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Valizadeh Shahbazlou S, Vandghanooni S, Dabirmanesh B, Eskandani M, Hasannia S. Ultrasensitive Quantification of MUC16 Antigen/Amine-Terminated Aptamer Interaction by Surface Plasmon Resonance: Kinetic and Thermodynamic Studies. Adv Pharm Bull 2024; 14:388-399. [PMID: 39206405 PMCID: PMC11347734 DOI: 10.34172/apb.2024.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/13/2023] [Accepted: 01/07/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose MUC16 is a commonly employed biomarker to identify and predict ovarian cancer (OC). Precise measurement of MUC16 levels is essential for the accurate diagnosis, prediction, and management of OC. This research seeks to introduce a new surface plasmon resonance (SPR) biosensor design that utilizes aptamer-based technology to enable the sensitive and real-time detection of MUC16. Methods In this study, the sensor chip was immobilized with an anti-MUC16 aptamer (Ap) by utilizing 11-mercaptoundecanoic acid (MUA) as a linker to attach the amine-terminated Ap to the chip using EDC/NHS chemistry. Results The results indicated that the newly created aptasensor had a detection limit of 0.03 U/mL for MUC16 concentration, with a linear range of 0.09 to 0.27 U/mL. The findings demonstrate good precision and accuracy (<15%) for each MUC16 concentration, with recoveries ranging from 93% to 96%. Additionally, the aptasensor exhibited high selectivity, good repeatability, stability, and applicability in real human serum samples, indicating its potential as a valuable tool for the diagnosis and treatment of OC. Conclusion According to the outcomes, the designed aptasensor exhibited acceptable specificity to detect the CA125 antigen and could be utilized for the serum detection of target antigen by SPR method.
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Affiliation(s)
| | - Somayeh Vandghanooni
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Morteza Eskandani
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sadegh Hasannia
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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2
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Jia Y, Chen S, Wang Q, Li J. Recent progress in biosensor regeneration techniques. NANOSCALE 2024; 16:2834-2846. [PMID: 38291996 DOI: 10.1039/d3nr05456j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Biosensors are widely used in various applications, from medical diagnostics to environmental monitoring. Their widespread and continuous use necessitates regeneration methods to ensure cost-effectiveness and sustainability. In the realm of advancing human-centric bioelectronics for continuous monitoring, employing these sensors for real-time, in situ detection of biomarkers presents a considerable challenge. This mini-review examines diverse strategies utilized for the regeneration of biosensors, categorizing them based on their underlying mechanisms and discussing representative works. We explore methods ranging from surface engineering/re-functionalization, chemical treatments, allosteric regulation of bioreceptors, to manipulations of electric/magnetic fields, highlighting their working principles and exemplary studies. The advantages of each method, such as simplicity, high regeneration efficiency, and versatility, are discussed alongside their challenges, including degradation over cycles, limited applicability, and potential damage to sensors. As the demand for continuous and real-time biosensing escalates, the development of efficient and reliable regeneration strategies becomes essential. This mini-review offers an overview of the current landscape of biosensor regeneration, aiming to guide future research and innovations in this area.
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Affiliation(s)
- Yizhen Jia
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Shulin Chen
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Qi Wang
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jinghua Li
- Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH 43210, USA.
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3
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Chen L, Yang G, Qu F. Advances of aptamer-based small-molecules sensors in body fluids detection. Talanta 2024; 268:125348. [PMID: 37925822 DOI: 10.1016/j.talanta.2023.125348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
The field of aptamer-based sensing has evolved considerably over the past three decades. The aptamer sensor-based detection of small-molecule targets in body fluids is designed for real-time or rapid, low-cost, non- or minimally invasive tracking and diagnosis of human health status. It can be achieved by specifically monitoring biomarkers or metabolites excreted from various body fluids, including blood, urine, cerebrospinal fluid, saliva, ect. This article reviews a comprehensive collection of aptamer-based sensors for detecting small-molecule in various body fluids. A comparative analysis of aptamer features, emerging chemistry, advanced sensing materials, transduction techniques, and detection performance is conducted, and the strengths and pitfalls of each approach are discussed. Finally, the development process and application challenges of aptamer-based sensors in the detection of small-molecule in body fluids are presented and discussed.
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Affiliation(s)
- Li Chen
- School of Life Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Ge Yang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Feng Qu
- School of Life Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, 100081, China.
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4
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Economou A, Kokkinos C, Bousiakou L, Hianik T. Paper-Based Aptasensors: Working Principles, Detection Modes, and Applications. SENSORS (BASEL, SWITZERLAND) 2023; 23:7786. [PMID: 37765843 PMCID: PMC10536119 DOI: 10.3390/s23187786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Aptamers are short oligonucleotides designed to possess high binding affinity towards specific target compounds (ions, molecules, or cells). Due to their function and unique advantages, aptamers are considered viable alternatives to antibodies as biorecognition elements in bioassays and biosensors. On the other hand, paper-based devices (PADs) have emerged as a promising and powerful technology for the fabrication of low-cost analytical tools, mainly intended for on-site and point-of-care applications. The present work aims to provide a comprehensive overview of paper-based aptasensors. The review describes the fabrication methods and working principles of paper-based devices, the properties of aptamers as bioreceptors, the different modes of detection used in conjunction with aptasensing PADs, and representative applications for the detection of ions, small molecules, proteins, and cells. The future challenges and prospects of these devices are also discussed.
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Affiliation(s)
- Anastasios Economou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Christos Kokkinos
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece;
| | - Leda Bousiakou
- IMD Laboratories Co., R&D Section, Lefkippos Technology Park, National Centre for Scientific Research (NCSR) Demokritos, Agia Paraskevi, P.O. Box 60037, 15130 Athens, Greece;
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 84248 Bratislava, Slovakia;
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5
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Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
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Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
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6
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Cheng EL, Kacherovsky N, Pun SH. Aptamer-Based Traceless Multiplexed Cell Isolation Systems. ACS APPLIED MATERIALS & INTERFACES 2022; 14:44136-44146. [PMID: 36149728 DOI: 10.1021/acsami.2c11783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In both biomedical research and clinical cell therapy manufacturing, there is a need for cell isolation systems that recover purified cells in the absence of any selection agent. Reported traceless cell isolation methods using engineered antigen-binding fragments or aptamers have been limited to processing a single cell type at a time. There remains an unmet need for cell isolation processes that rapidly sort multiple target cell types. Here, we utilized two aptamers along with their designated complementary strands (reversal agents) to tracelessly isolate two cell types from a mixed cell population with one aptamer-labeling step and two sequential cell elution steps with reversal agents. We engineered a CD71-binding aptamer (rvCD71apt) and a reversal agent pair to be used simultaneously with our previously reported traceless purification approach using the CD8 aptamer (rvCD8apt) and its reversal agent. We verified the compatibility of the two aptamer displacement mechanisms by flow cytometry and the feasibility of incorporating rvCD71apt with a magnetic solid state. We then combined rvCD71apt with rvCD8apt to isolate activated CD4+ T cells and resting CD8+ cells by eluting these target cells into separate fractions with orthogonal strand displacements. This is the first demonstration of isolating different cell types using two aptamers and reversal agents at the same time. Potentially, different or more aptamers can be included in this traceless multiplexed isolation system for diverse applications with a shortened operation time and a lower production cost.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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Mohamad N, Azizan NI, Mokhtar NFK, Mustafa S, Mohd Desa MN, Hashim AM. Future perspectives on aptamer for application in food authentication. Anal Biochem 2022; 656:114861. [PMID: 35985482 DOI: 10.1016/j.ab.2022.114861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Food fraudulence and food contamination are major concerns, particularly among consumers with specific dietary, cultural, lifestyle, and religious requirements. Current food authentication methods have several drawbacks and limitations, necessitating the development of a simpler, more sensitive, and rapid detection approach for food screening analysis, such as an aptamer-based biosensor system. Although the use of aptamer is growing in various fields, aptamer applications for food authentication are still lacking. In this review, we discuss the limitations of existing food authentication technologies and describe the applications of aptamer in food analyses. We also project several potential targets or marker molecules to be targeted in the SELEX process. Finally, this review highlights the drawbacks of current aptamer technologies and outlines the potential route of aptamer selection and applications for successful food authentication. This review provides an overview of the use of aptamer in food research and its potential application as a molecular reporter for rapid detection in food authentication process. Developing databases to store all biochemical profiles of food and applying machine learning algorithms against the biochemical profiles are urged to accelerate the identification of more reliable biomarker molecules as aptamer targets for food authentication.
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Affiliation(s)
- Nornazliya Mohamad
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Inani Azizan
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nur Fadhilah Khairil Mokhtar
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shuhaimi Mustafa
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Nasir Mohd Desa
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Faculty of Medicine and Health Science, Universiti Putra Malaysia, 43400, UPM, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Halal Products Research Institute, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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8
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Hamedani NS, Happich FL, Klein EM, Rühl H, Mayer G, Oldenburg J, Müller J, Pötzsch B. Aptamer loaded superparamagnetic beads for selective capturing and gentle release of activated protein C. Sci Rep 2022; 12:7091. [PMID: 35490167 PMCID: PMC9056527 DOI: 10.1038/s41598-022-11198-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/18/2022] [Indexed: 02/07/2023] Open
Abstract
Activated protein C (APC) is a serine protease with anticoagulant and cytoprotective activities which make it an attractive target for diagnostic and therapeutic applications. In this work, we present one-step activation of APC from a commercial source of protein C (PC, Ceprotin) followed by rapid and efficient purification using an APC-specific aptamer, HS02-52G, loaded on MyOne superparamagnetic beads. Due to the Ca2+-dependent binding of APC to HS02-52G, an efficient capturing of APC was applied in the presence of Ca2+ ions, while a gentle release of captured APC was achieved in the elution buffer containing low EDTA concentration (5 mM). The captured and eluted APC showed more than 95% purity according to SDS-PAGE gel analysis and an enzyme-linked fluorescent assay (VIDAS Protein C). The purification yield of 45% was calculated when 4.2 µg APC was used, however this yield reduced to 21% if the starting amount of APC increased to 28.5 µg. Altogether, this method is recommended for rapid and efficient PC activation and APC purification. The purified APC can be used directly for downstream processes where high concentration of pure and active APC is needed.
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Affiliation(s)
- Nasim Shahidi Hamedani
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany.
| | - Felix Lucian Happich
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Eva-Maria Klein
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Heiko Rühl
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Jens Müller
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany
| | - Bernd Pötzsch
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127, Bonn, Germany
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9
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Kumar V, Kim KH. Use of molecular imprinted polymers as sensitive/selective luminescent sensing probes for pesticides/herbicides in water and food samples. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118824. [PMID: 35016982 DOI: 10.1016/j.envpol.2022.118824] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
As non-biological molecules, molecular imprinted polymers (MIPs) can be made as antibody mimics for the development of luminescence sensors for various targets. The combination of MIPs with nanomaterials is further recognized as a useful option to improve the sensitivity of luminescence sensors. In this work, the recent progresses made in the fabrication of fluorescence, phosphorescence, chemiluminescence, and electrochemiluminescence sensors based on such combination have been reviewed with emphasis on the detection of pesticides/herbicides. Accordingly, the materials that are most feasible for the detection of such targets are recommended based on the MIP technologies.
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Affiliation(s)
- Vanish Kumar
- National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar, Punjab, 140306, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-ro, Seoul, 04763, South Korea.
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10
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Oranzie M, Douman SF, Uhuo OV, Mokwebo KV, Sanga N, Iwuoha EI. Chronocoulometric signalling of BNP using a novel quantum dot aptasensor. Analyst 2022; 147:4829-4837. [DOI: 10.1039/d2an01357f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study is a first-time report of the development of a quantum dot based aptasensor for brain natriuretic peptide (BNP) detection using chronocoulometry for real-time analysis.
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Affiliation(s)
- Marlon Oranzie
- SensorLab (University of the Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville 7535, Cape Town, South Africa
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Samantha F. Douman
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Onyinyechi V. Uhuo
- SensorLab (University of the Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Kefilwe V. Mokwebo
- SensorLab (University of the Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Nelia Sanga
- SensorLab (University of the Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville 7535, Cape Town, South Africa
| | - Emmanuel I. Iwuoha
- SensorLab (University of the Western Cape Sensor Laboratories), Chemical Sciences Building, University of the Western Cape, Bellville 7535, Cape Town, South Africa
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11
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Aptamer-Modified Hydrogels. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 178:147-168. [PMID: 33796881 DOI: 10.1007/10_2021_166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Hydrogels have attracted much attention especially due to their biocompatibility and their potential for stimulus responsiveness. By combining hydrogels with aptamers, biological recognition and responsiveness can be added to hydrogels, thereby opening path to advanced applications in biosensing and biomedicine. Within this chapter aptamers will be introduced and their contributions to biological responsiveness of hydrogels will be described. Especially the aptamer-based mechanisms that result in biological responsiveness will be explained and examples for the application of these mechanisms will be given ranging from rather simple sensing approaches to advanced materials for tissue engineering and drug delivery. Since aptamers are not only highly specific bioreceptors, but represent switchable structures that can be easily manipulated using well-known DNA techniques, the combination of aptamers and hydrogels facilitates the rational design of well-programmable and target-responsive smart hydrogels.
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Oravczová V, Garaiová Z, Hianik T. Nanoparticles and Nanomotors Modified by Nucleic Acids Aptamers for Targeted Drug Delivery. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Mokhtari J, Nourisefat M, Zamiri B, Fotouhi L, Zarnani AH, Moosavi-Movahedi AA, Karimian K. Novel Method for the Isolation of Proteins and Small Target Molecules from Biological and Aqueous Media by Salt-Assisted Phase Transformation of Their PEGylated Recognition Counterparts. ACS OMEGA 2021; 6:7585-7597. [PMID: 33778269 PMCID: PMC7992175 DOI: 10.1021/acsomega.0c06149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
An efficient and simple method for the application of PEGylated affinity ligands in precipitative isolation of protein target molecules (TMs) from a biological fluid such as blood serum or small target molecules from an aqueous medium is presented for the first time. This approach is based on the high binding specificity of PEGylated recognition molecules (PEG-RMs) to their TMs and the unique physicochemical properties of PEG that result in their salt-assisted phase transformation. Addition of PEG-RM to blood serum results in the formation of an RM-specific macromolecular complex (PEG-RM + TM → PEG-RM.TM) that undergoes facile salt-assisted phase transformation to a separable semisolid with ammonium sulfate. PEG-RM.TM is then dissociated into its components by pH reduction or an increase of ionic strength (PEG-RM.TM → PEG-RM + TM). PEG-RM is salted out to afford pure TM in solution. The same phenomenon is observed when RM or TM are small molecules. The general applicability of the method was validated by PEGylation of two proteins (protein A, sheep antihuman IgG) and a small molecule (salicylic acid) used as model RMs for the isolation of Igs, IgG, and serum albumin from blood serum. The isolated protein TMs were shown to be pure and aggregate-free by gel electrophoresis and dynamic light scattering (DLS). IgG isolated by this method was further characterized by peptide mass fingerprinting. PEGylated protein A was used to demonstrate the recyclability and scale-up potential of PEG-RM. IgG isolated by this method from blood serum of a hepatitis C-vaccinated individual was tested for its binding to sheep antihuman IgG by UV spectroscopy, and its bioactivity was ascertained by comparison of its enzyme-linked immunosorbent assay (ELISA) result to that of a blood sample from the same individual. Reciprocity of RM and TM was ascertained using PEGylated salicylic acid to obtain pure serum albumin, and PEGylated serum albumin was utilized for near-exclusive isolation of one drug from an aqueous equimolar mixture of three drugs (salicylic acid, 91%; capecitabine, 6%; and deferiprone, 3%). Advantages of this approach, including target specificity and general applicability and celerity, over other affinity methods for the isolation of proteins are discussed at a molecular level.
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Affiliation(s)
- Javad Mokhtari
- Arasto Pharmaceutical Chemicals Inc., Yousefabad, Jahanarar Avenue, 23rd St. No. 8, Tehran 1438933741, Iran
- Departments of Chemistry, Science and Research Branch, Azad University, Tehran 1477893855, Iran
| | - Maryam Nourisefat
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
| | - Bita Zamiri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
| | - Leila Fotouhi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
| | - Amir-Hassan Zarnani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417466191, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran 1936773493, Iran
| | | | - Khashayar Karimian
- Arasto Pharmaceutical Chemicals Inc., Yousefabad, Jahanarar Avenue, 23rd St. No. 8, Tehran 1438933741, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417466191 Iran
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Bor G, Man E, Ugurlu O, Ceylan AE, Balaban S, Durmus C, Pinar Gumus Z, Evran S, Timur S. in vitro
Selection of Aptamer for Imidacloprid Recognition as Model Analyte and Construction of a Water Analysis Platform. ELECTROANAL 2020. [DOI: 10.1002/elan.202000075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Gulsah Bor
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ezgi Man
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ozge Ugurlu
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ayse Elcin Ceylan
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Simge Balaban
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Ceren Durmus
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Z. Pinar Gumus
- Central Research Test and Analysis Laboratory Application and Research Center Ege University 35100 Izmir Turkey
| | - Serap Evran
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
| | - Suna Timur
- Department of Biochemistry Faculty of Science Ege University 35100 Izmir Turkey
- Central Research Test and Analysis Laboratory Application and Research Center Ege University 35100 Izmir Turkey
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15
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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16
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Arshavsky-Graham S, Urmann K, Salama R, Massad-Ivanir N, Walter JG, Scheper T, Segal E. Aptamers vs. antibodies as capture probes in optical porous silicon biosensors. Analyst 2020; 145:4991-5003. [PMID: 32519701 DOI: 10.1039/d0an00178c] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade aptamers have emerged as a promising class of bioreceptors for biosensing applications with significant advantages over conventional antibodies. However, experimental studies comparing aptasensors and immunosensors, under equivalent conditions, are limited and the results are inconclusive, in terms of benefits and limitations of each bioreceptor type. In the present work, the performance of aptamer and antibody bioreceptors for the detection of a his-tagged protein, used as a model target, is compared. The bioreceptors are immobilized onto a nanostructured porous silicon (PSi) thin film, used as the optical transducer, and the target protein is detected in a real-time and label-free format by reflective interferometric Fourier transform spectroscopy. For the antibodies, random-oriented immobilization onto the PSi nanostructure results in a poor biosensing performance. Contrary, Fc-oriented immobilization of the antibodies shows a similar biosensing performance to that exhibited by the aptamer-based biosensor, in terms of binding rate, dynamic detection range, limit of detection and selectivity. The aptasensor outperforms in terms of its reusability and storability, while the immunosensor could not be regenerated for subsequent experiments.
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Affiliation(s)
- Sofia Arshavsky-Graham
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstr. 5, 30167 Hannover, Germany.
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17
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Prante M, Schüling T, Roth B, Bremer K, Walter J. Characterization of an Aptamer Directed against 25-Hydroxyvitamin D for the Development of a Competitive Aptamer-Based Assay. BIOSENSORS 2019; 9:E134. [PMID: 31766203 PMCID: PMC6956098 DOI: 10.3390/bios9040134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/22/2022]
Abstract
Detection of the small molecule 25-hydroxyvitamin D (25(OH)D) as the most relevant marker for vitamin D supply suffers from a high variability of results using the current detection methods, such as high-performance liquid chromatography (HPLC) and immunoassays. A new detection approach using a highly specific aptamer directed against 25(OH)D was established in this study based on the target-induced dissociation (TID) sensing approach. In this work, the aptamer was investigated regarding its structural properties as well as its binding affinity by using microscale thermophoresis (MST). Moreover, complementary oligonucleotides were designed based on the aptamer structure and were evaluated in MST experiments. Binding experiments of immobilized aptamers were conducted in microarray experiments. It could be shown that the aptamer exhibited the usual B-DNA structure and did not form any G-quadruplexes. The design of complementary oligonucleotides for the TID assay identified a putative 25(OH)D binding site within the aptamer. The limit of detection of the established competitive assay was determined to be 5.4 nM, which sets the stage for the development of a biosensor system.
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Affiliation(s)
- Marc Prante
- Institute of Technical Chemistry, Leibniz University of Hannover, 30167 Hannover, Germany; (M.P.); (T.S.)
| | - Torsten Schüling
- Institute of Technical Chemistry, Leibniz University of Hannover, 30167 Hannover, Germany; (M.P.); (T.S.)
| | - Bernhard Roth
- Hannover Centre for Optical Technologies, Leibniz University of Hannover, 30167 Hannover, Germany; (B.R.); (K.B.)
- Cluster of Excellence PhoenixD, (Photonics, Optics, and Engineering—Innovation Across Disciplines), 30167 Hannover, Germany
| | - Kort Bremer
- Hannover Centre for Optical Technologies, Leibniz University of Hannover, 30167 Hannover, Germany; (B.R.); (K.B.)
| | - Johanna Walter
- Institute of Technical Chemistry, Leibniz University of Hannover, 30167 Hannover, Germany; (M.P.); (T.S.)
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18
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Kurth T, Witt S, Bolten S, Waniek JJ, Kortmann C, Lavrentieva A, Scheper T, Walter JG. Development of Aptamer-Based TID Assays Using Thermophoresis and Microarrays. BIOSENSORS 2019; 9:E124. [PMID: 31615077 PMCID: PMC6955894 DOI: 10.3390/bios9040124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023]
Abstract
Aptamers are single-stranded oligonucleotides which can be used as alternative recognition elements for protein detection, because aptamers bind their targets with a high affinity similar to antibodies. Due to the targetinduced conformational changes of aptamers, these oligonucleotides can be applied in various biosensing platforms. In this work, aptamers directed against the vascular endothelial growth factor (VEGF) were used as a model system. VEGF plays a key role in physiological angiogenesis and vasculogenesis. Furthermore, VEGF is involved in the development and growth of cancer and other diseases like agerelated macular degeneration, rheumatoid arthritis, diabetes mellitus, and neurodegenerative disorders. Detecting the protein biomarker VEGF is therefore of great importance for medical research and diagnostics. In this research, VEGFbinding aptamers were investigated for the systematic development of a targetinduced dissociation (TID) assay utilizing thermophoresis and microarrays. The established aptamer-microarray allowed for the detection of 0.1 nM of VEGF. Furthermore, the systematic development of the TID method using the VEGF model protein could help to develop further TID assays for the detection of various protein biomarkers.
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Affiliation(s)
- Tracy Kurth
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Sandra Witt
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Svenja Bolten
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Janice-Joy Waniek
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Carlotta Kortmann
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Antonina Lavrentieva
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Johanna-Gabriela Walter
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, 30167 Hannover, Germany.
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19
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Celikbas E, Balaban S, Evran S, Coskunol H, Timur S. A Bottom-Up Approach for Developing Aptasensors for Abused Drugs: Biosensors in Forensics. BIOSENSORS 2019; 9:E118. [PMID: 31581533 PMCID: PMC6955935 DOI: 10.3390/bios9040118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
Aptamer-based point-of-care (POC) diagnostics platforms may be of substantial benefit in forensic analysis as they provide rapid, sensitive, user-friendly, and selective analysis tools for detection. Aptasensors have not yet been adapted commercially. However, the significance of the applications of aptasensors in the literature exceeded their potential. Herein, in this review, a bottom-up approach is followed to describe the aptasensor development and application procedure, starting from the synthesis of the corresponding aptamer sequence for the selected analyte to creating a smart surface for the sensitive detection of the molecule of interest. Optical and electrochemical biosensing platforms, which are designed with aptamers as recognition molecules, detecting abused drugs are critically reviewed, and existing and possible applications of different designs are discussed. Several potential disciplines in which aptamer-based biosensing technology can be of greatest value, including forensic drug analysis and biological evidence, are then highlighted to encourage researchers to focus on developing aptasensors in these specific areas.
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Affiliation(s)
- Eda Celikbas
- Department of Biochemistry, Institute of Natural and Applied Sciences, Ege University, 35100 Bornova, Izmir, Turkey;
| | - Simge Balaban
- Department of Biochemistry, Institute of Natural and Applied Sciences, Ege University, 35100 Bornova, Izmir, Turkey;
| | - Serap Evran
- Department of Biochemistry, Institute of Natural and Applied Sciences, Ege University, 35100 Bornova, Izmir, Turkey;
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
| | - Hakan Coskunol
- Department of Mental Health and Diseases, Faculty of Medicine, Ege University, 35100 Bornova, Izmir, Turkey;
| | - Suna Timur
- Department of Biochemistry, Institute of Natural and Applied Sciences, Ege University, 35100 Bornova, Izmir, Turkey;
- Department of Biochemistry, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
- Central Research Testing and Analysis Laboratory Research and Application Center, Ege University, 35100 Bornova, Izmir, Turkey
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20
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Li Y, Stern D, Lock LL, Mills J, Ou SH, Morrow M, Xu X, Ghose S, Li ZJ, Cui H. Emerging biomaterials for downstream manufacturing of therapeutic proteins. Acta Biomater 2019; 95:73-90. [PMID: 30862553 DOI: 10.1016/j.actbio.2019.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/26/2019] [Accepted: 03/06/2019] [Indexed: 12/23/2022]
Abstract
Downstream processing is considered one of the most challenging phases of industrial manufacturing of therapeutic proteins, accounting for a large portion of the total production costs. The growing demand for therapeutic proteins in the biopharmaceutical market in addition to a significant rise in upstream titers have placed an increasing burden on the downstream purification process, which is often limited by high cost and insufficient capacities. To achieve efficient production and reduced costs, a variety of biomaterials have been exploited to improve the current techniques and also to develop superior alternatives. In this work, we discuss the significance of utilizing traditional biomaterials in downstream processing and review the recent progress in the development of new biomaterials for use in protein separation and purification. Several representative methods will be highlighted and discussed in detail, including affinity chromatography, non-affinity chromatography, membrane separations, magnetic separations, and precipitation/phase separations. STATEMENT OF SIGNIFICANCE: Nowadays, downstream processing of therapeutic proteins is facing great challenges created by the rapid increase of the market size and upstream titers, starving for significant improvements or innovations in current downstream unit operations. Biomaterials have been widely used in downstream manufacturing of proteins and efforts have been continuously devoted to developing more advanced biomaterials for the implementation of more efficient and economical purification methods. This review covers recent advances in the development and application of biomaterials specifically exploited for various chromatographic and non-chromatographic techniques, highlighting several promising alternative strategies.
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Affiliation(s)
- Yi Li
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - David Stern
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Lye Lin Lock
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Jason Mills
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Shih-Hao Ou
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Marina Morrow
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Xuankuo Xu
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States.
| | - Sanchayita Ghose
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Zheng Jian Li
- Biologics Process Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, MA 01434, United States
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering, and Institute for NanoBioTechnology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, United States; Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.
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21
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Munzar JD, Ng A, Juncker D. Duplexed aptamers: history, design, theory, and application to biosensing. Chem Soc Rev 2019; 48:1390-1419. [PMID: 30707214 DOI: 10.1039/c8cs00880a] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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22
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Nabiabad HS, Piri K, Amini M. Expression of active chimeric-tissue plasminogen activator in tobacco hairy roots, identification of a DNA aptamer and purification by aptamer functionalized-MWCNTs chromatography. Protein Expr Purif 2018; 152:137-145. [PMID: 26876003 DOI: 10.1016/j.pep.2016.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 11/26/2022]
Abstract
Tissue-type plasminogen activator (tPA) is a serine protease that plays a crucial role in the fibrinolytic system. We increased the activity of tPA by splicing the active site of dodder-cuscutain gene to human tPA. The chimeric cDNA of tPA was constructed by Splicing by Overlap Extension Polymerase Chain Reaction (SOEing-PCR) method and transferred to the hairy roots of tobacco using different strains of Agrobacterium rhizogenes. Chimeric-tPA was purified by lysine-sepharose chromatography and specific aptamers were designed using SELEX method. Multi wall carbon nanotubes were functionalized with selected aptamers, packed in a column, and used for purification. The results demonstrated that selected aptamer having KD values of 0.320 nM and IC50 of 28.9 nM possessed good affinity to tPA, and the chimeric-tPA was properly purified by aptamer-chromatography. Hairy roots expressing chimeric-tPA and normal-tPA produced 900 and 450 ngmg-1 of total protein, respectively. The activities of chimeric-tPA and normal-tPA were 90 and 60 IUml-1, respectively. Compared to the normal-tPA, chimeric-tPA showed more activity.
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Affiliation(s)
- Haidar Saify Nabiabad
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamadan, Iran
| | - Khosro Piri
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamadan, Iran.
| | - Massoume Amini
- Department of Biotechnology, College of Agriculture, Bu-Ali Sina University, Hamadan, Iran
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23
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Khodadadi M, Malekpour A, Mehrgardi MA. Aptamer functionalized magnetic nanoparticles for effective extraction of ultratrace amounts of aflatoxin M1 prior its determination by HPLC. J Chromatogr A 2018; 1564:85-93. [DOI: 10.1016/j.chroma.2018.06.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 04/03/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
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24
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Shaikh YS, Seibert C, Kampeis P. Novel In Situ Magnetic Separator for Magnetic Particle-Based Enzyme Purification or Biocatalysis. CHEM-ING-TECH 2018. [DOI: 10.1002/cite.201600107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yonas S. Shaikh
- Trier University of Applied Sciences; Environmental Campus Birkenfeld; Institute for Biotechnical Process Design; P.O. Box 1380 55761 Birkenfeld Germany
| | - Christian Seibert
- Trier University of Applied Sciences; Environmental Campus Birkenfeld; Institute for Biotechnical Process Design; P.O. Box 1380 55761 Birkenfeld Germany
| | - Percy Kampeis
- Trier University of Applied Sciences; Environmental Campus Birkenfeld; Institute for Biotechnical Process Design; P.O. Box 1380 55761 Birkenfeld Germany
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25
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Witt M, Phung NL, Stalke A, Walter JG, Stahl F, von Neuhoff N, Scheper T. Comparing two conventional methods of emulsion PCR and optimizing of Tegosoft-based emulsion PCR. Eng Life Sci 2017; 17:953-958. [PMID: 32624844 DOI: 10.1002/elsc.201700047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/26/2017] [Accepted: 07/14/2017] [Indexed: 12/25/2022] Open
Abstract
The selection of aptamers represents a promising route in the development of high affinity ligands. In these processes the formation of by-products is a common problem during the PCR-based amplification of complex oligonucleotide libraries. One approach to overcome this drawback is to separate each template oligonucleotide into an individual reaction compartment provided by a droplet. This method, termed emulsion PCR (ePCR), has already emerged to a standard method in sample preparation for 2nd generation sequencing. In this work, we compare different literature protocols that have been developed to generate stable emulsions for ePCR. We investigate different emulsification methods and evaluate the importance of the initial template concentration. We demonstrate that emulsion stability is of utmost importance for the successful inhibition of by-product formation and give an optimized protocol for generation of an emulsified PCR.
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Affiliation(s)
- Martin Witt
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Ngoc Linh Phung
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Amelie Stalke
- Institute for Cellular and Molecular Pathology Hannover Medical School Hannover Germany
| | | | - Frank Stahl
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
| | - Nils von Neuhoff
- Department of Pediatric Hematology-Oncology University of Duisburg-Essen Essen Germany
| | - Thomas Scheper
- Institute of Technical Chemistry Leibniz University Hannover Hannover Germany
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26
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Modh H, Scheper T, Walter JG. Detection of ochratoxin A by aptamer-assisted real-time PCR-based assay (Apta-qPCR). Eng Life Sci 2017; 17:923-930. [PMID: 32624841 DOI: 10.1002/elsc.201700048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/09/2017] [Accepted: 07/04/2017] [Indexed: 12/18/2022] Open
Abstract
Detection of food toxins with high sensitivity is very important and challenging. Ochratoxin A (OTA) is frequently present as food contaminant in contaminated grains and grain derivatives such as bread and beer. In this work, a target-induced dissociation (TID) based aptamer-assisted real-time PCR-based assay (apta-qPCR) is developed that features effective detection of OTA. Apta-qPCR effectively combines the capabilities of aptamer to be amplified, being a nucleotide sequence, with its specific interaction with the corresponding target molecule. Compared to commonly used fluorescence-based and colorimetric methods, the sensitivity of qPCR to detect a nucleotide sequence (aptamer) has ameliorated the sensitivity of the aptamer-based detection of OTA. Here, the OTA aptamer was immobilized on the magnetic beads coated with d(T)25 (dT beads). A sequence complementary to the OTA-binding portion of the aptamer was used as a linker between dT beads and the aptamer sequence. When OTA was added, the aptamer was released from the dT beads due to TID. The resulting assay was able to detect 0.009 ng/mL OTA with a wide dynamic range of 0.039-1000 ng/mL. Apta-qPCR can be easily transferred to other small molecules for highly sensitive detection using corresponding aptamers.
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Affiliation(s)
- Harshvardhan Modh
- Institute of Technical Chemistry Leibniz University of Hannover Hannover Germany
| | - Thomas Scheper
- Institute of Technical Chemistry Leibniz University of Hannover Hannover Germany
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27
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Urmann K, Modrejewski J, Scheper T, Walter JG. Aptamer-modified nanomaterials: principles and applications. ACTA ACUST UNITED AC 2017. [DOI: 10.1515/bnm-2016-0012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractAptamers are promising alternative binders that can substitute antibodies in various applications. Due to the advantages of aptamers, namely their high affinity, specificity and stability, along with the benefits originating from the chemical synthesis of aptamers, they have attracted attention in various applications including their use on nanostructured material. This necessitates the immobilization of aptamers on a solid support. Since aptamer immobilization may interfere with its binding properties, the immobilization of aptamers has to be investigated and optimized. Within this review, we give general insights into the principles and factors controlling the binding affinity of immobilized aptamers. Specific features of aptamer immobilization on nanostructured surfaces and nanoparticles are highlighted and a brief overview of applications of aptamer-modified nanostructured materials is given.
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28
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Forier C, Boschetti E, Ouhammouch M, Cibiel A, Ducongé F, Nogré M, Tellier M, Bataille D, Bihoreau N, Santambien P, Chtourou S, Perret G. DNA aptamer affinity ligands for highly selective purification of human plasma-related proteins from multiple sources. J Chromatogr A 2017; 1489:39-50. [PMID: 28179082 DOI: 10.1016/j.chroma.2017.01.031] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/04/2017] [Accepted: 01/06/2017] [Indexed: 01/18/2023]
Abstract
Nucleic acid aptamers are promising ligands for analytical and preparative-scale affinity chromatography applications. However, a full industrial exploitation requires that aptamer-grafted chromatography media provide a number of high technical standards that remained largely untested. Ideally, they should exhibit relatively high binding capacity associated to a very high degree of specificity. In addition, they must be highly resistant to harsh cleaning/sanitization conditions, as well as to prolonged and repeated exposure to biological environment. Here, we present practical examples of aptamer affinity chromatography for the purification of three human therapeutic proteins from various sources: Factor VII, Factor H and Factor IX. In a single chromatographic step, three DNA aptamer ligands enabled the efficient purification of their target protein, with an unprecedented degree of selectivity (from 0.5% to 98% of purity in one step). Furthermore, these aptamers demonstrated a high stability under harsh sanitization conditions (100h soaking in 1M NaOH). These results pave the way toward a wider adoption of aptamer-based affinity ligands in the industrial-scale purification of not only plasma-derived proteins but also of any other protein in general.
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Affiliation(s)
| | | | | | | | - Frédéric Ducongé
- CEA, I2BM, MIRCen, UMR 9199, Université Paris Saclay, Fontenay aux Roses, France
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29
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Lin X, Cheng C, Terry P, Chen J, Cui H, Wu J. Rapid and sensitive detection of bisphenol a from serum matrix. Biosens Bioelectron 2016; 91:104-109. [PMID: 28006678 DOI: 10.1016/j.bios.2016.12.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/28/2022]
Abstract
Bisphenol A (BPA) is an endocrine disrupting compound that may have adverse developmental, reproductive, neurological, and immune system effects. Low-level exposure to BPA is ubiquitous in human populations due to its widespread use in consumer products. Therefore, highly sensitive methods are needed to quantify BPA in various matrices including water, serum, and food products. In this study, we developed a simple, rapid, highly sensitive and specific sensor based on an aptamer probe and AC electrokinetics capacitive sensing method that successfully detected BPA at femto molar (fM) levels, which is an improvement over prior work by a factor of 10. We were able to detect BPA spiked in human serum as well as in maternal and cord blood within 30s. The sensor is responsive to BPA down to femto molar levels, but not to structurally similar compounds including bisphenol F (BPF) or bisphenol S (BPS) even at much higher concentration. Further development of this platform may prove useful in monitoring exposure to BPA and other small molecules in various matrices.
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Affiliation(s)
- Xiaogang Lin
- Key Laboratory of Optoelectronic Technology and System of the Education Ministry of China, Chongqing University, Chongqing 400044, China; Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA
| | - Cheng Cheng
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA
| | - Paul Terry
- Department of Medicine, Graduate School of Medicine, the University of Tennessee Medical Center, USA
| | - Jiangang Chen
- Department of Public Health, the University of Tennessee, Knoxville, TN 37996, USA.
| | - Haochen Cui
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA.
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30
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Tello A, Cao R, Marchant MJ, Gomez H. Conformational Changes of Enzymes and Aptamers Immobilized on Electrodes. Bioconjug Chem 2016; 27:2581-2591. [PMID: 27748603 DOI: 10.1021/acs.bioconjchem.6b00553] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Conformation constitutes a vital property of biomolecules, especially in the cases of enzymes and aptamers, and is essential in defining their molecular recognition ability. When biomolecules are immobilized on electrode surfaces, it is very important to have a control on all the possible conformational changes that may occur, either upon the recognition of their targets or by undesired alterations. Both enzymes and aptamers immobilized on electrodes are susceptible to conformational changes as a response to the nature of the charge of the surface and of the surrounding environment (pH, temperature, ionic strength, etc.). The main goal of this review is to analyze how the conformational changes of enzymes and aptamers immobilized on electrode surfaces have been treated in reports on biosensors and biofuel cells. This topic was selected due to insufficient information found on the actual conformational changes involved in the function of these bioelectrochemical devices despite its importance.
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Affiliation(s)
- Alejandra Tello
- Universidad Andres Bello , Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, República 239, Santiago, Chile
| | - Roberto Cao
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso , Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - María José Marchant
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso , Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - Humberto Gomez
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso , Avenida Universidad 330, Curauma, Valparaíso, Chile
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31
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Aptamer and PNIPAAm co-conjugated nanoparticles regulate activity of enzyme with different temperature. Talanta 2016; 159:47-54. [DOI: 10.1016/j.talanta.2016.05.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/22/2016] [Accepted: 05/29/2016] [Indexed: 11/20/2022]
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32
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Aptamer-based depletion of small molecular contaminants: A case study using ochratoxin A. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-015-0486-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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33
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Kimura Y, Saito N, Hanada K, Liu J, Okabe T, Kawashima SA, Yamatsugu K, Kanai M. Supramolecular Ligands for Histone Tails by Employing a Multivalent Display of Trisulfonated Calix[4]arenes. Chembiochem 2015; 16:2599-604. [DOI: 10.1002/cbic.201500448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yasuaki Kimura
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Nae Saito
- Drug Discovery Initiative; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kayo Hanada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jiaan Liu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shigehiro A. Kawashima
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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34
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Lönne M, Bolten S, Lavrentieva A, Stahl F, Scheper T, Walter JG. Development of an aptamer-based affinity purification method for vascular endothelial growth factor. ACTA ACUST UNITED AC 2015; 8:16-23. [PMID: 28352569 PMCID: PMC4980704 DOI: 10.1016/j.btre.2015.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 08/14/2015] [Accepted: 08/19/2015] [Indexed: 11/29/2022]
Abstract
Since aptamers bind their targets with high affinity and specificity, they are promising alternative ligands in protein affinity purification. As aptamers are chemically synthesized oligonucleotides, they can be easily produced in large quantities regarding GMP conditions allowing their application in protein production for therapeutic purposes. Several advantages of aptamers compared to antibodies are described in general within this paper. Here, an aptamer directed against the human Vascular Endothelial Growth Factor (VEGF) was used as affinity ligand for establishing a purification platform for VEGF in small scale. The aptamer was covalently immobilized on magnetic beads in a controlled orientation resulting in a functional active affinity matrix. Target binding was optimized by introduction of spacer molecules and variation of aptamer density. Further, salt-induced target elution was demonstrated as well as VEGF purification from a complex protein mixture proving the specificity of protein-aptamer binding.
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Affiliation(s)
- Maren Lönne
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, D-30167 Hannover, Germany
| | - Svenja Bolten
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, D-30167 Hannover, Germany
| | - Antonina Lavrentieva
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, D-30167 Hannover, Germany
| | - Frank Stahl
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, D-30167 Hannover, Germany
| | - Thomas Scheper
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, D-30167 Hannover, Germany
| | - Johanna-Gabriela Walter
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, D-30167 Hannover, Germany
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Urmann K, Tenenbaum E, Walter JG, Segal E. Porous Silicon Biosensors Employing Emerging Capture Probes. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20346-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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36
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Fields C, Li P, O'Mahony JJ, Lee GU. Advances in affinity ligand-functionalized nanomaterials for biomagnetic separation. Biotechnol Bioeng 2015; 113:11-25. [DOI: 10.1002/bit.25665] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 05/21/2015] [Accepted: 05/24/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Conor Fields
- School of Chemistry and Chemical Biology; University College Dublin, Belfield, Dublin 4; Ireland
| | - Peng Li
- School of Chemistry and Chemical Biology; University College Dublin, Belfield, Dublin 4; Ireland
| | - James J. O'Mahony
- School of Chemistry and Chemical Biology; University College Dublin, Belfield, Dublin 4; Ireland
| | - Gil U. Lee
- School of Chemistry and Chemical Biology; University College Dublin, Belfield, Dublin 4; Ireland
- Conway Institute for Biomolecular and Biomedical Sciences; University College Dublin, Belfield, Dublin 4; Ireland
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37
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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Urmann K, Walter JG, Scheper T, Segal E. Label-free optical biosensors based on aptamer-functionalized porous silicon scaffolds. Anal Chem 2015; 87:1999-2006. [PMID: 25551423 DOI: 10.1021/ac504487g] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A proof-of-concept for a label-free and reagentless optical biosensing platform based on nanostructured porous silicon (PSi) and aptamers is presented in this work. Aptamers are oligonucleotides (single-stranded DNA or RNA) that can bind their targets with high affinity and specificity, making them excellent recognition elements for biosensor design. Here we describe the fabrication and characterization of aptamer-conjugated PSi biosensors, where a previously characterized his-tag binding aptamer (6H7) is used as model system. Exposure of the aptamer-functionalized PSi to the target proteins as well as to complex fluids (i.e., bacteria lysates containing target proteins) results in robust and well-defined changes in the PSi optical interference spectrum, ascribed to specific aptamer-protein binding events occurring within the nanoscale pores, monitored in real time. The biosensors show exceptional stability and can be easily regenerated by a short rinsing step for multiple biosensing analyses. This proof-of-concept study demonstrates the possibility of designing highly stable and specific label-free optical PSi biosensors, employing aptamers as capture probes, holding immense potential for application in detection of a broad range of targets, in a simple yet reliable manner.
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Affiliation(s)
- Katharina Urmann
- Institute of Technical Chemistry, Leibniz University of Hannover , Callinstrasse 5, 30167 Hannover, Germany
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39
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Abstract
Aptamers are valuable alternative ligands for affinity separations. Here, we describe the aptamer-based affinity separation of His-tagged proteins using an aptamer directed against the His-tag. The immobilization of the aptamer to magnetic beads is described as well as the aptamer-based purification and proper methods for the characterization of the process. Moreover, indications for the transfer of the process to other aptamers are given.
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Affiliation(s)
- Guohong Zhu
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstr. 5, 30167, Hannover, Germany
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40
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Waybrant B, Pearce TR, Kokkoli E. Effect of polyethylene glycol, alkyl, and oligonucleotide spacers on the binding, secondary structure, and self-assembly of fractalkine binding FKN-S2 aptamer-amphiphiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7465-7474. [PMID: 24849928 DOI: 10.1021/la500403v] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Previously we identified an aptamer, named FKN-S2, which binds the cell surface protein fractalkine with high affinity and specificity. In this paper a hydrophobic dialkyl C16 tail was added to the aptamer to create an aptamer-amphiphile. We investigated how the tail and a spacer molecule of varying length and hydrophobicity, inserted between the tail and the aptamer headgroup, affect the binding, structure, and self-assembly properties of the aptamer-amphiphile. We synthesized aptamer-amphiphiles with no spacer (NoSPR), polyethylene glycol (PEG4, PEG8, PEG24), alkyl (C12 and C24), or oligonucleotide (T10 and T5: 10 and 5 thymine, and A10: 10 adenine) spacers. The addition of the tail reduced the binding affinity of the aptamer-amphiphile over 7.5-fold compared to the free aptamer. The hydrophobic alkyl spacers resulted in the greatest loss of affinity, and the hydrophilic PEG spacers improved amphiphile affinity but did not restore it to that of the free aptamer. Interestingly, oligonucleotide spacers produced the highest affinity amphiphiles. Nucleotide composition did not affect affinity, however, as the T10 and A10 spacers had equal affinity. The oligonucleotide spacer amphiphiles had the highest affinity because the oligonucleotide spacer increased the affinity of free aptamer; the FKN-S2 aptamer plus the oligonucleotide spacer had a higher affinity than the free FKN-S2 aptamer. Circular dichroism (CD) spectroscopy and thermal melting studies indicated the aptamer forms a stem-loop and intramolecular G-quadruplex, and the tail strongly stabilized the formation of the G-quadruplex in a buffer. Cryogenic transmission electron microscopy (cryo-TEM) imaging showed the aptamer-amphiphiles, independent of the spacer used, self-assembled into micelles and nanotapes, flat bilayer structures that were often twisted. Finally, liposomes functionalized with the FKN-S2 amphiphile were incubated with fractalkine expressing cells, and the amount of binding was dependent on the concentration of the amphiphile on the liposome surface.
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Affiliation(s)
- Brett Waybrant
- Department of Chemical Engineering and Materials Science, and ‡Department of Biomedical Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
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41
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Brower KP, Ryakala VK, Bird R, Godawat R, Riske FJ, Konstantinov K, Warikoo V, Gamble J. Single-step affinity purification of enzyme biotherapeutics: A platform methodology for accelerated process development. Biotechnol Prog 2014; 30:708-17. [DOI: 10.1002/btpr.1870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/06/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Kevin P. Brower
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Venkat K. Ryakala
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Ryan Bird
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Rahul Godawat
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Frank J. Riske
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Konstantin Konstantinov
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Veena Warikoo
- Late Stage Process Development; Genzyme - A Sanofi Company; 45 New York Avenue, Framingham MA 01701
| | - Jean Gamble
- Analytical Development; Genzyme - A Sanofi Company; One The Mountain Road, Framingham MA 01701
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Meyer M, Scheper T, Walter JG. Aptamers: versatile probes for flow cytometry. Appl Microbiol Biotechnol 2013; 97:7097-109. [PMID: 23838792 DOI: 10.1007/s00253-013-5070-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/17/2013] [Accepted: 06/17/2013] [Indexed: 12/21/2022]
Abstract
Aptamers are nucleic acid oligomers with distinct conformational shapes that allow them to bind targets with high affinity and specificity. Aptamers are selected from a random oligonucleotide library by their capability to bind a certain molecular target. A variety of targets ranging from small molecules like amino acids to complex targets and whole cells have been used to select aptamers. These characteristics and the ability to create specific aptamers against virtually any cell type in a process termed "systematic evolution by exponential enrichment" make them interesting tools for flow cytometry. In this contribution, we review the application of aptamers as probes for flow cytometry, especially cell-phenotyping and detection of various cancer cell lines and virus-infected cells and pathogens. We also discuss the potential of aptamers combined with nanoparticles such as quantum dots for the generation of new multivalent detector molecules with enhanced affinity and sensitivity. With regard to recent advancements in aptamer selection and the decreasing costs for oligonucleotide synthesis, aptamers may rise as potent competitors for antibodies as molecular probes in flow cytometry.
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Affiliation(s)
- Michael Meyer
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany
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43
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Lönne M, Zhu G, Stahl F, Walter JG. Aptamer-modified nanoparticles as biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:121-54. [PMID: 23824145 DOI: 10.1007/10_2013_231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are short oligonucleotides that are capable of selectively binding to their corresponding target. Therefore, they can be thought of as a nucleic acid-based alternative to antibodies and can substitute for their amino acid-based counterparts in analytical applications, including as receptors in biosensors. Here they offer several advantages because their nucleic acid nature and their binding via an induced fit mechanism enable novel sensing strategies. In this article, the utilization of aptamers as novel bio-receptors in combination with nanoparticles as transducer elements is reviewed. In addition to these analytical applications, the medical relevance of aptamer-modified nanoparticles is described.
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Affiliation(s)
- Maren Lönne
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstr. 5, 30167, Hannover, Germany
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44
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BiotecVisions 2012, November. Biotechnol J 2012. [DOI: 10.1002/biot.201200058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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