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Sun R, Zhou Y, Fang Y, Qin Y, Zheng Y, Jiang L. DNA aptamer-linked sandwich structure enhanced SPRi sensor for rapid, sensitive, and quantitative detection of SARS-CoV-2 spike protein. Anal Bioanal Chem 2024; 416:1667-1677. [PMID: 38342787 DOI: 10.1007/s00216-024-05172-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/13/2024]
Abstract
The harm and impact of the COVID-19 pandemic have highlighted the importance of fast, sensitive, and cost-effective virus detection methods. In this study, we developed a DNA aptamer sensor using nanoparticle-enhanced surface plasmon resonance imaging (SPRi) technology to achieve efficient labeling-free detection of SARS-CoV-2 S protein. We used the same DNA aptamer to modify the surface of the SPRi sensor chip and gold nanoparticles (AuNPs), respectively, for capturing target analytes and amplifying signals, achieving ideal results while greatly reducing costs and simplifying the preparation process. The SPRi sensing method exhibits a good linear relationship (R2 = 0.9926) in the concentration range of 1-20 nM before adding AuNPs to amplify the signal, with a limit of detection (LOD) of 0.32 nM. After amplifying the signal, there is a good linear relationship (R2 = 0.9829) between the concentration range of 25-1000 pM, with a LOD of 5.99 pM. The simulation results also verified the effectiveness of AuNPs in improving SPRi signal response. The SPRi sensor has the advantage of short detection time and can complete the detection within 10 min. In addition, the specificity and repeatability of this method can achieve excellent results. This is the first study to simultaneously capture a viral marker protein and amplify the signal using polyadenylic acid (polyA)-modified DNA aptamers on the SPR platform. This scheme can be used as a fast and inexpensive detection method for diagnosis at the point of care (POC) to combat current and future epidemics caused by the virus.
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Affiliation(s)
- Rengang Sun
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Yadong Zhou
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China.
| | - Yunzhu Fang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Yirui Qin
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Yekai Zheng
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Li Jiang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China.
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Development and classification of RNA aptamers for therapeutic purposes: an updated review with emphasis on cancer. Mol Cell Biochem 2022; 478:1573-1598. [DOI: 10.1007/s11010-022-04614-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
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Gholikhani T, Kumar S, Valizadeh H, Mahdinloo S, Adibkia K, Zakeri-Milani P, Barzegar-Jalali M, Jimenez B. Advances in Aptamers-Based Applications in Breast Cancer: Drug Delivery, Therapeutics, and Diagnostics. Int J Mol Sci 2022; 23:ijms232214475. [PMID: 36430951 PMCID: PMC9695968 DOI: 10.3390/ijms232214475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Aptamers are synthetic single-stranded oligonucleotides (such as RNA and DNA) evolved in vitro using Systematic Evolution of Ligands through Exponential enrichment (SELEX) techniques. Aptamers are evolved to have high affinity and specificity to targets; hence, they have a great potential for use in therapeutics as delivery agents and/or in treatment strategies. Aptamers can be chemically synthesized and modified in a cost-effective manner and are easy to hybridize to a variety of nano-particles and other agents which has paved a way for targeted therapy and diagnostics applications such as in breast tumors. In this review, we systematically explain different aptamer adoption approaches to therapeutic or diagnostic uses when addressing breast tumors. We summarize the current therapeutic techniques to address breast tumors including aptamer-base approaches. We discuss the next aptamer-based therapeutic and diagnostic approaches targeting breast tumors. Finally, we provide a perspective on the future of aptamer-based sensors for breast therapeutics and diagnostics. In this section, the therapeutic applications of aptamers will be discussed for the targeting therapy of breast cancer.
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Affiliation(s)
- Tooba Gholikhani
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
- NanoRa Pharmaceuticals Ltd., Tabriz 5166-15731, Iran
| | - Shalen Kumar
- IQ Science Limited, Wellington 5010, New Zealand
| | - Hadi Valizadeh
- Drug Applied Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Somayeh Mahdinloo
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Khosro Adibkia
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Parvin Zakeri-Milani
- Liver and Gastrointestinal Diseases Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Mohammad Barzegar-Jalali
- Pharmaceutical Analysis Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Balam Jimenez
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Correspondence:
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Shanaa OA, Rumyantsev A, Sambuk E, Padkina M. In Vivo Production of RNA Aptamers and Nanoparticles: Problems and Prospects. Molecules 2021; 26:molecules26051422. [PMID: 33800717 PMCID: PMC7961669 DOI: 10.3390/molecules26051422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/26/2022] Open
Abstract
RNA aptamers are becoming increasingly attractive due to their superior properties. This review discusses the early stages of aptamer research, the main developments in this area, and the latest technologies being developed. The review also highlights the advantages of RNA aptamers in comparison to antibodies, considering the great potential of RNA aptamers and their applications in the near future. In addition, it is shown how RNA aptamers can form endless 3-D structures, giving rise to various structural and functional possibilities. Special attention is paid to the Mango, Spinach and Broccoli fluorescent RNA aptamers, and the advantages of split RNA aptamers are discussed. The review focuses on the importance of creating a platform for the synthesis of RNA nanoparticles in vivo and examines yeast, namely Saccharomyces cerevisiae, as a potential model organism for the production of RNA nanoparticles on a large scale.
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Affiliation(s)
- Ousama Al Shanaa
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Atomic Energy Commission of Syria, Damascus P.O.B 6091, Syria
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
| | - Andrey Rumyantsev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Elena Sambuk
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
| | - Marina Padkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 Saint Petersburg, Russia; (A.R.); (E.S.)
- Correspondence: (O.A.S.); (M.P.); Tel.: +7-812-328-2822 (O.A.S.); +7-812-327-9827 (M.P.)
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5
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Ni S, Zhuo Z, Pan Y, Yu Y, Li F, Liu J, Wang L, Wu X, Li D, Wan Y, Zhang L, Yang Z, Zhang BT, Lu A, Zhang G. Recent Progress in Aptamer Discoveries and Modifications for Therapeutic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9500-9519. [PMID: 32603135 DOI: 10.1021/acsami.0c05750] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are oligonucleotide sequences with a length of about 25-80 bases which have abilities to bind to specific target molecules that rival those of monoclonal antibodies. They are attracting great attention in diverse clinical translations on account of their various advantages, including prolonged storage life, little batch-to-batch differences, very low immunogenicity, and feasibility of chemical modifications for enhancing stability, prolonging the half-life in serum, and targeted delivery. In this Review, we demonstrate the emerging aptamer discovery technologies in developing advanced techniques for producing aptamers with high performance consistently and efficiently as well as requiring less cost and resources but offering a great chance of success. Further, the diverse modifications of aptamers for therapeutic applications including therapeutic agents, aptamer-drug conjugates, and targeted delivery materials are comprehensively summarized.
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Affiliation(s)
- Shuaijian Ni
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanyuan Yu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Fangfei Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Jin Liu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Luyao Wang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Xiaoqiu Wu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Dijie Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Youyang Wan
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Aiping Lu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Ge Zhang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
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Allemailem KS, Almatroudi A, Alsahli MA, Basfar GT, Alrumaihi F, Rahmani AH, Khan AA. Recent advances in understanding oligonucleotide aptamers and their applications as therapeutic agents. 3 Biotech 2020; 10:551. [PMID: 33269185 PMCID: PMC7686427 DOI: 10.1007/s13205-020-02546-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
The innovative discovery of aptamers was based on target-specific treatment in clinical diagnostics and therapeutics. Aptamers are synthetic, single-stranded oligonucleotides, simply described as chemical antibodies, which can bind to diverse targets with high specificity and affinity. Aptamers are synthesized by the SELEX technique, and possess distinctive properties as small size (10-50 kDa), higher stability, easy manufacture and less immunogenicity. These oligonucleotides are easily degraded by nucleases, so require some important modifications like capping and incorporation of modified nucleotides. RNA aptamers can be modified chemically on 2' positions using -NH3, -F, -deoxy, or -OMe groups to enhance their nuclease resistance. Aptamers have been employed for multiple purposes, as direct drugs or aptamer-drug conjugates targeted against different diseased cells. Different aptamer-conjugated nanovehicles (e.g., micelles, liposomes, silica nano-shells) have been designed to transport diverse anticancer-drugs like doxorubicin and cisplatin in bulk to minimize systemic cytotoxicity. Some drug-loaded nanovehicles (up to 97% loading capacity) and conjugated with specific aptamer resulted in more than 60% tumor inhibition as compared to unconjugated drug-loaded nanovehicles which showed only 31% cancer inhibition. In addition, aptamers have been widely used in basic research, food safety, environmental monitoring, clinical diagnostics and therapeutics. Different FDA-approved RNA and DNA aptamers are now available in the market, used for the treatment of diverse diseases, especially cancer. These aptamers include Macugen, Pegaptanib, etc. Despite a good progress in aptamer use, the present-day chemotherapeutics and drug targeting systems still face great challenges. Here in this review article, we are discussing nucleic acid aptamers, preparation, role in the transportation of different nanoparticle vehicles and their applications as therapeutic agents.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohammed A. Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ghaiyda Talal Basfar
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, P.O. Box 6699, Buraydah, 51452 Saudi Arabia
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7
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Pleshakova TO, Kaysheva AL, Shumov ID, Ziborov VS, Bayzyanova JM, Konev VA, Uchaikin VF, Archakov AI, Ivanov YD. Detection of Hepatitis C Virus Core Protein in Serum Using Aptamer-Functionalized AFM Chips. MICROMACHINES 2019; 10:E129. [PMID: 30781415 PMCID: PMC6413090 DOI: 10.3390/mi10020129] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/24/2022]
Abstract
In the present study, we demonstrate atomic force microscopy (AFM)-based detection of hepatitis C virus (HCV) particles in serum samples using a chip with aptamer-functionalized surface (apta-based AFM chip). The target particles, containing core antigen of HCV (HCVcoreAg protein), were biospecifically captured onto the chip surface from 1 mL of test solution containing 10 µL of serum collected from a hepatitis C patient. The registration of aptamer/antigen complexes on the chip surface was performed by AFM. The aptamers used in the present study were initially developed for therapeutic purposes; herein, these aptamers have been successfully utilized as probe molecules for HCVcoreAg detection in the presence of a complex protein matrix (human serum). The results obtained herein can be used for the development of detection systems that employ affine enrichment for protein detection.
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Affiliation(s)
| | | | - Ivan D Shumov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
| | - Vadim S Ziborov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
- Joint Institute for High Temperatures of Russian Academy of Sciences, Moscow 125412, Russia.
| | - Jana M Bayzyanova
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | - Vladimir A Konev
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | - Vasiliy F Uchaikin
- Pirogov Russian National Research Medical University (RNRMU), Moscow 117997, Russia.
| | | | - Yuri D Ivanov
- Institute of Biomedical Chemistry, Moscow 119121, Russia.
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8
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Pleshakova TO, Kaysheva AL, Bayzyanova JМ, Anashkina АS, Uchaikin VF, Ziborov VS, Konev VA, Archakov AI, Ivanov YD. The detection of hepatitis c virus core antigen using afm chips with immobolized aptamers. J Virol Methods 2017; 251:99-105. [PMID: 29042217 DOI: 10.1016/j.jviromet.2017.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/09/2017] [Accepted: 10/14/2017] [Indexed: 10/18/2022]
Abstract
In the present study, the possibility of hepatitis C virus core antigen (HCVcoreAg) detection in buffer solution, using atomic force microscope chip (AFM-chip) with immobilized aptamers, has been demonstrated. The target protein was detected in 1mL of solution at concentrations from 10-10М to 10-13М. The registration of aptamer/antigen complexes on the chip surface was carried out by atomic force microscopy (AFM). The further mass-spectrometric (MS) identification of AFM-registered objects on the chip surface allowed reliable identification of HCVcoreAg target protein in the complexes. Aptamers, which were designed for therapeutic purposes, have been shown to be effective in HCVcoreAg detection as probe molecules.
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Affiliation(s)
- T O Pleshakova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - A L Kaysheva
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia.
| | - J М Bayzyanova
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - А S Anashkina
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - V F Uchaikin
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - V S Ziborov
- Joint Institute for High Temperatures RAS, Izhorskaya St. 13/19, Moscow, 125412, Russia
| | - V A Konev
- Pirogov Russian National Research Medical University (RNRMU), Ostrovitianov str. 1, Moscow, 117997, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
| | - Y D Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya St. 10, Moscow, 119121, Russia
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9
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Kolovskaya OS, Zamay TN, Zamay AS, Glazyrin YE, Spivak EA, Zubkova OA, Kadkina AV, Erkaev EN, Zamay GS, Savitskaya AG, Trufanova LV, Petrova LL, Berezovski MV. DNA-aptamer/protein interaction as a cause of apoptosis and arrest of proliferation in Ehrlich ascites adenocarcinoma cells. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2014. [DOI: 10.1134/s1990747813050061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Zamay TN, Kolovskaya OS, Glazyrin YE, Zamay GS, Kuznetsova SA, Spivak EA, Wehbe M, Savitskaya AG, Zubkova OA, Kadkina A, Wang X, Muharemagic D, Dubynina A, Sheina Y, Salmina AB, Berezovski MV, Zamay AS. DNA-aptamer targeting vimentin for tumor therapy in vivo. Nucleic Acid Ther 2014; 24:160-70. [PMID: 24410722 DOI: 10.1089/nat.2013.0471] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In recent years, new prospects for the use of nucleic acids as anticancer drugs have been discovered. Aptamers for intracellular targets can regulate cellular functions and cause cell death or proliferation. However, intracellular aptamers have limited use for therapeutic applications due to their low bioavailability. In this work, we selected DNA aptamers to cell organelles and nucleus of cancer cells, and showed that an aptamer NAS-24 binds to vimentin and causes apoptosis of mouse ascites adenocarcinoma cells in vitro and in vivo. To deliver the aptamer NAS-24 inside cells, natural polysaccharide arabinogalactan was used as a carrier reagent. The mixture of arabinogalactan and NAS-24 was injected intraperitonealy for 5 days into mice with adenocarcinoma and inhibited adenocarcinoma growth more effectively than free arabinogalactan or the aptamer alone. The use of aptamers to intracellular targets together with arabinogalactan becomes a promising approach for anticancer therapy.
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Affiliation(s)
- Tatyana N Zamay
- 1 Department of Biochemistry, Medical, Pharmaceutical, and Toxicological Chemistry, Krasnoyarsk State Medical University , Krasnoyarsk, Russia
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11
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Kolovskaya OS, Savitskaya AG, Zamay TN, Reshetneva IT, Zamay GS, Erkaev EN, Wang X, Wehbe M, Salmina AB, Perianova OV, Zubkova OA, Spivak EA, Mezko VS, Glazyrin YE, Titova NM, Berezovski MV, Zamay AS. Development of bacteriostatic DNA aptamers for salmonella. J Med Chem 2013; 56:1564-72. [PMID: 23387511 DOI: 10.1021/jm301856j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Salmonella is one of the most dangerous and common food-borne pathogens. The overuse of antibiotics for disease prevention has led to the development of multidrug resistant Salmonella. Now, more than ever, there is a need for new antimicrobial drugs to combat these resistant bacteria. Aptamers have grown in popularity since their discovery, and their properties make them attractive candidates for therapeutic use. In this work, we describe the selection of highly specific DNA aptamers to S. enteritidis and S. typhimurium. To evolve species-specific aptamers, twelve rounds of selection to live S. enteritidis and S. typhimurium were performed, alternating with a negative selection against a mixture of related pathogens. Studies have shown that synthetic pools combined from individual aptamers have the capacity to inhibit growth of S. enteritidis and S. typhimurium in bacterial cultures; this was the result of a decrease in their membrane potential.
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Affiliation(s)
- Olga S Kolovskaya
- Research Institute of Molecular Medicine and Pathobiochemistry, Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka str., Krasnoyarsk 660022, Russia
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12
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Sun N, Funke SA, Willbold D. Mirror image phage display--generating stable therapeutically and diagnostically active peptides with biotechnological means. J Biotechnol 2012; 161:121-5. [PMID: 22728425 DOI: 10.1016/j.jbiotec.2012.05.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/03/2012] [Accepted: 05/08/2012] [Indexed: 11/30/2022]
Abstract
Peptides are attracting increasing attention as therapeutics. D-enantiomeric peptides are remarkably resistant to in vivo proteolysis and elicit low immunogenic responses when compared with the respective L-peptides. Therefore, D-peptides can serve as therapeutic and early diagnosis agents for drug development. Here we discuss the application of mirror image phage display in pharmaceutical biotechnology aiming to identify protease resistant D-peptides with biotechnological approaches.
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Affiliation(s)
- Na Sun
- ICS-6, Forschungszentrum Jülich, 52425 Jülich, Germany
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D'Alonzo D, Guaragna A, Palumbo G. Exploring the role of chirality in nucleic acid recognition. Chem Biodivers 2012; 8:373-413. [PMID: 21404424 DOI: 10.1002/cbdv.201000303] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.
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Affiliation(s)
- Daniele D'Alonzo
- Dipartimento di Chimica Organica e Biochimica, Università di Napoli Federico II, Complesso Universitario Monte Sant'Angelo, via Cinthia, 4, I-80126 Napoli.
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14
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Kang KN, Lee YS. RNA aptamers: a review of recent trends and applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 131:153-69. [PMID: 22491855 DOI: 10.1007/10_2012_136] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA aptamers, small oligonucleotides derived by an in-vitro selection process called SELEX (Systematic Evolution of Ligands by EXperimental enrichment), are important candidates for therapeutic and diagnostic applications. RNA aptamers have high affinity and specificity for their target molecules. In this review, we describe methods for generating RNA aptamers (the SELEX technique and modified SELEX processes) and therapeutic applications for diseases such as neovascular age-related macular degeneration (AMD), inflammatory diseases, and obesity. We also analyze the social networks among researchers and organizations (universities, research institutes, firms, etc.) that are active in the pursuit of aptamer-based therapeutic approaches. This study provides relevant information on recent research trends in RNA aptamers.
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Affiliation(s)
- Kyung-Nam Kang
- Korea Institute of Intellectual Property, KIPS Center, 9th FL. 647-9, Yeoksam-dong, Gangnam-gu, Seoul, 135-980, Korea,
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15
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Abstract
Aptamers are small molecular ligands composed of short oligonucleotides that bind targets with high affinity. In contrast to antibodies, as synthetic oligonucleotides, aptamers have lower production costs and elicit no antigenic reactions. Therefore, aptamers are potential agents for disease diagnosis and treatment. In this study, we validate a fluorescently labeled RNA aptamer, which has been reported to bind specifically to mouse CD30 proteins in solution, for human CD30 protein recognition on intact cells. The aptamer probe was tested with cultured anaplastic large cell lymphoma and Hodgkin's lymphoma cells that express high levels of CD30. Flow cytometry and fluorescence microscopy showed specific and sensitive binding of the aptamer probe to CD30-expressing lymphoma cells at low concentrations (0.3 nM). Studies performed on multiple cell lines and nuclear cells from healthy donors confirmed that the CD30 aptamer and anti-CD30 antibody, the standard clinical probe, recognized the same set of cells. The potential application of multicolor flow cytometry analysis using the CD30 aptamer probe and antibodies was also shown. In conclusion, the developed CD30 aptamer probe could act as a replacement and/or a supplement for antibodies in the diagnosis of the CD30-expressing lymphomas.
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16
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Rahimi F, Murakami K, Summers JL, Chen CHB, Bitan G. RNA aptamers generated against oligomeric Abeta40 recognize common amyloid aptatopes with low specificity but high sensitivity. PLoS One 2009; 4:e7694. [PMID: 19901993 PMCID: PMC2770325 DOI: 10.1371/journal.pone.0007694] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/30/2009] [Indexed: 12/02/2022] Open
Abstract
Aptamers are useful molecular recognition tools in research, diagnostics, and therapy. Despite promising results in other fields, aptamer use has remained scarce in amyloid research, including Alzheimer's disease (AD). AD is a progressive neurodegenerative disease believed to be caused by neurotoxic amyloid β-protein (Aβ) oligomers. Aβ oligomers therefore are an attractive target for development of diagnostic and therapeutic reagents. We used covalently-stabilized oligomers of the 40-residue form of Aβ (Aβ40) for aptamer selection. Despite gradually increasing the stringency of selection conditions, the selected aptamers did not recognize Aβ40 oligomers but reacted with fibrils of Aβ40, Aβ42, and several other amyloidogenic proteins. Aptamer reactivity with amyloid fibrils showed some degree of protein-sequence dependency. Significant fibril binding also was found for the naïve library and could not be eliminated by counter-selection using Aβ40 fibrils, suggesting that aptamer binding to amyloid fibrils was RNA-sequence-independent. Aptamer binding depended on fibrillogenesis and showed a lag phase. Interestingly, aptamers detected fibril formation with ≥15-fold higher sensitivity than thioflavin T (ThT), revealing substantial β-sheet and fibril formation undetected by ThT. The data suggest that under physiologic conditions, aptamers for oligomeric forms of amyloidogenic proteins cannot be selected due to high, non-specific affinity of oligonucleotides for amyloid fibrils. Nevertheless, the high sensitivity, whereby aptamers detect β-sheet formation, suggests that they can serve as superior amyloid recognition tools.
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Affiliation(s)
- Farid Rahimi
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Kazuma Murakami
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jamie L. Summers
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Chi-Hong B. Chen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Brain Research Institute, University of California Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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17
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Funke SA, Willbold D. Mirror image phage display--a method to generate D-peptide ligands for use in diagnostic or therapeutical applications. MOLECULAR BIOSYSTEMS 2009; 5:783-6. [PMID: 19603110 DOI: 10.1039/b904138a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mirror image phage display is a straightforward approach to identify new potentially therapeutically active D-enantiomeric peptides. Such D-peptides are more resistant to proteolytic degradation compared to L-peptides. In this review, several examples of mirror image phage display derived D-peptides with therapeutical potential are introduced and discussed.
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18
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Henry SP, Levin AA, White K, Mennear JH. Assessment of the Effects of ISIS 2302, an Anti-Sense Inhibitor of Human ICAM-1, on Cellular and Humoral Immunity in Mice. J Immunotoxicol 2008; 3:199-211. [DOI: 10.1080/15476910601046538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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19
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Cowperthwaite MC, Ellington AD. Bioinformatic analysis of the contribution of primer sequences to aptamer structures. J Mol Evol 2008; 67:95-102. [PMID: 18594898 DOI: 10.1007/s00239-008-9130-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 05/12/2008] [Accepted: 05/15/2008] [Indexed: 02/07/2023]
Abstract
Aptamers are nucleic acid molecules selected in vitro to bind a particular ligand. While numerous experimental studies have examined the sequences, structures, and functions of individual aptamers, considerably fewer studies have applied bioinformatics approaches to try to infer more general principles from these individual studies. We have used a large Aptamer Database to parse the contributions of both random and constant regions to the secondary structures of more than 2000 aptamers. We find that the constant, primer-binding regions do not, in general, contribute significantly to aptamer structures. These results suggest that (a) binding function is not contributed to nor constrained by constant regions; (b) in consequence, the landscape of functional binding sequences is sparse but robust, favoring scenarios for short, functional nucleic acid sequences near origins; and (c) many pool designs for the selection of aptamers are likely to prove robust.
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Affiliation(s)
- Matthew C Cowperthwaite
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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20
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Sparrow LG, Lawrence MC, Gorman JJ, Strike PM, Robinson CP, McKern NM, Ward CW. N-linked glycans of the human insulin receptor and their distribution over the crystal structure. Proteins 2008; 71:426-39. [DOI: 10.1002/prot.21768] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Bhindi R, Fahmy RG, Lowe HC, Chesterman CN, Dass CR, Cairns MJ, Saravolac EG, Sun LQ, Khachigian LM. Brothers in arms: DNA enzymes, short interfering RNA, and the emerging wave of small-molecule nucleic acid-based gene-silencing strategies. THE AMERICAN JOURNAL OF PATHOLOGY 2007; 171:1079-88. [PMID: 17717148 PMCID: PMC1988859 DOI: 10.2353/ajpath.2007.070120] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The past decade has seen the rapid evolution of small-molecule gene-silencing strategies, driven largely by enhanced understanding of gene function in the pathogenesis of disease. Over this time, many genes have been targeted by specifically engineered agents from different classes of nucleic acid-based drugs in experimental models of disease to probe, dissect, and characterize further the complex processes that underpin molecular signaling. Arising from this, a number of molecules have been examined in the setting of clinical trials, and several have recently made the successful transition from the bench to the clinic, heralding an exciting era of gene-specific treatments. This is particularly important because clear inadequacies in present therapies account for significant morbidity, mortality, and cost. The broad umbrella of gene-silencing therapeutics encompasses a range of agents that include DNA enzymes, short interfering RNA, antisense oligonucleotides, decoys, ribozymes, and aptamers. This review tracks current movements in these technologies, focusing mainly on DNA enzymes and short interfering RNA, because these are poised to play an integral role in antigene therapies in the future.
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MESH Headings
- Animals
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/therapeutic use
- DNA, Catalytic/chemistry
- DNA, Catalytic/metabolism
- DNA, Catalytic/therapeutic use
- Gene Silencing
- Gene Targeting
- Genetic Therapy/methods
- Humans
- Mice
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/therapeutic use
- RNA, Catalytic/chemistry
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/metabolism
- RNA, Small Interfering/therapeutic use
- Rabbits
- Rats
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Affiliation(s)
- Ravinay Bhindi
- Centre for Vascular Research, The University of New South Wales, Sydney, NSW 2052, Australia
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22
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Affiliation(s)
- John J Rossi
- Division of Molecular Biology, Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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23
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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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24
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Du M, Ulrich H, Zhao X, Aronowski J, Jayaraman V. Water soluble RNA based antagonist of AMPA receptors. Neuropharmacology 2007; 53:242-51. [PMID: 17588619 PMCID: PMC2001231 DOI: 10.1016/j.neuropharm.2007.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 04/27/2007] [Accepted: 05/14/2007] [Indexed: 11/18/2022]
Abstract
Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are one of the important receptor classes involved in glutamate-mediated excitotoxicity. Although small molecule antagonists of this receptor have been shown to have neuroprotective properties, their low solubilities pose severe side effects in clinical trials. Here we have used the SELEX method to obtain water-soluble nuclease-resistant RNA ligands that bind to the agonist binding site of AMPA receptors. Using whole-cell current recordings, we have characterized the functional consequences of a representative aptamer from this class and show that it is a competitive antagonist of AMPA receptors and in the concentration range where it acts as an inhibitor of the AMPA receptor the RNA has no effect on the GluR6 homomeric kainate receptors. Additionally, using a fluorescence resonance energy transfer (FRET) probe, we show that this RNA ligand stabilizes the open cleft conformation of the ligand binding domain, consistent with the known structures of small antagonist-bound states of the soluble domain of this protein. Finally, using rat primary cortical neurons, we show that this RNA ligand significantly reduces neurotoxicity associated with oxygen glucose deprivation. The water-soluble and antagonistic properties of this aptamer coupled with its neuroprotective properties make it an excellent candidate for potential use in diseases or pathological conditions involving glutamate-mediated excitotoxicity.
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Affiliation(s)
- Mei Du
- 6431 Fannin, Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030, USA
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25
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Morse DP. Direct selection of RNA beacon aptamers. Biochem Biophys Res Commun 2007; 359:94-101. [PMID: 17533112 PMCID: PMC2030492 DOI: 10.1016/j.bbrc.2007.05.072] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
A method for the direct selection of RNA molecules that can be easily converted into beacon aptamers is presented. Beacon aptamers are fluorescently labeled nucleic acids that signal the presence of a specific ligand through changes in fluorescence intensity. Typically, ligand binding causes an increase in fluorescence intensity by inducing a conformational change that separates a fluorophore/quencher pair. The method presented here simultaneously selects for ligand binding and induction of an appropriate conformational change. The method was tested by selecting RNA molecules that can detect the aminoglycoside antibiotic tobramycin. After 14 rounds of selection, two sequence families emerged. Upon conversion into beacon aptamers, representatives of the two selected sequence families specifically detected tobramycin, while a negative control RNA that did not survive the selection protocol did not function as a tobramycin beacon aptamer.
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Affiliation(s)
- Daniel P Morse
- Department of Chemistry, United States Naval Academy, Annapolis, MD 21402, USA.
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26
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Böldicke T. Blocking translocation of cell surface molecules from the ER to the cell surface by intracellular antibodies targeted to the ER. J Cell Mol Med 2007; 11:54-70. [PMID: 17367501 PMCID: PMC4401220 DOI: 10.1111/j.1582-4934.2007.00002.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Intracellular antibodies (intrabodies) constitute a potent tool to neutralize the function of target proteins inside specific cell compartments (cytosol, nucleus, mitochondria and ER). The intrabody technology is an attractive alternative to the generation of gene-targeted knockout animals and complements or replaces knockdown techniques such as antisense-RNA, RNAi and RNA aptamers. This article focuses on intrabodies targeted to the ER. Intracellular anti-bodies expressed and retained inside the ER (ER intrabodies) are shown to be highly efficient in blocking the translocation of secreted and cell surface molecules from the ER to the cell surface.The advantage of ER intrabodies over cytoplasmic intrabodies is that they are correctly folded and easier to select. A particular advantage of the intrabody technology over existing ones is the possibility of inhibiting selectively post-translational modifications of proteins.The main applications of ER intrabodies so far have been (i) inactivation of oncogenic receptors and (ii) functional inhibition of virus envelope proteins and virus-receptor molecules on the surface of host cells.In cancer research, the number of in vivo mouse models for evaluation of the therapeutic potential of intrabodies is increasing.In the future, endosomal localized receptors involved in bacterial and viral infections, intracellular oncogenic receptors and enzymes involved in glycosylation of tumour antigens might be new targets for ER intrabodies.
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Affiliation(s)
- Thomas Böldicke
- Helmholtz Centre for Infection Research, Department of Gene Regulation and Differentiation,Braunschweig, Germany.
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27
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König J, Julius C, Baumann S, Homann M, Göringer HU, Feldbrügge M. Combining SELEX and the yeast three-hybrid system for in vivo selection and classification of RNA aptamers. RNA (NEW YORK, N.Y.) 2007; 13:614-22. [PMID: 17283213 PMCID: PMC1831868 DOI: 10.1261/rna.334307] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are small nucleic acid ligands that bind to their targets with specificity and high affinity. They are generated by a combinatorial technology, known as SELEX. This in vitro approach uses iterative cycles of enrichment and amplification to select binders from nucleic acid libraries of high complexity. Here we combine SELEX with the yeast three-hybrid system in order to select for RNA aptamers with in vivo binding activity. As a target molecule, we chose the RNA recognition motif-containing RNA-binding protein Rrm4 from the corn pathogen Ustilago maydis. Rrm4 is an ELAV-like protein containing three N-terminal RNA recognition motifs (RRMs). It has been implicated in microtubule-dependent RNA transport during pathogenic development. After 11 SELEX cycles, four aptamer classes were identified. These sequences were further screened for their in vivo binding activity applying the yeast three-hybrid system. Of the initial aptamer classes only members of two classes were capable of binding in vivo. Testing representatives of both classes against Rrm4 variants mutated in one of the three RRM domains revealed that these aptamers interacted with the third RRM. Thus, the yeast three-hybrid system is a useful extension to the SELEX protocol for the identification and characterization of aptamers with in vivo binding activity.
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Affiliation(s)
- Julian König
- Department of Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, Marburg, Germany
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