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Chen J, Xu D, Huang Q, Wang S, Li F, Wu S, Wang W, Zhou N. A novel dual-recognition fluorescent biosensor for sialyl-Lewis x sensitive detection. Mikrochim Acta 2024; 191:479. [PMID: 39042166 DOI: 10.1007/s00604-024-06555-2] [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: 02/21/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024]
Abstract
Sialyl-Lewisx (SLex) is a tetrasugar, which plays an important role in initial inflammation and cancer cell metastasis, and can be used as a marker for cancer diagnosis and prognosis or a therapeutic target. Detecting SLex from complex biological media remains a significant challenge. Herein, a single-stranded DNA aptamer of SLex was screened based on the double-stranded DNA library-modified magnetic bead (MB)-SELEX technology. After 14 rounds of screening, 12,639 sequences were obtained and divided into nine families. Three representative sequences were selected based on the number of sequence repeats and Gibbs binding free energy, and the aptamer SLex-Apt2 with 80 nt length (Kd = 23.01 nM) had the best affinity and relatively high specificity for targeting SLex. Then, a novel dual-recognition fluorescent biosensor for SLex-sensitive detection based on aptamer SLex-Apt2 bio-dots and 3-aminobenzoboric acid-modified MB was developed. This method can detect SLex as low as 32 μM and has a good linear response in the range 100 μM to 2 mM. It has the advantages of low preparation cost, good targeting, and avoiding the occurrence of false-positive and false-negative detection results, which makes the biosensor more valuable in biological detection and clinical diagnosis.
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Affiliation(s)
- Jinri Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China.
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Jiangsu Key Laboratory of Marine Biotechnology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China.
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Dong Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
| | - Fuhou Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
| | - Shaojie Wu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
| | - Weixia Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Jiangsu Key Laboratory of Marine Biotechnology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, 59 Cangwu Road, Haizhou, 222005, Lianyungang, China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Panda PK, Saraf S, Tiwari A, Verma A, Raikwar S, Jain A, Jain SK. Novel Strategies for Targeting Prostate Cancer. Curr Drug Deliv 2020; 16:712-727. [PMID: 31433757 DOI: 10.2174/1567201816666190821143805] [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: 01/28/2019] [Revised: 04/24/2019] [Accepted: 08/06/2019] [Indexed: 12/15/2022]
Abstract
Prostate cancer (PCa) is a worldwide issue, with a rapid increase in its occurrence and mortality. Over the years, various strategies have been implemented to overcome the hurdles that exist in the treatment of PCa. Consistently, there is a change in opinion about the methodologies in clinical trial that have engrossed towards the treatment of PCa. Currently, there is a need to resolve these newly recognized challenges by developing newer rational targeting systems. The ongoing clinical protocol for the therapy using different targeting systems is undertaken followed by local targeting to cancer site. A number of new drug targeting systems like liposomes, nanoemulsions, magnetic nanoparticles (MNPs), solid lipid nanoparticles, drug-peptide conjugate systems, drug-antibody conjugate systems, epigenetic and gene therapy approaches, and therapeutic aptamers are being developed to suit this protocol. Recent advancements in the treatment of PCa with various nanocarriers have been reported with respect to newly identified biological barriers and intended to solve the contexts. This review encompasses the input of nanotechnology in particular targeting of PCa which might escape the lifethreatening side effects and potentially contribute to bring fruitful clinical outcomes.
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Affiliation(s)
- Pritish Kumar Panda
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Shivani Saraf
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Ankita Tiwari
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Amit Verma
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Sarjana Raikwar
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
| | - Ankit Jain
- Institute of Pharmaceutical Research, GLA University, NH-2, Mathura-Delhi Road, Mathura (U.P.), 281 406, India
| | - Sanjay K Jain
- Pharmaceutics Research Projects Laboratory, Department of Pharmaceutical Sciences, Dr. Hari Singh Gour Central University, Sagar (M.P.), 470 003, India
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Wu HB, Wang ZW, Shi F, Ren ZL, Li LC, Hu XP, Hu R, Li BW. Av β3 Single-Stranded DNA Aptamer Attenuates Vascular Smooth Muscle Cell Proliferation and Migration via Ras-PI3K/MAPK Pathway. Cardiovasc Ther 2020; 2020:6869856. [PMID: 32042311 PMCID: PMC6995496 DOI: 10.1155/2020/6869856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/15/2019] [Accepted: 11/05/2019] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES To observe the effect of avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. BACKGROUND Percutaneous transluminal coronary angioplasty (PTCA) is currently the preferred method for the treatment of coronary heart disease. However, vascular restenosis still occurs after PTCA treatment, severely affecting the clinical efficacy of PTCA. Integrin avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. METHODS In this experiment, we used systematic evolution of ligands by exponential enrichment (SELEX) to screen out avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. RESULTS In the present study, we found that avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. P < 0.05). Avβ3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism. P < 0.05). AvP < 0.05). Av. CONCLUSIONS The findings suggest that avβ3 ssDNA inhibited the proliferation and migration of VSMCs by suppressing the activation of Ras-PI3K/MAPK signaling.β3 single-stranded (ss) DNA on proliferation and migration of vascular smooth muscle cells (VSMCs) and its potential mechanism.
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MESH Headings
- Animals
- Apoptosis
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Cell Movement
- Cell Proliferation
- Cells, Cultured
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Focal Adhesion Kinase 1/genetics
- Focal Adhesion Kinase 1/metabolism
- Gene Expression Regulation
- Integrin alphaVbeta3/genetics
- Integrin alphaVbeta3/metabolism
- Mitogen-Activated Protein Kinases/genetics
- Mitogen-Activated Protein Kinases/metabolism
- Muscle, Smooth, Vascular/enzymology
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/enzymology
- Myocytes, Smooth Muscle/pathology
- Osteopontin/genetics
- Osteopontin/metabolism
- Phosphatidylinositol 3-Kinases/genetics
- Phosphatidylinositol 3-Kinases/metabolism
- Phosphorylation
- Rats, Sprague-Dawley
- Signal Transduction
- ras Proteins/genetics
- ras Proteins/metabolism
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Affiliation(s)
- Hong-Bing Wu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhi-Wei Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Feng Shi
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zong-Li Ren
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Luo-Cheng Li
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiao-Ping Hu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Rui Hu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bo-Wen Li
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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Kang L, Rosenkrans ZT, Cai W. 64Cu-Labeled Aptamers for Tumor-Targeted Radionuclide Delivery. Methods Mol Biol 2019; 1974:223-231. [PMID: 31099007 DOI: 10.1007/978-1-4939-9220-1_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamers are a class of oligonucleotides with high binding affinity and specificity with their targets. Additionally, aptamers are nontoxic, very thermally stable, and able to reversibly undergo denaturation and have a small size. Cancer-related aptamers can be used for tumor-targeted drug delivery, such as to deliver diagnostic and therapeutic radionuclides to target cancers. We describe the process for preparing a 64Cu-labeled modified A10 aptamer to target prostate cancer by conjugating and radiolabeling. The modified A10 aptamer was conjugated with p-SCN-Bn-NOTA as the chelator. Following this, the aptamer can be radiolabeled with the 64Cu radioisotope. NOTA was selected as the chelator of choice due to its commercial availability and widely demonstrated in vivo stability with the 64Cu radioisotope. Using this system, prostate cancer could potentially be targeted for noninvasive imaging using positron emission tomography (PET). Closely following this protocol allows many aptamers to be successfully radiolabeled to accurately and quantitatively trace their distribution in vivo for a wide range of medical applications.
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Affiliation(s)
- Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing, China.
| | - Zachary T Rosenkrans
- Department of Radiology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA
| | - Weibo Cai
- Department of Radiology, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, USA.
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Guo X, Ye T, Liu L, Hu X. Preparation and characterization of an aptamer-functionalized solid-phase microextraction fiber and its application in the selective monitoring of adenosine phosphates with liquid chromatography and tandem mass spectrometry. J Sep Sci 2018; 39:1533-41. [PMID: 27106768 DOI: 10.1002/jssc.201501264] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 11/08/2022]
Abstract
An aptamer with adenosine triphosphate as a ligand was immobilized onto the surface of a porous-polymer-coated fiber to obtain an aptamer-functionalized porous-polymer-coated solid-phase microextraction fiber. The fiber was observed with a crosslinked and porous morphological surface structure. It shows specific selectivity to adenosine triphosphate with a selectivity coefficient of 22.1 compared to the scrambled oligonucleotide functionalized fiber, and the selectivity factors over other analogues and reference compounds were from 6.1 to 77.5. When the fiber-based solid-phase microextraction was coupled with liquid chromatography and tandem mass spectrometry, detection limits of 2.7, 29, and 34 μg/L were achieved for adenosine triphosphate, adenosine diphosphate, and adenosine monophosphate, respectively. The spiking recoveries of 77.6-91.9% were achieved for trace adenosine phosphates in human serum sample. Furthermore, the fibers showed high stability and good reusability and could be used over 50 times for the real serum sample pretreatment without remarkable performance reduction.
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Affiliation(s)
- Xuan Guo
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
| | - Tingting Ye
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
| | - Luying Liu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
| | - Xiaogang Hu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry and Environment, South China Normal University, Guangzhou, P.R. China
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Díaz-Fernández A, Miranda-Castro R, de-Los-Santos-Álvarez N, Lobo-Castañón MJ. Post-translational modifications in tumor biomarkers: the next challenge for aptamers? Anal Bioanal Chem 2018; 410:2059-2065. [PMID: 29353432 DOI: 10.1007/s00216-018-0861-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/05/2017] [Accepted: 01/04/2018] [Indexed: 01/11/2023]
Abstract
Advances in proteomics have fueled the search for novel cancer biomarkers with higher selectivity. Differential expression of low abundant proteins has been the usual way of finding those biomarkers. The existence of a selective receptor for each biomarker is compulsory for their use in diagnostic/prognostic assays. Antibodies are the receptors of choice in most cases although aptamers are becoming familiar because of their facile and reproducible synthesis, chemical stability as well as comparable affinity and selectivity. In recent years, it has been reported that the pattern of post-translational modifications, altered under neoplastic disease, is a better predictive biomarker than the total protein level. Among others, abnormal glycosylation is attracting great attention. Lectins and antibodies are being used for identification and detection of the carbohydrate moiety with low level of discrimination among various glycoproteins. Such level of selectivity is critical to bring next-generation biomarkers to the clinic. Aptamers that can be rationally tailored for a certain molecule domain can become the golden receptor to specifically detect aberrant glycosylation at each protein or even at each glycosylation site, providing new diagnostic tools for early detection of cancer. Graphical abstract Aptamers may specifically differentiate normal from aberrant glycoproteins.
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Affiliation(s)
- Ana Díaz-Fernández
- Dpto. Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - Rebeca Miranda-Castro
- Dpto. Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
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Carlson GE, Martin EW, Shirure VS, Malgor R, Resto VA, Goetz DJ, Burdick MM. Dynamic biochemical tissue analysis detects functional L-selectin ligands on colon cancer tissues. PLoS One 2017; 12:e0173747. [PMID: 28282455 PMCID: PMC5345883 DOI: 10.1371/journal.pone.0173747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/24/2017] [Indexed: 12/31/2022] Open
Abstract
A growing body of evidence suggests that L-selectin ligands presented on circulating tumor cells facilitate metastasis by binding L-selectin presented on leukocytes. Commonly used methods for detecting L-selectin ligands on tissues, e.g., immunostaining, are performed under static, no-flow conditions. However, such analysis does not assay for functional L-selectin ligands, specifically those ligands that promote adhesion under shear flow conditions. Recently our lab developed a method, termed dynamic biochemical tissue analysis (DBTA), to detect functional selectin ligands in situ by probing tissues with L-selectin-coated microspheres under hemodynamic flow conditions. In this investigation, DBTA was used to probe human colon tissues for L-selectin ligand activity. The detection of L-selectin ligands using DBTA was highly specific. Furthermore, DBTA reproducibly detected functional L-selectin ligands on diseased, e.g., cancerous or inflamed, tissues but not on noncancerous tissues. In addition, DBTA revealed a heterogeneous distribution of functional L-selectin ligands on colon cancer tissues. Most notably, detection of L-selectin ligands by immunostaining using HECA-452 antibody only partially correlated with functional L-selectin ligands detected by DBTA. In summation, the results of this study demonstrate that DBTA detects functional selectin ligands to provide a unique characterization of pathological tissue.
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Affiliation(s)
- Grady E. Carlson
- Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
- Biomedical Engineering Program, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
| | - Eric W. Martin
- Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
- Biomedical Engineering Program, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
| | - Venktesh S. Shirure
- Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
| | - Ramiro Malgor
- Biomedical Engineering Program, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
- Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, United States of America
| | - Vicente A. Resto
- Department of Otolaryngology, University of Texas-Medical Branch, Galveston, Texas, United States of America
| | - Douglas J. Goetz
- Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
- Biomedical Engineering Program, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
| | - Monica M. Burdick
- Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
- Biomedical Engineering Program, Russ College of Engineering and Technology, Ohio University, Athens, Ohio, United States of America
- Edison Biotechnology Institute, Ohio University, Athens, Ohio, United States of America
- * E-mail:
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Abstract
Aptamers are single strand DNA or RNA molecules, selected by an iterative process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Due to various advantages of aptamers such as high temperature stability, animal free, cost effective production and its high affinity and selectivity for its target make them attractive alternatives to monoclonal antibody for use in diagnostic and therapeutic purposes. Aptamer has been generated against vesicular endothelial growth factor 165 involved in age related macular degeneracy. Macugen was the first FDA approved aptamer based drug that was commercialized. Later other aptamers were also developed against blood clotting proteins, cancer proteins, antibody E, agents involved in diabetes nephropathy, autoantibodies involved in autoimmune disorders, etc. Aptamers have also been developed against viruses and could work with other antiviral agents in treating infections.
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Affiliation(s)
- Abhishek Parashar
- Research Scholar, Animal Biochemistry Division, National Dairy Research Institute , Karnal, India
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9
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Cui HF, Li YJ, Wang J, Li XJ, Wang QL, Bai YF. Selection, identification, and characterization of aptamers for pro-gastrin-releasing peptide (31–98), a tumor marker for small cell lung cancer. RSC Adv 2016. [DOI: 10.1039/c5ra24703a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pro-gastrin-releasing peptide (31–98) (ProGRP31–98) is a highly reliable, sensitive, and specific tumor marker for small cell lung cancer (SCLC).
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Affiliation(s)
- Hui-Fang Cui
- Department of Bioengineering
- School of Life Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Ya-Jun Li
- Department of Bioengineering
- School of Life Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Jia Wang
- Department of Bioengineering
- School of Life Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Xiao-Jia Li
- Department of Bioengineering
- School of Life Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Qiong-Lin Wang
- Department of Bioengineering
- School of Life Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
| | - Yan-Feng Bai
- Department of Bioengineering
- School of Life Sciences
- Zhengzhou University
- Zhengzhou
- P. R. China
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10
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Ma H, Liu J, Ali MM, Mahmood MAI, Labanieh L, Lu M, Iqbal SM, Zhang Q, Zhao W, Wan Y. Nucleic acid aptamers in cancer research, diagnosis and therapy. Chem Soc Rev 2015; 44:1240-56. [PMID: 25561050 DOI: 10.1039/c4cs00357h] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligomers, identified from a random sequence pool, with the ability to form unique and versatile tertiary structures that bind to cognate molecules with superior specificity. Their small size, excellent chemical stability and low immunogenicity enable them to rival antibodies in cancer imaging and therapy applications. Their facile chemical synthesis, versatility in structural design and engineering, and the ability for site-specific modifications with functional moieties make aptamers excellent recognition motifs for cancer biomarker discovery and detection. Moreover, aptamers can be selected or engineered to regulate cancer protein functions, as well as to guide anti-cancer drug design or screening. This review summarizes their applications in cancer, including cancer biomarker discovery and detection, cancer imaging, cancer therapy, and anti-cancer drug discovery. Although relevant applications are relatively new, the significant progress achieved has demonstrated that aptamers can be promising players in cancer research.
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Affiliation(s)
- Haitao Ma
- The Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
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11
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Khedri M, Rafatpanah H, Abnous K, Ramezani P, Ramezani M. Cancer immunotherapy via nucleic acid aptamers. Int Immunopharmacol 2015; 29:926-936. [PMID: 26603636 DOI: 10.1016/j.intimp.2015.10.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023]
Abstract
Over the past decade, immune therapy has become a standard treatment for a variety of cancers. Monoclonal antibodies, immune adjuvants and vaccines against oncogenic viruses are now well-established cancer therapies. Immune modulation is a principal element of supportive care for many high-dose chemotherapy regimens. Aptamers are short nucleic acids that bind to defined targets with high affinity and specificity. The first aptamers have been selected around two decades ago by an in vitro process named SELEX (systematic evolution of ligands by exponential enrichment). Since then, numerous aptamers with specificities for a variety of targets from small molecules to proteins or even whole cells have been selected. Targeting immunomodulatory ligands in the progressive tumor lesions of the patients would be prophylactic or therapeutic and may reduce drug-associated toxicities. A new class of inhibitory and agonistic ligands composed of short oligonucleotide (ODN) aptamers was developed recently that exhibited bioactivities comparable or superior to that of antibodies. This paper addressed progress in cancer immunotherapy with nucleic acid aptamers and highlighted recent developments either in immune system targeting or in immunotherapy methods involved aptamers. We discussed aptamer limitations when used as therapeutic agents for cancer treatment and suggested ways to overcome those limitations.
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Affiliation(s)
- Mostafa Khedri
- Department of Immunology, Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafatpanah
- Department of Immunology, Immunology Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Pouria Ramezani
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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12
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Cansiz S, Zhang L, Wu C, Wu Y, Teng IT, Hou W, Wang Y, Wan S, Cai R, Jin C, Liu Q, Tan W. DNA Aptamer Based Nanodrugs: Molecular Engineering for Efficiency. Chem Asian J 2015; 10:2084-94. [PMID: 26177853 DOI: 10.1002/asia.201500434] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 12/21/2022]
Abstract
In the past two decades, the study of cancer therapy has gradually advanced to the "nano" era. Numerous novel nanomaterials armed with unique physical properties have been introduced into biomedical research. At the same time, functional nucleic acid molecules, especially aptamers, have aroused broad attention from the biomedical community. Benefiting from the advancement of molecular engineering strategies, it is now feasible to combine the cancer-specific recognition capability of aptamers with various other special functions of nanomaterials to develop cancer-specific drugs at the nanoscale. Nanodrugs are now offering an unprecedented opportunity to achieve the goal of efficient targeted delivery as well as controlled release. This review highlights some achievements made in multiple aptamer-based nanodrug systems that have emerged in recent years, including studies in the infant stage of "proof-of-concept".
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Affiliation(s)
- Sena Cansiz
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Liqin Zhang
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Cuichen Wu
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Yuan Wu
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - I-Ting Teng
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Weijia Hou
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Yanyue Wang
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Shuo Wan
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Ren Cai
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA
| | - Chen Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China
| | - Weihong Tan
- Departments of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611-7200, USA. .,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, 410082, P.R. China.
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13
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Hou Z, Meyer S, Propson NE, Nie J, Jiang P, Stewart R, Thomson JA. Characterization and target identification of a DNA aptamer that labels pluripotent stem cells. Cell Res 2015; 25:390-3. [PMID: 25591927 PMCID: PMC4349250 DOI: 10.1038/cr.2015.7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Susanne Meyer
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Nicholas E Propson
- 1] Morgridge Institute for Research, Madison, WI, USA [2] Current address: Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jeff Nie
- 1] Morgridge Institute for Research, Madison, WI, USA [2] Current address: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Peng Jiang
- Morgridge Institute for Research, Madison, WI, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, USA
| | - James A Thomson
- 1] Morgridge Institute for Research, Madison, WI, USA [2] Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA [3] Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
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14
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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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15
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Ouellet E, Lagally ET, Cheung KC, Haynes CA. A simple method for eliminating fixed-region interference of aptamer binding during SELEX. Biotechnol Bioeng 2014; 111:2265-79. [PMID: 24895227 DOI: 10.1002/bit.25294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 01/20/2023]
Abstract
Standard libraries for systematic evolution of ligands by exponential enrichment (SELEX) typically utilize flanking regions that facilitate amplification of aptamers recovered from each selection round. Here, we show that these flanking sequences can bias the selection process, due in part to their ability to interfere with the fold or function of aptamers localized within the random region of the library sequence. We then address this problem by investigating the use of complementary oligonucleotides as a means to block aptamer interference by each flanking region. Isothermal titration calorimetry (ITC) studies are combined with fold predictions to both define the various interference mechanisms and assess the ability of added complementary oligonucleotides to ameliorate them. The proposed blocking strategy is thereby refined and then applied to standard library forms of benchmark aptamers against human α-thrombin, streptavidin, and vascular endothelial growth factor (VEGF). In each case, ITC data show that the new method effectively removes fixed-region mediated interference effects so that the natural binding affinity of the benchmark aptamer is completely restored. We further show that the binding affinities of properly functioning aptamers within a selection library are not affected by the blocking protocol, and that the method can be applied to various common library formats comprised of different flanking region sequences. Finally, we present a rapid and inexpensive qPCR-based method for determining the mean binding affinity of retained aptamer pools and use it to show that introduction of the pre-blocking method into the standard SELEX protocol results in retention of high-affinity aptamers that would otherwise be lost during the first round of selection. Significant enrichment of the available pool of high-affinity aptamers is thereby achieved in the first few rounds of selection. By eliminating single-strand (aptamer-like) structures within or involving the fixed regions, the technique is therefore shown to isolate aptamer sequence and function within the desired random region of the library members, and thereby provide a new selection method that is complementary to other available SELEX protocols.
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Affiliation(s)
- Eric Ouellet
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4; Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3; Biomedical Engineering Program, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3
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16
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Bastian AA, Rodríguez-Pulido A, Gruszka A, Gerasimov JY, Herrmann A. Probing the shielding properties of aptameric protective groups. Chem Asian J 2014; 9:2225-31. [PMID: 24957252 DOI: 10.1002/asia.201402327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 11/10/2022]
Abstract
Site-specific derivatization of chemically equivalent functional groups has recently been facilitated by the introduction of high-affinity aptamers as non-covalent protective groups. More specifically, a series of RNA aptamers have proven to be highly efficient in enhancing the regioselectivity of reactions with the aminoglycoside antibiotic neomycin B, which carries several chemically indistinguishable amino and hydroxy groups. Since small-molecule targets tend to exhibit multiple modes of binding with a single aptamer, the impact of secondary binding sites on the regioselectivity should be considered. To address this issue, we investigated a series of well-characterized RNA aptamers that bind neomycin B and propose a mechanism that accounts for the regioselective outcome of these transformations. We further demonstrate that the regioselectivity induced by non-covalent aptamer protective groups is determined by the number of binding sites, their affinity, and the mode of interaction with the guest molecule.
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Affiliation(s)
- Andreas A Bastian
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747 AG Groningen (The Netherlands)
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17
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Perturbation of discrete sites on a single protein domain with RNA aptamers: targeting of different sides of the TATA-binding protein (TBP). Biosci Biotechnol Biochem 2013; 77:1739-46. [PMID: 23924740 DOI: 10.1271/bbb.130296] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Control of interactions among proteins is critical in the treatment of diseases, but the specificity required is not easily incorporated into small molecules. Macromolecules could be more suitable as antagonists in this situation, and RNA aptamers have become particularly promising. Here we describe a novel selection procedure for RNA aptamers against a protein that constitutes a single structural domain, the Drosophila TATA-binding protein (TBP). In addition to the conventional filter partitioning method with free TBP as target, we performed another experiment, in which the TATA-bound form of TBP was targeted. Aptamers generated by both selections were able to bind specifically to TBP, but the two groups showed characteristics which were clearly different in terms of their capability to compete with TATA-DNA, their effects on the TATA-bound form of TBP, and their effects on in vitro transcription. The method used to generate these two groups of aptamers can be used with other targets to direct aptamer specificity to discrete sites on the surface of a protein.
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18
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Radom F, Jurek PM, Mazurek MP, Otlewski J, Jeleń F. Aptamers: molecules of great potential. Biotechnol Adv 2013; 31:1260-74. [PMID: 23632375 DOI: 10.1016/j.biotechadv.2013.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/27/2013] [Accepted: 04/19/2013] [Indexed: 01/08/2023]
Abstract
Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.
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Affiliation(s)
- Filip Radom
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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19
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Hussain AF, Tur MK, Barth S. An aptamer-siRNA chimera silences the eukaryotic elongation factor 2 gene and induces apoptosis in cancers expressing αvβ3 integrin. Nucleic Acid Ther 2013; 23:203-12. [PMID: 23544955 DOI: 10.1089/nat.2012.0408] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Small interfering RNAs (siRNAs) silence gene expression by triggering the sequence-specific degradation of mRNAs, but the targeted delivery of such reagents remains challenging and a significant obstacle to therapeutic applications. One promising approach is the use of RNA aptamers that bind tumor-associated antigens to achieve the delivery of siRNAs to tumor cells displaying specific antigens. Wholly RNA-based constructs are advantageous because they are inexpensive to synthesize and their immunogenicity is low. We therefore joined an aptamer-recognizing alpha V and integrin beta 3 (αvβ3) integrin to a siRNA that targets eukaryotic elongation factor 2 and achieved for the first time the targeted delivery of a siRNA to tumor cells expressing αvβ3 integrin, causing the inhibition of cell proliferation and the induction of apoptosis specifically in tumor cells. The impact of our results on the development of therapeutic aptamer-siRNA constructs is discussed.
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Affiliation(s)
- Ahmad Fawzi Hussain
- Department of Experimental Medicine and Immunotherapy, Institute of Applied Medical Engineering, Helmholtz-Institute for Biomedical Engineering, Aachen, Germany
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20
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Arnaud J, Audfray A, Imberty A. Binding sugars: from natural lectins to synthetic receptors and engineered neolectins. Chem Soc Rev 2013; 42:4798-813. [PMID: 23353569 DOI: 10.1039/c2cs35435g] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The large diversity and complexity of glycan structures together with their crucial role in many biological or pathological processes require the development of new high-throughput techniques for analyses. Lectins are classically used for characterising, imaging or targeting glycoconjugates and, when printed on microarrays, they are very useful tools for profiling glycomes. Development of recombinant lectins gives access to reliable and reproducible material, while engineering of new binding sites on existing scaffolds allows tuning of specificity. From the accumulated knowledge on protein-carbohydrate interactions, it is now possible to use nucleotide and peptide (bio)synthesis for producing new carbohydrate-binding molecules. Such a biomimetic approach can also be addressed by boron chemistry and supra-molecular chemistry for the design of fully artificial glycosensors.
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Affiliation(s)
- Julie Arnaud
- Centre de Recherche sur les Macromolécules Végétales (CERMAV-CNRS), affiliated to Grenoble-Université and ICMG, Grenoble, France
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21
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Cho S, Lee BR, Cho BK, Kim JH, Kim BG. In vitro selection of sialic acid specific RNA aptamer and its application to the rapid sensing of sialic acid modified sugars. Biotechnol Bioeng 2012; 110:905-13. [PMID: 23042406 DOI: 10.1002/bit.24737] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/17/2012] [Accepted: 09/21/2012] [Indexed: 11/07/2022]
Abstract
Sialic acids (SAs) are located on the terminal positions of glycan on a cell surface, which play important role in the spread and metastasis of cancer cells and infection of pathogen. For their detection and diagnosis, the finding of SA specific ligand is an essential prerequisite. Here, RNA aptamer for N-acetylneuraminic acid (Neu5Ac), a representative of SAs, with the high affinity of 1.35 nM and the selectivity was screened by in vitro selection method. The strong binding of the screened aptamer was enough to protect the hydrolysis of Neu5Ac by neuraminidase with the stoichiometry of 1:1 molar ratio. For the rapid detection of SAs, the RNA aptamer was further engineered to the aptazyme sensor by conjugating with a ribozyme following the characterization of selected aptamer by RNase footprinting assay. Without additional desialylation, modification, or/and purification processes, the aptazyme indicated high catalytic activities in the presence of Neu5Ac over 20 µM in several minutes. Also, we observed that the aptazyme sensor shows high sensitivities to Neu5Ac-conjugated sugars as well as Neu5Ac monomer, but not in non-Neu5Ac modified sugars. The aptamer for Neu5Ac can support valuable tools in a wide range of bioanalytical applications as well as biosensors.
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Affiliation(s)
- Suhyung Cho
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, Republic of Korea
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22
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Zhou J, Bobbin ML, Burnett JC, Rossi JJ. Current progress of RNA aptamer-based therapeutics. Front Genet 2012; 3:234. [PMID: 23130020 PMCID: PMC3486975 DOI: 10.3389/fgene.2012.00234] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/15/2012] [Indexed: 01/07/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that specifically recognize and bind tightly to their cognate targets due to their stable three-dimensional structure. Nucleic acid aptamers have been developed for various applications, including diagnostics, molecular imaging, biomarker discovery, target validation, therapeutics, and drug delivery. Due to their high specificity and binding affinity, aptamers directly block or interrupt the functions of target proteins making them promising therapeutic agents for the treatment of human maladies. Additionally, aptamers that bind to cell surface proteins are well suited for the targeted delivery of other therapeutics, such as conjugated small interfering RNAs (siRNA) that induce RNA interference (RNAi). Thus, aptamer-siRNA chimeras may offer dual-functions, in which the aptamer inhibits a receptor function, while the siRNA internalizes into the cell to target a specific mRNA. This review focuses on the current progress and therapeutic potential of RNA aptamers, including the use of cell-internalizing aptamers as cell-type specific delivery vehicles for targeted RNAi. In particular, we discuss emerging aptamer-based therapeutics that provide unique clinical opportunities for the treatment various cancers and neurological diseases.
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Affiliation(s)
- Jiehua Zhou
- Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope Duarte, CA, USA
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23
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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25
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Abstract
Carbohydrate biomarkers play very important roles in a wide range of biological and pathological processes. Compounds that can specifically recognize a carbohydrate biomarker are useful for targeted delivery of imaging agents and for development of new diagnostics. Furthermore, such compounds could also be candidates for the development of therapeutic agents. A tremendous amount of active work on synthetic lectin mimics has been reported in recent years. Amongst all the synthetic lectins, boronic-acid-based lectins (boronolectins) have shown great promise. Along this line, four classes of boronolectins including peptide-, nucleic-acid-, polymer-, and small-molecule-based ones are discussed with a focus on the design principles and recent advances. We hope that by presenting the potentials of this field, this review will stimulate more research in this area.
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26
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Aravind A, Yoshida Y, Maekawa T, Kumar DS. Aptamer-conjugated polymeric nanoparticles for targeted cancer therapy. Drug Deliv Transl Res 2012; 2:418-36. [DOI: 10.1007/s13346-012-0104-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Cibiel A, Dupont DM, Ducongé F. Methods To Identify Aptamers against Cell Surface Biomarkers. Pharmaceuticals (Basel) 2011. [PMCID: PMC4058655 DOI: 10.3390/ph4091216] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aptamers are nucleic acid-based ligands identified through a process of molecular evolution named SELEX (Systematic Evolution of Ligands by Exponential enrichment). During the last 10-15 years, numerous aptamers have been developed specifically against targets present on or associated with the surface of human cells or infectious pathogens such as viruses, bacteria, fungi or parasites. Several of the aptamers have been described as potent probes, rivalling antibodies, for use in flow cytometry or microscopy. Some have also been used as drugs by inhibiting or activating functions of their targets in a manner similar to neutralizing or agonistic antibodies. Additionally, it is straightforward to conjugate aptamers to other agents without losing their affinity and they have successfully been used in vitro and in vivo to deliver drugs, siRNA, nanoparticles or contrast agents to target cells. Hence, aptamers identified against cell surface biomarkers represent a promising class of ligands. This review presents the different strategies of SELEX that have been developed to identify aptamers for cell surface-associated proteins as well as some of the methods that are used to study their binding on living cells.
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Affiliation(s)
- Agnes Cibiel
- CEA, DSV, IBM, Service Hospitalier Frédéric Joliot (SHFJ), 4 place du général Leclerc, 91401 Orsay, France; E-Mail: (A.C.)
- INSERM U1023, 4 place du général Leclerc, 91401 Orsay, France
- Université Paris Sud, 4 place du général Leclerc, 91401 Orsay, France
| | - Daniel Miotto Dupont
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark; E-Mail: (D.M.D.)
| | - Frédéric Ducongé
- CEA, DSV, IBM, Service Hospitalier Frédéric Joliot (SHFJ), 4 place du général Leclerc, 91401 Orsay, France; E-Mail: (A.C.)
- INSERM U1023, 4 place du général Leclerc, 91401 Orsay, France
- Université Paris Sud, 4 place du général Leclerc, 91401 Orsay, France
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-169-867-766; Fax: +33-169-867-786
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Jin S, Cheng Y, Reid S, Li M, Wang B. Carbohydrate recognition by boronolectins, small molecules, and lectins. Med Res Rev 2010; 30:171-257. [PMID: 19291708 PMCID: PMC2829346 DOI: 10.1002/med.20155] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Carbohydrates are known to mediate a large number of biological and pathological events. Small and macromolecules capable of carbohydrate recognition have great potentials as research tools, diagnostics, vectors for targeted delivery of therapeutic and imaging agents, and therapeutic agents. However, this potential is far from being realized. One key issue is the difficulty in the development of "binders" capable of specific recognition of carbohydrates of biological relevance. This review discusses systematically the general approaches that are available in developing carbohydrate sensors and "binders/receptors," and their applications. The focus is on discoveries during the last 5 years.
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Affiliation(s)
- Shan Jin
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Yunfeng Cheng
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Suazette Reid
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Minyong Li
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Binghe Wang
- Department of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-4098, USA
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30
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Affiliation(s)
- Claudia M Dollins
- Department of Surgery and Duke Translational Institute, Duke University Medical Center, Durham, NC 27710, USA
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31
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Lin PH, Yen SL, Lin MS, Chang Y, Louis SR, Higuchi A, Chen WY. Microcalorimetrics studies of the thermodynamics and binding mechanism between L-tyrosinamide and aptamer. J Phys Chem B 2008; 112:6665-73. [PMID: 18457441 DOI: 10.1021/jp8000866] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.
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Affiliation(s)
- Po-Hsun Lin
- Institute of Systems Biology and Bioinformatics, National Central University, Jhong-Li, Taiwan
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Missailidis S, Perkins A. Update: aptamers as novel radiopharmaceuticals: their applications and future prospects in diagnosis and therapy. Cancer Biother Radiopharm 2007; 22:453-68. [PMID: 17803440 DOI: 10.1089/cbr.2007.357] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The production of biomaterials with the capacity to bind tightly and specifically to cell surface receptors of malignant cells can greatly benefit cancer diagnosis and treatment. Whereas antibodies have the ability to specifically recognize some tumor cell makers, their large size and immunogenecity markedly limit their value. The development of nuclease-resistant oligonucleotide agents, termed aptamers, offers an alternative to antibodies as targeting, diagnostic, and delivery agents. Using the systematic evolution of ligands by exponential enrichment (SELEX) methodology or other variations, one can select specific sequences that have appropriate binding affinities and specificities against clinically relevant markers from large libraries of oligonucleotide ligands. Aptamers have been found to bind their targets with high specificity and with dissociation constants in the subnanomolar or picomolar range. However, the possibility for the selected aptamers to be developed as targeting agents for diagnostic imaging or targeted radiotherapy purposes has yet to be realized. Peptide-coupling reactions between amino and carboxylic groups offer the possibility of labeling the aptamers with a number of chelators that, coupled with appropriate radionuclides, would generate novel targeted radiopharmaceuticals for the diagnosis and therapy of disease. The unparalleled combinatorial chemical diversity, small size, and modification ability of aptamers is expected to meet the criteria for robust, generic drug discovery technology and open new horizons for the development of future radiopharmaceuticals.
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Affiliation(s)
- Sotiris Missailidis
- Department of Chemistry, The Open University, Walton Hall, Milton Keynes, UK.
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Mairal T, Ozalp VC, Lozano Sánchez P, Mir M, Katakis I, O'Sullivan CK. Aptamers: molecular tools for analytical applications. Anal Bioanal Chem 2007; 390:989-1007. [PMID: 17581746 DOI: 10.1007/s00216-007-1346-4] [Citation(s) in RCA: 382] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 04/30/2007] [Accepted: 05/07/2007] [Indexed: 01/21/2023]
Abstract
Aptamers are artificial nucleic acid ligands, specifically generated against certain targets, such as amino acids, drugs, proteins or other molecules. In nature they exist as a nucleic acid based genetic regulatory element called a riboswitch. For generation of artificial ligands, they are isolated from combinatorial libraries of synthetic nucleic acid by exponential enrichment, via an in vitro iterative process of adsorption, recovery and reamplification known as systematic evolution of ligands by exponential enrichment (SELEX). Thanks to their unique characteristics and chemical structure, aptamers offer themselves as ideal candidates for use in analytical devices and techniques. Recent progress in the aptamer selection and incorporation of aptamers into molecular beacon structures will ensure the application of aptamers for functional and quantitative proteomics and high-throughput screening for drug discovery, as well as in various analytical applications. The properties of aptamers as well as recent developments in improved, time-efficient methods for their selection and stabilization are outlined. The use of these powerful molecular tools for analysis and the advantages they offer over existing affinity biocomponents are discussed. Finally the evolving use of aptamers in specific analytical applications such as chromatography, ELISA-type assays, biosensors and affinity PCR as well as current avenues of research and future perspectives conclude this review.
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Affiliation(s)
- Teresa Mairal
- Nanobiotechnology and Bioanalysis Group, Department of Chemical Engineering, Universitat Rovira i Virgili, 43007, Tarragona, Spain
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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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Bagalkot V, Farokhzad OC, Langer R, Jon S. An aptamer-doxorubicin physical conjugate as a novel targeted drug-delivery platform. Angew Chem Int Ed Engl 2007; 45:8149-52. [PMID: 17099918 DOI: 10.1002/anie.200602251] [Citation(s) in RCA: 446] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vaishali Bagalkot
- Department of Life Science, Gwangju Institute of Science and Technology, 1 Oryoung-dong, Buk-gu, Gwangju 500712, South Korea
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Bagalkot V, Farokhzad OC, Langer R, Jon S. An Aptamer–Doxorubicin Physical Conjugate as a Novel Targeted Drug-Delivery Platform. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602251] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Win MN, Klein JS, Smolke CD. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nucleic Acids Res 2006; 34:5670-82. [PMID: 17038331 PMCID: PMC1636496 DOI: 10.1093/nar/gkl718] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA aptamers that bind the opium alkaloid codeine were generated using an iterative in vitro selection process. The binding properties of these aptamers, including equilibrium and kinetic rate constants, were determined through a rapid, high-throughput approach using surface plasmon resonance (SPR) analysis to measure real-time binding. The approach involves direct coupling of the target small molecule onto a sensor chip without utilization of a carrier protein. Two highest binding aptamer sequences, FC5 and FC45 with Kd values of 2.50 and 4.00 μM, respectively, were extensively studied. Corresponding mini-aptamers for FC5 and FC45 were subsequently identified through the described direct coupling Biacore assays. These assays were also employed to confirm the proposed secondary structures of the mini-aptamers. Both aptamers exhibit high specificity to codeine over morphine, which differs from codeine by a methyl group. Finally, the direct coupling method was demonstrated to eliminate potential non-specific interactions that may be associated with indirect coupling methods in which protein linkers are commonly employed. Therefore, in addition to presenting the first RNA aptamers to a subclass of benzylisoquinoline alkaloid molecules, this work highlights a method for characterizing small molecule aptamers that is more robust, precise, rapid and high-throughput than other commonly employed techniques.
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Affiliation(s)
| | | | - Christina D. Smolke
- To whom correspondence should be addressed. Tel: +1 626 395 2460; Fax: +1 626 568 8743;
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Abstract
The combination of targeted drug delivery and controlled-release technology may pave the road for more effective yet safer chemotherapeutic options for cancer therapy. Drug-encapsulated polymeric nanoparticle-aptamer bioconjugates represent an emerging technology that can facilitate the delivery of chemotherapeutics to primary and metastatic tumours. Aptamers are short nucleic acid molecules with binding properties and biochemical characteristics that may make them suitable for use as targeting molecules. The goal of this review is to summarise the key components that are required for creating effective cancer targeting nanoparticle-aptamer bioconjugates. The field of controlled release and the structure and properties of aptamers, as well as the criteria for constructing effective conjugates, will be discussed.
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Affiliation(s)
- Omid C Farokhzad
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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Tseng YJ, Yang FY, Au LC. An improved system for regenerative production of combinatorial RNA libraries. Anal Biochem 2006; 349:312-4. [PMID: 16384545 DOI: 10.1016/j.ab.2005.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 11/21/2005] [Accepted: 11/21/2005] [Indexed: 11/17/2022]
Affiliation(s)
- Yu-Ju Tseng
- Graduate Institute of Medical Technology, National Yang-Ming University, Taiwan, ROC
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Abstract
Nucleic acid molecules are designed to interact predominantly with proteins or complementary nucleic acids. Interaction of nucleic acids with carbohydrates, abundant constituents of glycoproteins and glycolipids, are not common in cells. Biomedical applications of nucleic acids targeted against oligosaccharides, which are involved in the function of receptors, immune answer, host interaction with invading infectious agents, and cancer metastasis, are feasible. In vitro selection of nucleic acids interacting with oligoand polysaccharides is a promising strategy to identify potential inhibitors of biochemical recognition processes in which carbohydrates are involved. Several RNA and DNA aptamers directed against carbohydrates have already been isolated and characterized. The results are summarized in this article, and an attempt is made to draw initial conclusions concerning the perspectives of the outlined approach.
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Affiliation(s)
- M Sprinzl
- Laboratorium für Biochemie, Universität Bayreuth, 95440 Bayreuth, Germany.
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Abstract
Numerous nucleic acid ligands, also termed decoys or aptamers, have been developed during the past 15 years that can inhibit the activity of many pathogenic proteins. Two of them, Macugen and E2F decoy, are in phase III clinical trials. Several properties of aptamers make them an attractive class of therapeutic compounds. Their affinity and specificity for a given protein make it possible to isolate a ligand to virtually any target, and adjusting their bioavailability expands their clinical utility. The ability to develop aptamers that retain activity in multiple organisms facilitates preclinical development. Antidote control of aptamer activity enables safe, tightly controlled therapeutics. Aptamers may prove useful in the treatment of a wide variety of human maladies, including infectious diseases, cancer, and cardiovascular disease. We review the observations that facilitated the development of this emerging class of therapeutics, summarize progress to date, and speculate on the eventual utility of such agents in the clinic.
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Affiliation(s)
- Shahid M Nimjee
- University Program of Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Ogawa A, Tomita N, Kikuchi N, Sando S, Aoyama Y. Aptamer selection for the inhibition of cell adhesion with fibronectin as target. Bioorg Med Chem Lett 2005; 14:4001-4. [PMID: 15225715 DOI: 10.1016/j.bmcl.2004.05.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Revised: 05/19/2004] [Accepted: 05/19/2004] [Indexed: 10/26/2022]
Abstract
An affinity column immobilizing a decapeptide H(2)N-RGDSPASSKP-CO(2)H was used to select RGD-binding aptamers from a pool of 86-mer single-strand oligodeoxynucleotides (ODNs) containing a random 40-mer sequence. The enriched library thus obtained was further selected against adsorbed fibronectin and individual aptamers were monocloned in E. coli and sequenced to give a couple of highly homologous ODNs, which indeed inhibited fibronectin-integrin mediated cell adhesion.
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Affiliation(s)
- Atsushi Ogawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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Onai Y, Suzuki JI, Nishiwaki Y, Gotoh R, Berens K, Dixon R, Yoshida M, Ito H, Isobe M. Blockade of cell adhesion by a small molecule selectin antagonist attenuates myocardial ischemia/reperfusion injury. Eur J Pharmacol 2004; 481:217-25. [PMID: 14642789 DOI: 10.1016/j.ejphar.2003.09.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reperfusion injury is related closely to inflammatory reactions such as the activation and accumulation of neutrophils. We investigated the efficacy of a novel small molecule selectin antagonist (bimosiamose) in a rat model of transient left coronary artery occlusion (30 min) and reperfusion (24 h). Treatment with bimosiamose (25 mg/kg, intravenously at reperfusion) showed a significant reduction in infarction area/area at risk of approximately 41% compared to vehicle control (P=0.01) and preserved the left ventricular function. The accumulation of polymorphonuclear neutrophils at the site of area at risk was decreased significantly, accompanied by 78% reduction of the myeloperoxidase activity. Parallel-plate flow chamber analysis revealed that bimosiamose showed a significant inhibition in rolling (62%, P<0.001) and adhesion (38%, P<0.05) of HL-60 cells to activated human umbilical vein endothelial cells compared with vehicle control. This study demonstrates for the first time that bimosiamose, a novel small molecule selectin antagonist, attenuates significantly ischemia/reperfusion injury.
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Affiliation(s)
- Yasuyuki Onai
- Department of Cardiovascular Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan
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Masud MM, Kuwahara M, Ozaki H, Sawai H. Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX. Bioorg Med Chem 2004; 12:1111-20. [PMID: 14980623 DOI: 10.1016/j.bmc.2003.12.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 12/03/2003] [Indexed: 11/26/2022]
Abstract
We produced a novel cationic-charged modified DNA aptamer for sialyllactose that is a ubiquitous component of the cell surface responsible for the infection of several viruses by using the magnetic-particle-based SELEX method. After 13 rounds of selection we selected 22 clones as sialyllactose-binding DNA aptamers composed of several modified thymidines. The DNA aptamers could form a three-way junction structure that likely forms a binding site for siallyllactose. The three-way junction structure contains several modified thymidines bearing a positively-charged amino group at the C5 position, which could enhance the binding ability for silalyllactose which has a negatively-charged carboxyl group. The dissociation constant of the aptamer that showed the strongest sialyllactose-binding ability among the clones of the aptamers was 4.9 microM.
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You KM, Lee SH, Im A, Lee SB. Aptamers as functional nucleic acids:In vitro selection and biotechnological applications. BIOTECHNOL BIOPROC E 2003. [DOI: 10.1007/bf02940259] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
We have assembled references of 700 articles published in 2001 that describe work performed using commercially available optical biosensors. To illustrate the technology's diversity, the citation list is divided into reviews, methods and specific applications, as well as instrument type. We noted marked improvements in the utilization of biosensors and the presentation of kinetic data over previous years. These advances reflect a maturing of the technology, which has become a standard method for characterizing biomolecular interactions.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Ulrich H, Magdesian MH, Alves MJM, Colli W. In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion. J Biol Chem 2002; 277:20756-62. [PMID: 11919187 DOI: 10.1074/jbc.m111859200] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma cruzi causing Chagas' disease needs to invade host cells to complete its life cycle. Macromolecules on host cell surfaces such as laminin, thrombospondin, heparan sulfate, and fibronectin are believed to be important in mediating parasite-host cell adhesions and in the invasion process of the host cell by the parasite. The SELEX technique (systematic evolution of ligands by exponential enrichment) was used to evolve nuclease-resistant RNA ligands (aptamer = to fit) that bind with affinities of 40-400 nm to parasite receptors for the host cell matrix molecules laminin, fibronectin, thrombospondin, and heparan sulfate. After eight consecutive rounds of in vitro selection four classes of RNA aptamers based on structural similarities were isolated and sequenced. All members of each class shared a common sequence motif and competed with the respective host cell matrix molecule that was used for displacement during the selection procedure. RNA pools following seven and eight selection rounds as well as individual aptamers sharing consensus motifs were active in inhibiting invasion of LLC-MK(2) monkey kidney cells by T. cruzi in vitro.
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Affiliation(s)
- Henning Ulrich
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, Caixa Postal 26077, São Paulo 05513-970, Brazil
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Affiliation(s)
- Amy Yan
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
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