1
|
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: 28] [Impact Index Per Article: 28.0] [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.
Collapse
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
| |
Collapse
|
2
|
Arciszewska K, Kowalska E, Bartnicki F, Bonarek P, Banaś AK, Strzałka W. DNA aptamer-based affinity chromatography system for purification of recombinant proteins tagged with lysine tag. J Chromatogr A 2023; 1692:463846. [PMID: 36780846 DOI: 10.1016/j.chroma.2023.463846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
Affinity chromatography (AC) is one of the techniques widely used for the purification of recombinant proteins. In our previous study, we presented a successful application of the Argi system [1] for the purification of recombinant proteins, based on the specific interaction between an arginine tag and a DNA aptamer. Exploring the possible application of positively charged peptide tags in the purification of recombinant proteins, in this study we developed and characterized an AC system based on the specific and reversible interaction between a DNA aptamer and a lysine tag (Lys-tag) comprising five lysine residues (5 K). We optimized the length of both the selected DNA aptamer and Lys-tag which were named B5K aptamer and 5K-tag, respectively. The results showed that the stability of the B5K aptamer and 5K-tag was dependent on the presence of potassium ions. The conditions for mild elution of 5K-tagged protein from B5K aptamer were determined. Our study proved that the developed system can be used for the purification of recombinant proteins from Escherichia coli total protein extracts.
Collapse
Affiliation(s)
- Klaudia Arciszewska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Filip Bartnicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Piotr Bonarek
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland
| | - Wojciech Strzałka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow 30-387, Poland.
| |
Collapse
|
3
|
Ning Y, Hu J, Lu F. Aptamers used for biosensors and targeted therapy. Biomed Pharmacother 2020; 132:110902. [PMID: 33096353 PMCID: PMC7574901 DOI: 10.1016/j.biopha.2020.110902] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/07/2023] Open
Abstract
Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.
Collapse
Affiliation(s)
- Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Jue Hu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan, 410208, PR China.
| |
Collapse
|
4
|
Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
Collapse
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| |
Collapse
|
5
|
Mahmoudi Gomari M, Saraygord-Afshari N, Farsimadan M, Rostami N, Aghamiri S, Farajollahi MM. Opportunities and challenges of the tag-assisted protein purification techniques: Applications in the pharmaceutical industry. Biotechnol Adv 2020; 45:107653. [PMID: 33157154 DOI: 10.1016/j.biotechadv.2020.107653] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/16/2023]
Abstract
Tag-assisted protein purification is a method of choice for both academic researches and large-scale industrial demands. Application of the purification tags in the protein production process can help to save time and cost, but the design and application of tagged fusion proteins are challenging. An appropriate tagging strategy must provide sufficient expression yield and high purity for the final protein products while preserving their native structure and function. Thanks to the recent advances in the bioinformatics and emergence of high-throughput techniques (e.g. SEREX), many new tags are introduced to the market. A variety of interfering and non-interfering tags have currently broadened their application scope beyond the traditional use as a simple purification tool. They can take part in many biochemical and analytical features and act as solubility and protein expression enhancers, probe tracker for online visualization, detectors of post-translational modifications, and carrier-driven tags. Given the variability and growing number of the purification tags, here we reviewed the protein- and peptide-structured purification tags used in the affinity, ion-exchange, reverse phase, and immobilized metal ion affinity chromatographies. We highlighted the demand for purification tags in the pharmaceutical industry and discussed the impact of self-cleavable tags, aggregating tags, and nanotechnology on both the column-based and column-free purification techniques.
Collapse
Affiliation(s)
- Mohammad Mahmoudi Gomari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Shahin Aghamiri
- Student research committee, Department of medical biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Wu S, Liu Y, Sun H, Zhong M, Dai B, Pan B, Shen Z. An ssDNA aptamer specific for detection and purification of hexahistidine-tagged proteins. Anal Biochem 2020; 607:113893. [PMID: 32739349 DOI: 10.1016/j.ab.2020.113893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/27/2022]
Abstract
Aptamers are small-sized RNA or ssDNA ligands with a unique structure, which have high specificity and affinity to their cognate targets. Thus, in addition to the extensive values in various bio-medical fields, aptamers can also be alternatively used as affinity ligands in the bioprocess, such as for protein purification. In the present study, a hexahistidine specific aptamer named AptHis-C, was developed through the SELEX methodology, which has high affinity to hexahistidine, and its dissociation constant was as low as 20.8 nM. The structural prediction revealed that AptHis-C contains two connected stem-loop conformations. AptHis-C can only specifically recognize recombinant proteins with the hexahistidine-tag in simple or complex situations, and not to those with other tags. When immobilized on magnetic beads, AptHis-C can be used as a tool for hexahistidine-tagged recombinant protein purification. Its effectiveness is as good as traditional Ni-based beads. Besides, due to the intrinsic characteristics of nucleic acids, such as high thermal/chemical stability, immobilized aptamer-magnetic beads can be reused many times without an obvious decrease of purification effectiveness. This aptamer may represent a novel method for the detection and purification of hexahistidine-tagged recombinant proteins.
Collapse
Affiliation(s)
- Shijia Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanting Liu
- Department of Oncology, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan, China
| | - Hongguang Sun
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Meizuo Zhong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bichun Dai
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Biyao Pan
- Aptamer-Theranostics R&D Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhijian Shen
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| |
Collapse
|
8
|
Chen Y, Ding X, Zhu D, Lin X, Xie Z. Preparation and evaluation of highly hydrophilic aptamer-based hybrid affinity monolith for on-column specific discrimination of ochratoxin A. Talanta 2019; 200:193-202. [PMID: 31036173 DOI: 10.1016/j.talanta.2019.03.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 03/10/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022]
Abstract
Nonspecific adsorption is a challenge of specific recognition on aptamer-based affinity monoliths. Here, a novel highly hydrophilic polyhedral oligomeric silsesquioxane (POSS)-containing aptamer-based hybrid-silica affinity monolith with a good recognition nature was prepared and used for specific discrimination of ochratoxin A (OTA). A homogeneous polymerization mixture consisted of POSS chemicals, hydrophilic monomers and aptamer solution was directly polymerized via the "one-pot" method. Preparation and characterization of the resultant affinity monolith were studied in detail. A highly hydrophilic nature was obtained and the typical hydrophilic interaction liquid chromatography (HILIC) was observed when acetonitrile (ACN) content in mobile phase was 25%, which reached the highest hydrophilicity of POSS-based hybrid monoliths. By using OTA as model analyte, the nonspecific adsorption was effectively suppressed. The recovery of the analogue ochratoxin B (OTB) was only about 0.1% even if the content of OTB was 50 times more than OTA, which was much better than other POSS-containing monoliths and polar siloxane-based hybrid monoliths. Applied to beer samples, the adsorption of background materials was drastically resisted, and efficient recognition of OTA was obtained with the recoveries of 94.9-99.8%. Much less disturbance was observed than that occurred in hydrophobic POSS-based affinity monolith. It lights an attractive implement with high hydrophilicity and specificity for online selective recognition of OTA.
Collapse
Affiliation(s)
- Yiqiong Chen
- Institute of Food Safety and Environment Monitoring, Fuzhou University, Fuzhou 350108, China
| | - Xinyue Ding
- Institute of Food Safety and Environment Monitoring, Fuzhou University, Fuzhou 350108, China
| | - Dandan Zhu
- Institute of Food Safety and Environment Monitoring, Fuzhou University, Fuzhou 350108, China
| | - Xucong Lin
- Institute of Food Safety and Environment Monitoring, Fuzhou University, Fuzhou 350108, China.
| | - Zenghong Xie
- Institute of Food Safety and Environment Monitoring, Fuzhou University, Fuzhou 350108, China
| |
Collapse
|
9
|
Vu CQ, Rotkrua P, Soontornworajit B, Tantirungrotechai Y. Effect of PDGF-B aptamer on PDGFRβ/PDGF-B interaction: Molecular dynamics study. J Mol Graph Model 2018; 82:145-156. [PMID: 29738888 DOI: 10.1016/j.jmgm.2018.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/23/2018] [Accepted: 04/21/2018] [Indexed: 12/27/2022]
Abstract
PDGFRβ/PDGF-B interaction plays a role in angiogenesis, and is mandatory in wound healing and cancer treatment. It has been reported that the PDGF-B aptamer was able to bind to PDGF-B, thus regulating the angiogenesis. However, the binding interaction between the aptamer and the growth factor, including the binding sites, has not been well investigated. This study applied a molecular dynamics (MD) simulation to investigate the aptamer-growth factor interaction in the presence or absence of a receptor (PDGFRβ). Characterization of the structure of an aptamer-growth factor complex revealed binding sites from each section in the complex. Upon the complex formation, PDGF-B and its aptamer exhibited less flexibility in their molecular movement, as indicated by the minimum values of RMSD, RMSF, loop-to-loop distance, and the summation of PCA eigenvalues. Our study of residue pairwise interaction demonstrated that the binding interaction was mainly contributed by electrostatic interaction between the positively-charged amino acid and the negatively-charged phosphate backbone. The role of the PDGF-B aptamer in PDGFRβ/PDGF-B interaction was also investigated. We demonstrated that the stability of the Apt-PDGF-B complex could prevent the presence of a competitor, of PDGFRβ, interrupting the binding process. Because the aptamer was capable of binding with PDGF-B, and blocking the growth factor from the PDGFRβ, it could down regulate the consequent signaling pathway. We provide evidence that the PDGF-BB aptamer is a promising molecule for regulation of angiogenesis. The MD study provides a molecular understanding to modification of the aptamer binding interaction, which could be used in a number of medical applications.
Collapse
Affiliation(s)
- Cong Quang Vu
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand
| | - Pichayanoot Rotkrua
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
| | - Boonchoy Soontornworajit
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand
| | - Yuthana Tantirungrotechai
- Department of Chemistry, Faculty of Science and Technology, Thammasat University, Pathumthani, Thailand.
| |
Collapse
|
10
|
Zhang C, Rodriguez E, Bi C, Zheng X, Suresh D, Suh K, Li Z, Elsebaei F, Hage DS. High performance affinity chromatography and related separation methods for the analysis of biological and pharmaceutical agents. Analyst 2018; 143:374-391. [PMID: 29200216 PMCID: PMC5768458 DOI: 10.1039/c7an01469d] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The last few decades have witnessed the development of many high-performance separation methods that use biologically related binding agents. The combination of HPLC with these binding agents results in a technique known as high performance affinity chromatography (HPAC). This review will discuss the general principles of HPAC and related techniques, with an emphasis on their use for the analysis of biological compounds and pharmaceutical agents. Various types of binding agents for these methods will be considered, including antibodies, immunoglobulin-binding proteins, aptamers, enzymes, lectins, transport proteins, lipids, and carbohydrates. Formats that will be discussed for these methods range from the direct detection of an analyte to indirect detection based on chromatographic immunoassays, as well as schemes based on analyte extraction or depletion, post-column detection, and multi-column systems. The use of biological agents in HPLC for chiral separations will also be considered, along with the use of HPAC as a tool to screen or study biological interactions. Various examples will be presented to illustrate these approaches and their applications in fields such as biochemistry, clinical chemistry, and pharmaceutical research.
Collapse
Affiliation(s)
- Chenhua Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Beloborodov SS, Bao J, Krylova SM, Shala-Lawrence A, Johnson PE, Krylov SN. Aptamer facilitated purification of functional proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1073:201-206. [PMID: 29287247 DOI: 10.1016/j.jchromb.2017.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/15/2017] [Accepted: 12/15/2017] [Indexed: 12/13/2022]
Abstract
DNA aptamers are attractive capture probes for affinity chromatography since, in contrast to antibodies, they can be chemically synthesized and, in contrast to tag-specific capture probes (such as Nickel-NTA or Glutathione), they can be used for purification of proteins free of genetic modifications (such as His or GST tags). Despite these attractive features of aptamers as capture probes, there are only a few reports on aptamer-based protein purification and none of them includes a test of the purified protein's activity, thus, leaving discouraging doubts about method's ability to purify proteins in their active state. The goal of this work was to prove that aptamers could facilitate isolation of active proteins. We refined a complete aptamer-based affinity purification procedure, which takes 4 h to complete. We further applied this procedure to purify two recombinant proteins, MutS and AlkB, from bacterial cell culture: 0.21 mg of 85%-pure AlkB from 4 mL of culture and 0.24 mg of 82%-pure MutS from 0.5 mL of culture. Finally, we proved protein activity by two capillary electrophoresis based assays: an enzymatic assay for AlkB and a DNA-binding assay for MutS. We suggest that in combination with aptamer selection for non-purified protein targets in crude cell lysate, aptamer-based purification provides a means of fast isolation of tag-free recombinant proteins in their native state without the use of antibodies.
Collapse
Affiliation(s)
- Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Agnesa Shala-Lawrence
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
| |
Collapse
|
12
|
Perret G, Boschetti E. Aptamer affinity ligands in protein chromatography. Biochimie 2017; 145:98-112. [PMID: 29054800 DOI: 10.1016/j.biochi.2017.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented. Then the focus is centered on aptamers which represent the last step so far to the long quest for affinity ligands associating very high specificity, availability and strong stability against most harsh cleaning agents required in chromatography. Then technologies of ligand selection from large libraries followed by the most appropriate chemical grafting approaches are described and supported by a number of bibliographic references. Experimental results assembled from relevant published paper are reported; they are selected by their practical applicability and potential use at large scale. The review concludes with specific remarks and future developments that are expected in the near future to turn this technology into a large acceptance for preparative applications.
Collapse
|
13
|
Kong F, Zhang M, Chen J, Fan L, Xiao H, Liu S, Cao C. Continuous protein concentration via free-flow moving reaction boundary electrophoresis. J Chromatogr A 2017; 1508:169-175. [DOI: 10.1016/j.chroma.2017.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
|
14
|
Wedepohl S, Dernedde J, Vahedi-Faridi A, Tauber R, Saenger W, Bulut H. Reducing Macro- and Microheterogeneity of N-Glycans Enables the Crystal Structure of the Lectin and EGF-Like Domains of Human L-Selectin To Be Solved at 1.9 Å Resolution. Chembiochem 2017; 18:1338-1345. [PMID: 28489325 DOI: 10.1002/cbic.201700220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 01/07/2023]
Abstract
L-Selectin, a cell-adhesion receptor on the surface of most leukocytes, contains seven N-glycosylation sites. In order to obtain the crystal structure of human L-selectin, we expressed a shortened version of L-selectin comprising the C-type lectin and EGF-like domains (termed LE) and systematically analysed mutations of the three glycosylation sites (Asn22, Asn66 and Asn139) in order to reduce macroheterogeneity. After we further removed microheterogeneity, we obtained crystals that diffracted X-rays up to 1.9 Å from a variant (LE010) with exchanges N22Q and N139Q and one GlcNAc2 Man5 N-glycan chain attached to Asn66. Crystal-structure analysis showed that the terminal mannose of GlcNAc2 Man5 of one LE010 molecule was coordinated to Ca2+ in the binding site of a symmetry-related LE010. The orientation of the lectin and EGF-like domain was similar to the described "bent" conformation of E- and P-selectins. The Ca2+ -binding site reflects the binding mode seen in E- and P-selectin structures co-crystallised with ligands.
Collapse
Affiliation(s)
- Stefanie Wedepohl
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité Universitätsmedizin Berlin, CVK, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jens Dernedde
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité Universitätsmedizin Berlin, CVK, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195, Berlin, Germany
| | - Rudolf Tauber
- Institut für Laboratoriumsmedizin, Klinische Chemie und Pathobiochemie, Charité Universitätsmedizin Berlin, CVK, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195, Berlin, Germany
| | - Haydar Bulut
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195, Berlin, Germany
| |
Collapse
|
15
|
|
16
|
Single-Step Purification of Monomeric l-Selectin via Aptamer Affinity Chromatography. SENSORS 2017; 17:s17020226. [PMID: 28125045 PMCID: PMC5336075 DOI: 10.3390/s17020226] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 12/20/2022]
Abstract
l-selectin is a transmembrane receptor expressed on the surface of white blood cells and responsible for the tethering of leukocytes to vascular endothelial cells. This initial intercellular contact is the first step of the complex leukocyte adhesion cascade that ultimately permits extravasation of leukocytes into the surrounding tissue in case of inflammation. Here we show the binding of a soluble histidine tagged l-selectin to a recently described shortened variant of an l-selectin specific DNA aptamer with surface plasmon resonance. The high specificity of this aptamer in combination with its high binding affinity of ~12 nM, allows for a single-step protein purification from cell culture supernatants. In comparison to the well-established Ni-NTA based technology, aptamer affinity chromatography (AAC) was easier to establish, resulted in a 3.6-fold higher protein yield, and increased protein purity. Moreover, due to target specificity, the DNA aptamer facilitated binding studies directly from cell culture supernatant, a helpful characteristic to quickly monitor successful expression of biological active l-selectin.
Collapse
|
17
|
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.
Collapse
Affiliation(s)
| | | | | | | | - Frédéric Ducongé
- CEA, I2BM, MIRCen, UMR 9199, Université Paris Saclay, Fontenay aux Roses, France
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Chen Y, Deng N, Wu C, Liang Y, Jiang B, Yang K, Liang Z, Zhang L, Zhang Y. Aptamer functionalized hydrophilic polymer monolith with gold nanoparticles modification for the sensitive detection of human α-thrombin. Talanta 2016; 154:555-9. [DOI: 10.1016/j.talanta.2016.02.054] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/18/2016] [Accepted: 02/23/2016] [Indexed: 12/15/2022]
|
19
|
Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers. J Nucleic Acids 2016; 2016:9718612. [PMID: 27042344 PMCID: PMC4794571 DOI: 10.1155/2016/9718612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/17/2016] [Indexed: 01/10/2023] Open
Abstract
Immobilization of nucleic acid aptamer recognition elements selected free in solution onto the surface of biosensor platforms has proven challenging. This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications. The results indicate a minimum distance (linker length) from the surface and thymine nucleobase linker provides reproducible binding across varying conditions. An indirect labeling method, where the target was labeled with a biotin followed by a brief Cy3-streptavidin incubation, provided a higher signal-to-noise ratio and over two orders of magnitude improvement in limit of detection, compared to direct Cy3-protein labeling. We also showed that the affinities of the aptamer/target interaction can change between direct and indirect labeling and conditions to optimize for the highest fluorescence intensity will increase the sensitivity of the assay but will not change the overall affinity. Additionally, some sequences which did not initially bind demonstrated binding when conditions were optimized. These results, in combination with studies demonstrating enhanced binding in nonselection buffers, provided insights into the structure and affinity of aptamers critical for biosensor applications and allowed for generalizations in starting conditions for researchers wishing to investigate aptamers on a microarray surface.
Collapse
|
20
|
Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
Collapse
Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
| |
Collapse
|
21
|
Use of aptamers in immunoassays. Mol Immunol 2016; 70:149-54. [PMID: 26774749 DOI: 10.1016/j.molimm.2015.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/02/2015] [Accepted: 12/15/2015] [Indexed: 12/19/2022]
Abstract
Aptamers, short single-chain DNA or RNA oligonucleotides, react specifically with small molecules, as well as with proteins. Unlike antibodies, they may be obtained relatively easily. Aptamers are now widely employed in immunological studies and could replace antibodies in immunoassays. In this short review, methods for immobilizing aptamers on various insoluble materials (so-called apta-sorbents) are described. Recent findings on their use in the detection and isolation of immunoglobulins and their application in various immunoassays are also discussed.
Collapse
|
22
|
Riese SB, Buscher K, Enders S, Kuehne C, Tauber R, Dernedde J. Structural requirements of mono- and multivalent L-selectin blocking aptamers for enhanced receptor inhibition in vitro and in vivo. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:901-908. [PMID: 26772426 DOI: 10.1016/j.nano.2015.12.379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 08/28/2015] [Accepted: 12/24/2015] [Indexed: 01/08/2023]
Abstract
UNLABELLED L-selectin mediates extravasation of leukocytes from blood into the surrounding tissue during inflammation and is therefore a therapeutical target in certain overwhelming immune reactions. In this study, we characterized an L-selectin specific blocking DNA aptamer with respect to nucleotide composition and target binding. Introduction of deletions and nucleotide exchanges resulted in an optimized DNA sequence but preservation of the IC50 in the low nanomolar range. The inhibitory potential was significantly increased when the aptamer was displayed as a di- and trimer connected via appropriate linker length. Similar to monoclonal antibodies, trimer yielded picomolar IC50 values in a competitive binding assay. In comparison to the monovalent aptamer, the trivalent assembly reduced PBMC interactions to L-selectin ligands 90-fold under shear and exerted superior inhibition of PBMC rolling in vivo. In conclusion, our work demonstrates the feasibility of optimizing aptamer sequences and shows that multivalent ligand presentation enables superior adhesion receptor targeting. FROM THE CLINICAL EDITOR During inflammation, leukocytes extravasate from blood vessels under chemotaxic signals. The presence of L-selectin on endothelium acts as a mediator for the extravasation process. In this study, the authors investigated an L-selectin specific blocking DNA aptamer in various forms, as inhibitors to leukocyte binding and extravasation. This new approach confirmed the potential use of aptamers in clinical setting.
Collapse
Affiliation(s)
- Sebastian B Riese
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Konrad Buscher
- Institute for Physiological Chemistry Pathobiochemistry, University of Muenster, Muenster, Germany; Department of Nephrology and Rheumatology, University Hospital Muenster, Muenster, Germany.
| | - Sven Enders
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Christian Kuehne
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Rudolf Tauber
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Jens Dernedde
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Cywiński PJ, Olejko L, Löhmannsröben HG. A time-resolved luminescent competitive assay to detect L-selectin using aptamers as recognition elements. Anal Chim Acta 2015; 887:209-215. [PMID: 26320804 DOI: 10.1016/j.aca.2015.06.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 12/01/2022]
Abstract
L-selectin is a protein with potential importance for numerous diseases and clinical disorders. In this paper, we present a new aptamer-based luminescent assay developed to detect L-selectin. The sensing system working principle is based on Förster Resonance Energy Transfer (FRET) from a donor terbium complex (TbC) to an acceptor cyanine dye (Cy5). In the present approach, the biotinylated aptamer is combined with Cy5-labelled streptavidin (Cy5-Strep) to yield an aptamer-based acceptor construct (Apta-Cy5-Strep), while L-selectin is conjugated using luminescent TbC. Upon aptamer binding to the TbC-labelled L-selectin (L-selectin-TbC), permanent donor-acceptor proximity is established which allows for radiationless energy transfer to occur. However, when unlabelled L-selectin is added, it competes with the L-selectin-TbC and the FRET signal decreases as the L-selectin concentration increases. FRET from the TbC to Cy5 was observed with time-gated time-resolved luminescence spectroscopy. A significant change in the corrected luminescence signal was observed in the dynamic range of 10-500 ng/mL L-selectin, the concentration range relevant for accelerated cognitive decline of Alzheimer's disease, with a limit of detection (LOD) equal to 10 ng/mL. The aptasensor-based assay is homogeneous and can be realized within one hour. Therefore, this method has the potential to become an alternative to tedious heterogeneous analytical methods, e.g. based on enzyme-linked immunosorbent assay (ELISA).
Collapse
Affiliation(s)
- Piotr J Cywiński
- Functional Materials and Devices, Fraunhofer Institute for Applied Polymer Research, Geiselberstr.69, 14476 Potsdam-Golm, Germany; Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany.
| | - Lydia Olejko
- Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Hans-Gerd Löhmannsröben
- Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| |
Collapse
|
25
|
Yu J, Yang L, Liang X, Dong T, Liu H. Reversible regulation of thrombin adsorption and desorption based on photoresponsive-aptamer modified gold nanoparticles. Talanta 2015; 144:312-7. [PMID: 26452827 DOI: 10.1016/j.talanta.2015.06.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/11/2015] [Accepted: 06/20/2015] [Indexed: 10/23/2022]
Abstract
In the protein separation, adsorption and desorption of target protein have been using different buffer condition. Different buffer will change the structure and activity of target protein in some cases. This work describes the use of different wavelength light for remote regulation of adsorption and desorption of target protein in the same buffer solutions. A dynamic system that captured and released protein in response to light is reported. Matrix gold nanoparticles and light-responsive affinity ligand comprising thrombin aptamer (APT15), polyethylene glycol linker, and azobenzene-modified complementary sequence were used. UV light induced a trans-cis isomerization of the azobenzene that destabilized the duplex of aptamer and azobenzene-modified complementary sequence, resulting in thrombin binding to aptamer sequence. Visible light irradiation resulted in DNA duplex rehybridization and thrombin released. Our work demonstrates that different light wavelengths effectively regulated the adsorption and desorption of thrombin in the same buffer, and this system also can capture and release prothrombin from plasma with different wavelength light. Furthermore, this method can be widely applied to a variety of different protein separation process.
Collapse
Affiliation(s)
- Jiemiao Yu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Liangrong Yang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Xiangfeng Liang
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Tingting Dong
- Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huizhou Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Key Laboratory of Green Process and Engineering, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| |
Collapse
|
26
|
Ahirwar R, Nahar P. Development of an aptamer-affinity chromatography for efficient single step purification of Concanavalin A from Canavalia ensiformis. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 997:105-9. [PMID: 26102634 DOI: 10.1016/j.jchromb.2015.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/27/2015] [Accepted: 06/04/2015] [Indexed: 11/25/2022]
Abstract
Herein, an aptamer-based affinity chromatography method for rapid and single step purification of Concanavalin A is developed and validated. We have used a 41ntssDNA aptamer of Con A (Con A aptabody) as an affinity reagent in the developed aptamer-affinity chromatography. Stationary phase of the method consists of surface functionalized agarose beads carrying covalently immobilized Con A-aptabody. Affinity purification of Con A from jack bean (Canavalia ensiformis) seed using developed aptamer-affinity columns has resulted in ≥66% recovery with 90% purity and 336-fold purification of Con A. The developed aptamer-affinity chromatography has shown efficient scalability and consistent purification when analysed over 13mm, 20mm and 25mm diameter columns having a bed height of 60mm each. Also, the developed aptamer-agarose columns were found to be reusable with recovery decrease of 12.9% in seven sequential cycles of purification. Therefore, the developed aptamer-affinity chromatography provides a novel, efficient and single-step methodology for isolation and purification of Con A.
Collapse
Affiliation(s)
- Rajesh Ahirwar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
| | - Pradip Nahar
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India.
| |
Collapse
|
27
|
Du F, Guo L, Qin Q, Zheng X, Ruan G, Li J, Li G. Recent advances in aptamer-functionalized materials in sample preparation. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
28
|
|
29
|
Qiao L, Lv B, Feng X, Li C. A new application of aptamer: One-step purification and immobilization of enzyme from cell lysates for biocatalysis. J Biotechnol 2015; 203:68-76. [PMID: 25835950 DOI: 10.1016/j.jbiotec.2015.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 12/24/2022]
Abstract
Aptamers are nucleic acid-based high affinity ligands that are able to capture their corresponding target through molecular recognition. In this study, several DNA aptamers with high affinity and specificity for β-glucuronidases (PGUS-E) were obtained by our modified SELEX method. Among them, Apt5 and Apt9 were selected as representatives and covalently linked to magnetic beads, respectively. The aptamer-modified magnetic beads were characterized and successfully applied to one-step purification and immobilization of PGUS-E from the complex cell lysates. By conveniently adjusting the pH and ion strength, the PGUS-E purities reached 84% for Apt5-modified beads and 88% for Apt9-modified beads. Moreover, the maximum PGUS-E capturing capacity of the Apt5 and Apt9 modified magnetic beads were found to be 31.75μg/mg and 32.95μg/mg, respectively. The immobilized PGUS-E on aptamer-based magnetic beads showed good reusability, and the conversion of glycyrrhizin still remained more than 70% after 7 cycles. In addition, the aptamer-modified beads support can be easily regenerated, and the conversion rate of glycyrrhizin (GL) was still 62% after the 7th cycle of regeneration. This investigation can be easily extended to other enzyme systems and may help open a generic route to develop a novel enzyme immobilization technology for biocatalysis based on aptamer.
Collapse
Affiliation(s)
- Lifeng Qiao
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, Xinjiang, PR China
| | - Bo Lv
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xudong Feng
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Chun Li
- School of Life Science and Technology, Beijing Institute of Technology, Beijing, 100081, PR China.
| |
Collapse
|
30
|
He X, Chen J, Yie SM, Ye SR, Dong DD, Li K. Using a sequence of estrogen response elements as a DNA aptamer for estrogen receptors in vitro. Nucleic Acid Ther 2015; 25:152-61. [PMID: 25734367 DOI: 10.1089/nat.2014.0521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Estrogen receptors (ERs) are overexpressed in approximately 70% of breast cancer cases, and they play an important role in tumorigenesis. ERs are strong predictive factors for measuring responses to hormonal therapies. Aptamers are short and single stranded oligonucleotides that are able to recognize target molecules with high affinity. In the present study, we selected and synthesized an oligonucleotide, which has a similar sequence to estrogen response element in the Xenopus Vitellogenin A2 gene. The synthesized oligonucleotide was evaluated by using immunostaining of paraffin-embedded breast cancer tissues and treating MCF-7 human mammary carcinoma cell line in vitro. We found that the synthesized oligonucleotide had a high binding affinity to ER similar to estradiol. Using a specific anti-ER antibody as a standard control, we showed that the synthesized oligonucleotide specifically recognized and immunostained tumor cells of breast cancer without cross-reaction with normal tissues. The overall agreement of ER detection between the anti-ER antibody and the ER aptamer was 97.1% (kappa value=0.943; 95% CI=0.879-1.006; p<0.002). Similar to tamoxifen or fulvestrant, the oligonucleotide also had an inhibitory effect on cell proliferation of MCF-7 cell line in a dose- and time-dependent fashion but had no cytotoxic effect on human normal mammary epithelial cells. Therefore, the synthesized oligonucleotide may be used as an aptamer for immunostaining of paraffin-embedded tissue sections for breast cancer diagnosis, as well as a potential ER antagonist in the treatment of breast cancer.
Collapse
Affiliation(s)
- Xu He
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jie Chen
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Shang-mian Yie
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.,2Research and Development Center, Sichuan HeLi Bio-pharmaceutical Co. Ltd., Sichuan HeBang Group, Chengdu, Sichuan, China
| | - Shang-rong Ye
- 2Research and Development Center, Sichuan HeLi Bio-pharmaceutical Co. Ltd., Sichuan HeBang Group, Chengdu, Sichuan, China
| | - Dan-Dan Dong
- 3Department of Pathology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Ke Li
- 3Department of Pathology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| |
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- Guohong Zhu
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstr. 5, 30167, Hannover, Germany
| | | |
Collapse
|
32
|
Abstract
Affinity chromatography is one of the most selective and versatile forms of liquid chromatography for the separation or analysis of chemicals in complex mixtures. This method makes use of a biologically related agent as the stationary phase, which provides an affinity column with the ability to bind selectively and reversibly to a given target in a sample. This review examines the early work in this method and various developments that have lead to the current status of this technique. The general principles of affinity chromatography are briefly described as part of this discussion. Past and recent efforts in the generation of new binding agents, supports, and immobilization methods for this method are considered. Various applications of affinity chromatography are also summarized, as well as the influence this field has played in the creation of other affinity-based separation or analysis methods.
Collapse
Affiliation(s)
- David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, 704 Hamilton Hall, 639 N 12 Street, Lincoln, NE, 68588-0304, USA,
| | | |
Collapse
|
33
|
Brothier F, Pichon V. Miniaturized DNA aptamer-based monolithic sorbent for selective extraction of a target analyte coupled on-line to nanoLC. Anal Bioanal Chem 2014; 406:7875-86. [PMID: 25335821 DOI: 10.1007/s00216-014-8256-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 10/01/2014] [Accepted: 10/08/2014] [Indexed: 10/24/2022]
Abstract
A complete characterization of a novel target-specific DNA aptamer-based miniaturized solid phase extraction (SPE)-sorbent coupled on-line to nanoLC is presented. A miniaturized oligosorbent (mOS) was prepared via the in situ sol-gel synthesis of a hybrid organic-inorganic monolith in 100 μm i.d. capillary columns using tetraethoxysilane and 3-aminopropyltriethoxysilane as precursors, followed by covalent binding of a 5'-amino-modified DNA aptamer with a C12 spacer arm specific for a molecule of small molecular weight. Ochratoxin A (OTA), one of the most abundant naturally occurring mycotoxins, was chosen as model analyte to demonstrate the principle of such an approach. The mOS was coupled on-line to RP-nanoLC-LIF. Selective extraction of OTA on several mOSs was demonstrated with an average extraction recovery above 80 % when percolating spiked binding buffer and a low recovery on control monoliths grafted with a non-specific aptamer. Reproducibility of mOSs preparation was highlighted by comparing extraction yields. Otherwise, the mOSs demonstrated no cross-reactivity towards an OTA structural analogue, i.e., ochratoxin B. Due to the high specific surface area of the hybrid silica-based monolith, the coverage density of DNA aptamers covalently immobilized in the capillaries was very high and reached 6.27 nmol μL(-1), thus leading to a capacity above 5 ng of OTA. This miniaturized device was then applied to the selective extraction of OTA from beer samples. It revealed to be effective in isolating OTA from this complex matrix, thus improving the reliability of its analysis at the trace level.
Collapse
Affiliation(s)
- Fabien Brothier
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM)-UMR CBI 8231 (CNRS-ESPCI), ESPCI ParisTech, PSL Research University, 10 rue Vauquelin, 75231, Paris Cedex 05, France
| | | |
Collapse
|
34
|
Aptamer-based-sorbents for sample treatment--a review. Anal Bioanal Chem 2014; 407:681-98. [PMID: 25286873 DOI: 10.1007/s00216-014-8129-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 10/24/2022]
Abstract
To improve selectivity during sample pretreatment, various selective tools inducing a molecular recognition mechanism during the extraction procedure have been developed, such as sorbents constituted of immobilized antibodies, i.e., immunosorbents, or molecularly imprinted polymers. More recently, as an alternative to both previous approaches, aptamers immobilized onto a solid support, i.e., oligosorbents, were proposed. Thanks to the high affinity and high selectivity of the interaction that some aptamers offer toward some target analytes, they also provide powerful techniques that make selective extraction and the concentration of a target analyte from liquid matrices in one step or sample purification of extracts from solid matrices possible. This review describes the development and the properties of these oligosorbents developed for different types of targets-pharmaceuticals, mycotoxins, proteins, cells, etc. After describing the immobilization procedures, we discuss different parameters characterizing the potential of aptamer-based supports as extraction sorbents. Close relations exist between extraction recoveries and the affinity and amounts of aptamers immobilized on the extraction device. In addition, analyte-aptamer interactions may be affected by matrix components and by additives in the samples. This may also lower extraction recoveries and affect the stability and the possible reusability of the aptamer-based sorbent. All these points are discussed and illustrated. Numerous examples of applications of these sorbents to the treatment of complex samples such as food samples, environmental samples, and biological fluids are also reported. Their association with analytical devices, from conventional to miniaturized analytical systems, is also discussed.
Collapse
|
35
|
Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. MOLECULAR THERAPY-NUCLEIC ACIDS 2014; 3:e201. [PMID: 25291143 PMCID: PMC4217074 DOI: 10.1038/mtna.2014.49] [Citation(s) in RCA: 347] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022]
Abstract
Limited chemical diversity of nucleic acid libraries has long been suspected to be a major constraining factor in the overall success of SELEX (Systematic Evolution of Ligands by EXponential enrichment). Despite this constraint, SELEX has enjoyed considerable success over the past quarter of a century as a result of the enormous size of starting libraries and conformational richness of nucleic acids. With judicious introduction of functional groups absent in natural nucleic acids, the “diversity gap” between nucleic acid–based ligands and protein-based ligands can be substantially bridged, to generate a new class of ligands that represent the best of both worlds. We have explored the effect of various functional groups at the 5-position of uracil and found that hydrophobic aromatic side chains have the most profound influence on the success rate of SELEX and allow the identification of ligands with very low dissociation rate constants (named Slow Off-rate Modified Aptamers or SOMAmers). Such modified nucleotides create unique intramolecular motifs and make direct contacts with proteins. Importantly, SOMAmers engage their protein targets with surfaces that have significantly more hydrophobic character compared with conventional aptamers, thereby increasing the range of epitopes that are available for binding. These improvements have enabled us to build a collection of SOMAmers to over 3,000 human proteins encompassing major families such as growth factors, cytokines, enzymes, hormones, and receptors, with additional SOMAmers aimed at pathogen and rodent proteins. Such a large and growing collection of exquisite affinity reagents expands the scope of possible applications in diagnostics and therapeutics.
Collapse
|
36
|
Rozenblum GT, Kaufman T, Vitullo AD. Myelin Basic Protein and a Multiple Sclerosis-related MBP-peptide Bind to Oligonucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e192. [PMID: 25202925 PMCID: PMC4222649 DOI: 10.1038/mtna.2014.43] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/24/2014] [Indexed: 02/07/2023]
Abstract
Aptamer ligands for myelin basic protein (MBP) were obtained using the systematic evolution of ligand by exponential enrichment (SELEX) method. Two clones were isolated from a pool of oligonucleotides and tested for MBP targeting. Using purified MBP, we demonstrated the binding activity of the aptamers and we also showed the affinity of MBP for oligonucleotides of specific length. Moreover, one selected aptamer competitively inhibited the binding of an MBP-specific antibody to MBP and the aptamer was found more sensitive than a commercial antibody. In addition, we showed the ability of the aptamer to detect myelin-rich regions in paraffin-embedded mouse brain tissue. Therefore, the MBP-binding activity of the selected oligonucleotide may prove useful as a tool for life science and medical research for myelin detection and might be a good lead for testing it in autoimmune diseases such as multiple sclerosis.
Collapse
Affiliation(s)
- Guido Tomás Rozenblum
- Departamento de Investigaciones Biomédicas y Biotecnológicas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD-Universidad Maimónides, Buenos Aires, Argentina
| | - Tomás Kaufman
- Departamento de Investigaciones Biomédicas y Biotecnológicas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD-Universidad Maimónides, Buenos Aires, Argentina
| | - Alfredo Daniel Vitullo
- Departamento de Investigaciones Biomédicas y Biotecnológicas, Centro de Estudios Biomédicos, Biotecnológicos, Ambientales y Diagnóstico, CEBBAD-Universidad Maimónides, Buenos Aires, Argentina
| |
Collapse
|
37
|
Lee JW, Cho JH, Cho EJ. Aptamer-based optical switch for biosensors. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.3.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
38
|
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
| |
Collapse
|
39
|
Saraswat M, Musante L, Ravidá A, Shortt B, Byrne B, Holthofer H. Preparative purification of recombinant proteins: current status and future trends. BIOMED RESEARCH INTERNATIONAL 2013; 2013:312709. [PMID: 24455685 PMCID: PMC3877584 DOI: 10.1155/2013/312709] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/17/2013] [Indexed: 12/18/2022]
Abstract
Advances in fermentation technologies have resulted in the production of increased yields of proteins of economic, biopharmaceutical, and medicinal importance. Consequently, there is an absolute requirement for the development of rapid, cost-effective methodologies which facilitate the purification of such products in the absence of contaminants, such as superfluous proteins and endotoxins. Here, we provide a comprehensive overview of a selection of key purification methodologies currently being applied in both academic and industrial settings and discuss how innovative and effective protocols such as aqueous two-phase partitioning, membrane chromatography, and high-performance tangential flow filtration may be applied independently of or in conjunction with more traditional protocols for downstream processing applications.
Collapse
Affiliation(s)
- Mayank Saraswat
- Centre for Bioanalytical Sciences (CBAS), Dublin City University (DCU), Dublin 9, Ireland
| | - Luca Musante
- Centre for Bioanalytical Sciences (CBAS), Dublin City University (DCU), Dublin 9, Ireland
| | - Alessandra Ravidá
- Centre for Bioanalytical Sciences (CBAS), Dublin City University (DCU), Dublin 9, Ireland
| | - Brian Shortt
- Centre for Bioanalytical Sciences (CBAS), Dublin City University (DCU), Dublin 9, Ireland
| | - Barry Byrne
- Centre for Bioanalytical Sciences (CBAS), Dublin City University (DCU), Dublin 9, Ireland
| | - Harry Holthofer
- Centre for Bioanalytical Sciences (CBAS), Dublin City University (DCU), Dublin 9, Ireland
| |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Filip Radom
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
| | | | | | | | | |
Collapse
|
41
|
Šmuc T, Ahn IY, Ulrich H. Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics. J Pharm Biomed Anal 2013; 81-82:210-7. [PMID: 23666257 DOI: 10.1016/j.jpba.2013.03.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/11/2013] [Accepted: 03/20/2013] [Indexed: 02/07/2023]
Abstract
Aptamers are small nucleic acid molecules capable of binding to a wide range of target molecules with high affinity and specificity. They have been developed and widely used not only as research tools, but also as biosensors, specific antagonists, and diagnostic markers and as protein purification platform for many pharmaceutical and clinical applications. Here, in this paper we will explore biochemical aspects of aptamer-target interactions and show why aptamers rival antibodies in target recognition and purification procedures. This review will focus on strategies of using aptamers as affinity ligands for molecules of therapeutic and pharmaceutical interest including applications in chromatography and capillary electrophoresis for protein and small molecule purification. Moreover, we will also discuss aptamers whose binding parameters can be controlled on demand for diagnostic approaches and used as sensitive receptors in biosensorics. Aptamers have opened up exciting fields in basic and applied research of pharmaceutical and biotechnological interest.
Collapse
Affiliation(s)
- Tina Šmuc
- Laboratory for Bio-instrumentation, Centre of Excellence for Biosensors, Instrumentation and Process Control, Velika pot 22, 5250 Solkan, Slovenia
| | | | | |
Collapse
|
42
|
Augusto F, Hantao LW, Mogollón NG, Braga SC. New materials and trends in sorbents for solid-phase extraction. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2012.08.012] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
43
|
|
44
|
Yoshida Y, Waga I, Horii K. Quantitative and sensitive protein detection strategies based on aptamers. Proteomics Clin Appl 2012; 6:574-80. [PMID: 22996907 DOI: 10.1002/prca.201200037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 01/24/2023]
Abstract
Aptamers are functional oligonucleotides of single-stranded RNA or DNA that can selectively recognize their targets with high affinity. Hence, they have been widely developed for analytical, diagnostic, and therapeutic applications. In this review, we have summarized recent advances in the development of aptamer-based detection systems. Aptamers can be amplified exponentially by PCR, which is one of the advantages of aptamers over antibodies. Recently, we have developed immuno-aptamers that bind to mouse or rabbit IgG and constructed a novel sensitive detection system based on a conventional ELISA, called the immuno-aptamer PCR assay. In this article, the aptamer-based ready-to-use sensors and another PCR-based aptamer assays are also described; moreover, we have discussed highly sensitive aptamer-based detection systems.
Collapse
|
45
|
Tippkötter N, Al-Kaidy H, Wollny S, Ulber R. Functionalized Magnetizable Particles for Downstream Processing in Single-Use Systems. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201200130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
46
|
Han B, Zhao C, Yin J, Wang H. High performance aptamer affinity chromatography for single-step selective extraction and screening of basic protein lysozyme. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 903:112-7. [PMID: 22841745 DOI: 10.1016/j.jchromb.2012.07.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 07/04/2012] [Accepted: 07/11/2012] [Indexed: 12/24/2022]
Abstract
A DNA aptamer based high-performance affinity chromatography is developed for selective extraction and screening of a basic protein lysozyme. First, a poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolithic column was synthesized in situ by thermally initiated radical polymerization, and then an anti-lysozyme DNA aptamer was covalently immobilized on the surface of the monolith through a 16-atom spacer arm. The target protein lysozyme but non-target proteins can be trapped by the immobilized anti-lysozyme DNA aptamer. In contrast, lysozyme cannot be trapped by the immobilized oligodeoxynucleotide that does not contain the sequence of the anti-lysozyme DNA aptamer. The study clearly demonstrates the trapping of lysozyme by the immobilized anti-lysozyme DNA aptamer is mainly due to specific recognition rather than simple electrostatic interaction of positively charged protein and the negatively charged DNA. The inter-day precision was determined as 0.8% for migration time and 4.2% for peak area, respectively. By the use of aptamer affinity monolith, a screening strategy is developed to selectively extract lysozyme from chicken egg white, showing the advantages of high efficiency, low cost and ease-of-operation.
Collapse
Affiliation(s)
- Bin Han
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100086, PR China
| | | | | | | |
Collapse
|
47
|
Walter JG, Stahl F, Scheper T. Aptamers as affinity ligands for downstream processing. Eng Life Sci 2012. [DOI: 10.1002/elsc.201100197] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Johanna-Gabriela Walter
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| | - Frank Stahl
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| | - Thomas Scheper
- Institut für Technische Chemie; Leibniz Universität Hannover; Callinstr. 3; 30167; Hannover; Germany
| |
Collapse
|
48
|
Nakamura Y, Ishiguro A, Miyakawa S. RNA plasticity and selectivity applicable to therapeutics and novel biosensor development. Genes Cells 2012; 17:344-64. [PMID: 22487172 PMCID: PMC3444689 DOI: 10.1111/j.1365-2443.2012.01596.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 02/03/2012] [Indexed: 12/25/2022]
Abstract
Aptamers are short, single-stranded nucleic acid sequences that are selected in vitro from large oligonucleotide libraries based on their high affinity to a target molecule. Hence, aptamers can be thought of as a nucleic acid analog to antibodies. However, several viewpoints hold that the potential of aptamers arises from interesting characteristics that are distinct from, or in some cases, superior to those of antibodies. This review summarizes the recent achievements in aptamer programs developed in our laboratory against basic and therapeutic protein targets. Through these studies, we became aware of the remarkable conformational plasticity and selectivity of RNA, on which the published report has not shed much light even though this is evidently a crucial feature for the strong specificity and affinity of RNA aptamers.
Collapse
Affiliation(s)
- Yoshikazu Nakamura
- Department of Basic Medical Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | | | | |
Collapse
|
49
|
Donovan MJ, Meng L, Gulbakan B, Chen Y, Parekh P, Sefah K, Tan W. Aptamer Moieties in Biochemical Applications. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
50
|
Hage DS, Anguizola JA, Bi C, Li R, Matsuda R, Papastavros E, Pfaunmiller E, Vargas J, Zheng X. Pharmaceutical and biomedical applications of affinity chromatography: recent trends and developments. J Pharm Biomed Anal 2012; 69:93-105. [PMID: 22305083 DOI: 10.1016/j.jpba.2012.01.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/04/2012] [Accepted: 01/06/2012] [Indexed: 10/14/2022]
Abstract
Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered.
Collapse
Affiliation(s)
- David S Hage
- Chemistry Department, University of Nebraska, Lincoln, NE 68588-0304, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|