50
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Gopinath SCB. Methods developed for SELEX. Anal Bioanal Chem 2006; 387:171-82. [PMID: 17072603 DOI: 10.1007/s00216-006-0826-2] [Citation(s) in RCA: 245] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2006] [Revised: 08/29/2006] [Accepted: 09/01/2006] [Indexed: 02/07/2023]
Abstract
SELEX (systematic evolution of ligands by exponential enrichment) is a process that involves the progressive purification from a combinatorial library of nucleic acid ligands with a high affinity for a particular target by repeated rounds of partitioning and amplification. With the development of aptamer technology over the last decade, various modified SELEX processes have arisen that allow various aptamers to be developed against a wide variety of molecules, irrespective of the target size. In the present review, the separation methods used in such SELEX processes are reviewed.
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Affiliation(s)
- Subash Chandra Bose Gopinath
- Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
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