1
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Wang L, Yao L, Ma Q, Mao Y, Qu H, Zheng L. Investigation on small molecule-aptamer dissociation equilibria based on antisense displacement probe. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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2
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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: 16] [Impact Index Per Article: 16.0] [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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3
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Drees A, Trinh TL, Fischer M. The Influence of Protein Charge and Molecular Weight on the Affinity of Aptamers. Pharmaceuticals (Basel) 2023; 16:ph16030457. [PMID: 36986556 PMCID: PMC10054347 DOI: 10.3390/ph16030457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/13/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Aptamers offer several advantages over antibodies. However, to ensure high affinity and specificity, a better understanding of the interactions between the nucleic-acid-based aptamers and their targets is mandatory. Therefore, we investigated the influence of two physical properties of proteins-molecular mass and charge-on the affinity of nucleic-acid-based aptamers. For this purpose, first, the affinity of two random oligonucleotides towards twelve proteins was determined. No binding was observed for proteins with a negative net charge towards the two oligonucleotides, while up to nanomolar affinity was determined for positively charged proteins with a high pI value. Second, a literature analysis comprising 369 aptamer-peptide/protein pairs was performed. The dataset included 296 different target peptides and proteins and is thus currently one of the largest databases for aptamers for proteins and peptides. The targets considered covered isoelectric points of 4.1-11.8 and a molecular weight range of 0.7-330 kDa, while the dissociation constants ranged from 50 fM to 29.5 µM. This also revealed a significant inverse correlation between the protein's isoelectric point and the affinity of aptamers. In contrast, no trend was observed between the affinity and the molecular weight of the target protein with either approach.
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Affiliation(s)
- Alissa Drees
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Tung Lam Trinh
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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4
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Assays to Estimate the Binding Affinity of Aptamers. Talanta 2022; 238:122971. [PMID: 34857318 DOI: 10.1016/j.talanta.2021.122971] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.
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5
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Ouyang Y, Biniuri Y, Fadeev M, Zhang P, Carmieli R, Vázquez-González M, Willner I. Aptamer-Modified Cu 2+-Functionalized C-Dots: Versatile Means to Improve Nanozyme Activities-"Aptananozymes". J Am Chem Soc 2021; 143:11510-11519. [PMID: 34286967 PMCID: PMC8856595 DOI: 10.1021/jacs.1c03939] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The covalent linkage of aptamer binding
sites to nanoparticle nanozymes
is introduced as a versatile method to improve the catalytic activity
of nanozymes by concentrating the reaction substrates at the catalytic
nanozyme core, thereby emulating the binding and catalytic active-site
functions of native enzymes. The concept is exemplified with the synthesis
of Cu2+ ion-functionalized carbon dots (C-dots), modified
with the dopamine binding aptamer (DBA) or the tyrosinamide binding
aptamer (TBA), for the catalyzed oxidation of dopamine to aminochrome
by H2O2 or the oxygenation of l-tyrosinamide
to the catechol product, which is subsequently oxidized to amidodopachrome,
in the presence of H2O2/ascorbate mixture. Sets
of structurally functionalized DBA-modified Cu2+ ion-functionalized
C-dots or sets of structurally functionalized TBA-modified Cu2+ ion-functionalized C-dots are introduced as nanozymes of
superior catalytic activities (aptananozymes) toward the oxidation
of dopamine or the oxygenation of l-tyrosinamide, respectively.
The aptananozymes reveal enhanced catalytic activities as compared
to the separated catalyst and respective aptamer constituents. The
catalytic functions of the aptananozymes are controlled by the structure
of the aptamer units linked to the Cu2+ ion-functionalized
C-dots. In addition, the aptananozyme shows chiroselective catalytic
functions demonstrated by the chiroselective-catalyzed oxidation of l/d-DOPA to l/d-dopachrome. Binding
studies of the substrates to the different aptananozymes and mechanistic
studies associated with the catalytic transformations are discussed.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yonatan Biniuri
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Fadeev
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Pu Zhang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Raanan Carmieli
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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6
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Schnichels S, Hurst J, de Vries JW, Ullah S, Frößl K, Gruszka A, Löscher M, Bartz-Schmidt KU, Spitzer MS, Herrmann A. Improved Treatment Options for Glaucoma with Brimonidine-Loaded Lipid DNA Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9445-9456. [PMID: 33528240 DOI: 10.1021/acsami.0c18626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Glaucoma is the second leading cause of irreversible blindness worldwide. Among others, elevated intraocular pressure (IOP) is one of the hallmarks of the disease. Antiglaucoma drugs such as brimonidine can lower the IOP but their adherence to the ocular surface is low, leading to a low drug uptake. This results in a frequent dropping regime causing low compliance by the patients. Lipid DNA nanoparticles (NPs) have the intrinsic ability to bind to the ocular surface and can be loaded with different drugs. Here, we report DNA NPs functionalized for loading of brimonidine through specific aptamers and via hydrophobic interactions with double stranded micelles. Both NP systems exhibited improved affinity toward the cornea and retained release of the drug as compared to controls both in vitro and in vivo. Both NP types were able to lower the IOP in living animals significantly more than pristine brimonidine. Importantly, the brimonidine-loaded NPs showed no toxicity and improved efficacy and hence should improve compliance. In conclusion, this drug-delivery system offers high chances of an improved treatment for glaucoma and thus preserving vision in the aging population.
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Affiliation(s)
- Sven Schnichels
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - José Hurst
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Jan Willem de Vries
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Sami Ullah
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Katharina Frößl
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Agnieszka Gruszka
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Marina Löscher
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Karl-Ulrich Bartz-Schmidt
- Centre for Ophthalmology, University Eye Hospital Tübingen, Elfriede-Aulhorn-Straße 7, Tübingen D-72076, Germany
| | - Martin S Spitzer
- Clinic for Ophthalmology, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, Hamburg D-20246, Germany
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstrasse 50, Aachen 52056, Germany
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, Aachen 52074, Germany
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7
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Chen Y, Jiang B, Yuan H, Zhu X, Liu J, Zhang X, Liang Z, Wang L, Zhang L, Zhang Y. Fully integrated protein absolute quantification platform for analysis of multiple tumor markers in human plasma. Talanta 2021; 226:122102. [PMID: 33676658 DOI: 10.1016/j.talanta.2021.122102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 11/18/2022]
Abstract
In this study, we developed a fully integrated protein absolute quantification platform for simultaneous analysis of multiple tumor markers in human plasma, by which multiple target proteins (alpha-fetoprotein, prostate-specific antigen, carcino-embryonic antigen and mucin-1) were firstly enriched by aptamers immobilized capillary column using graphene oxide modified polymer microsphere as the separation matrix, and then the eluted target proteins were online denatured, reduced, desalted and digested by our developed fully automated sample treatment device (FAST), finally the resulting peptides were analyzed by parallel reaction monitoring (PRM) on LTQ-orbitrap velos mass spectrometry. Compared to traditional ELISA assay, the platform exhibited significant advantages such as short analysis time, low limit of detection, and ease of automation. Furthermore, our developed platform was also applied in the absolute quantification of tumor markers from clinical human plasma samples, and the results were comparable to those obtained by clinical immunoassay. All the results demonstrated that such a platform could provide a promising tool for achieving high sensitivity, high accuracy, and high throughput detection of disease related protein markers in the routine physical examination and clinical disease diagnosis.
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Affiliation(s)
- Yuanbo Chen
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Jiang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Huiming Yuan
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
| | - Xudong Zhu
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhui Liu
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaodan Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Zhen Liang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
| | - Liming Wang
- The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Lihua Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China.
| | - Yukui Zhang
- National Chromatographic Research and Analysis Center, Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
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8
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Alkhamis O, Yang W, Farhana R, Yu H, Xiao Y. Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease. Nucleic Acids Res 2020; 48:e120. [PMID: 33053182 PMCID: PMC7672472 DOI: 10.1093/nar/gkaa849] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
In vitro aptamer isolation methods can yield hundreds of potential candidates, but selecting the optimal aptamer for a given application is challenging and laborious. Existing aptamer characterization methods either entail low-throughput analysis with sophisticated instrumentation, or offer the potential for higher throughput at the cost of providing a relatively increased risk of false-positive or -negative results. Here, we describe a novel method for accurately and sensitively evaluating the binding between DNA aptamers and small-molecule ligands in a high-throughput format without any aptamer engineering or labeling requirements. This approach is based on our new finding that ligand binding inhibits aptamer digestion by T5 exonuclease, where the extent of this inhibition correlates closely with the strength of aptamer-ligand binding. Our assay enables accurate and efficient screening of the ligand-binding profiles of individual aptamers, as well as the identification of the best target binders from a batch of aptamer candidates, independent of the ligands in question or the aptamer sequence and structure. We demonstrate the general applicability of this assay with a total of 106 aptamer-ligand pairs and validate these results with a gold-standard method. We expect that our assay can be readily expanded to characterize small-molecule-binding aptamers in an automated, high-throughput fashion.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Weijuan Yang
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Rifat Farhana
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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9
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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: 21] [Impact Index Per Article: 5.3] [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.
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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
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10
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Kasai K. Frontal affinity chromatography: An excellent method of analyzing weak biomolecular interactions based on a unique principle. Biochim Biophys Acta Gen Subj 2020; 1865:129761. [PMID: 33086119 DOI: 10.1016/j.bbagen.2020.129761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Not only strong biomolecular interactions but also weak interactions play important roles in ensuring appropriate operations of many biological systems. Although a thorough investigation of the latter is essential in understanding life science, few suitable research tools are available because of inherent difficulties. SCOPE OF REVIEW Frontal affinity chromatography (FAC) is a versatile method that overcomes the inherent difficulties to provide accurate information on weak interactions. Since its concept and merit are not widely recognized, a comprehensive interpretation of FAC is provided in this review to encourage its application among researchers. MAJOR CONCLUSION FAC is based on a unique principle of measuring the binding strength by the delayed migration of an analyte through an affinity column. Its utility was elucidated via the lectin-glycan interactions. GENERAL SIGNIFICANCE FAC has a great potential as a research tool to solve many difficult problems in general bioscience that are relevant to almost all researchers.
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Affiliation(s)
- Kenichi Kasai
- Teikyo University, 2-11-1 Kaga, Itabashiku, Tokyo 1738605, Japan.
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11
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Zhang F, Huang PJJ, Liu J. Sensing Adenosine and ATP by Aptamers and Gold Nanoparticles: Opposite Trends of Color Change from Domination of Target Adsorption Instead of Aptamer Binding. ACS Sens 2020; 5:2885-2893. [PMID: 32847353 DOI: 10.1021/acssensors.0c01169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The 27 mer DNA aptamer for adenosine and adenosine 5'-triphosphate (ATP) is a popular model system for designing biosensors. Various strategies have been reported for label-free colorimetric detection using gold nanoparticles (AuNPs). It is generally accepted that free aptamers can protect AuNPs against salt-induced aggregation, whereas target-bound aptamers cannot. However, these studies only considered the aptamer binding to its target, and the adsorption of the aptamer on AuNPs, but none considered the adsorption of target molecules by AuNPs. We herein report that the adsorption of adenosine destabilized citrate-capped AuNPs with an apparent Kd of just 7.7 μM adenosine, whereas that of ATP stabilized the AuNPs because of the negative charges from the triphosphate group. The adsorbed ATP inhibited the adsorption of DNA. Using the aptamer and a nonbinding mutant, ATP and guanosine 5'-triphosphate (GTP) had the same colorimetric response, and so did adenosine and guanosine, regardless of the DNA sequence, indicating that the color change mainly reflected the adsorption of the nucleosides and nucleotides instead of aptamer binding. The related literature examples using this aptamer were classified into three types and individually analyzed, where the reported color changes can all be explained by the adsorption of target analytes.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People’s Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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12
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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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13
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Wang X, Cheng Y, Cai S, Chen J, Xu P, Chen Y, Yu H, Xu T, Zhang S, Li X. Resonant-Cantilever-Detected Kinetic/Thermodynamic Parameters for Aptamer-Ligand Binding on a Liquid-Solid Interface. Anal Chem 2020; 92:11127-11134. [PMID: 32551574 DOI: 10.1021/acs.analchem.0c01142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acid aptamers have been widely used as recognition elements on various biosensing interfaces, but quantitative kinetic/thermodynamic analysis for revealing the aptamer-ligand binding mechanism, which occurs on a liquid-solid interface, has not been realized due to a lack of usable biophysical tools. Herein we apply a resonant microcantilever sensor to continuously record the frequency shift according to the binding-induced mass change on the liquid-solid interface. The frequency-shift curve is used for tracing the reaction process and is fitted with classic equations to calculate a set of kinetic/thermodynamic parameters, such as rate constants (ka = 902.95 M-1 s-1, kd = 0.000141 s-1), equilibrium constants (KD = 1.55 μM), the Gibbs free energy (ΔG° = -32.57 kJ/mol), and the activation energy (Ea = 38.03 kJ/mol) for the immobilized aptamer and free ATP. This quantitative analysis method is label-free, calibration-free, and highly sensitive. The kinetic/thermodynamic parameter detection method provides new resolution to the in-depth understanding of the ligand-aptamer interaction on the liquid-solid interface for biosensing or lab-on-a-chip applications.
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Affiliation(s)
- Xuefeng Wang
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yarong Cheng
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Shengran Cai
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianzhong Chen
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Xu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Chen
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haitao Yu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tiegang Xu
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Zhang
- College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, China
| | - Xinxin Li
- State Key Lab of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Liu Y, Le C, Tyrrell DL, Le XC, Li XF. Aptamer Binding Assay for the E Antigen of Hepatitis B Using Modified Aptamers with G-Quadruplex Structures. Anal Chem 2020; 92:6495-6501. [PMID: 32250595 DOI: 10.1021/acs.analchem.9b05740] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The e antigen of hepatitis B (HBeAg) is positively associated with an increased risk of developing liver cancer and cirrhosis in chronic hepatitis B (CHB) patients. Clinical monitoring of HBeAg provides guidance to the treatment of CHB and the assessment of disease progression. We describe here an affinity binding assay for HBeAg, which takes advantage of G-quadruplex aptamers for enhanced binding and stability. We demonstrate a strategy to improve the binding affinity of aptamers by modifying their sequences upon their G-quadruplex and secondary structures. On the basis of predicting a stable G-quadruplex and a secondary structure, we truncated 19 nucleotides (nt) from the primer regions of an 80-nt aptamer, and the resulting 61-nt aptamer enhanced binding affinity by 19 times (Kd = 1.2 nM). We mutated a second aptamer (40 nt) in one loop region and incorporated pyrrolo-deoxycytidine to replace deoxycytidine in another loop. The modified 40-nt aptamer, with a stable G-quadruplex and two modified loops, exhibited a 100 times higher binding affinity for HBeAg (Kd = 0.4 nM) than the unmodified original aptamer. Using the two newly modified aptamers, one serving as the capture and the other as the reporter, we have developed an improved sandwich binding assay for HBeAg. Analyses of HBeAg in serum samples (concentration ranging from 0.1 to 60 ng/mL) of 10 hepatitis B patients, showing consistent results with clinical tests, demonstrate a successful application of the aptamer modification strategy and the associated aptamer binding assay.
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Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Connie Le
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada, T6G 2E1
| | - D Lorne Tyrrell
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada, T6G 2E1
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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15
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Acquah C, Chan YW, Pan S, Yon LS, Ongkudon CM, Guo H, Danquah MK. Characterisation of aptamer-anchored poly(EDMA-co-GMA) monolith for high throughput affinity binding. Sci Rep 2019; 9:14501. [PMID: 31601836 PMCID: PMC6787036 DOI: 10.1038/s41598-019-50862-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/13/2019] [Indexed: 11/17/2022] Open
Abstract
Immobilisation of aptameric ligands on solid stationary supports for effective binding of target molecules requires understanding of the relationship between aptamer-polymer interactions and the conditions governing the mass transfer of the binding process. Herein, key process parameters affecting the molecular anchoring of a thrombin-binding aptamer (TBA) onto polymethacrylate monolith pore surface, and the binding characteristics of the resulting macroporous aptasensor were investigated. Molecular dynamics (MD) simulations of the TBA-thrombin binding indicated enhanced Guanine 4 (G4) structural stability of TBA upon interaction with thrombin in an ionic environment. Fourier-transform infrared spectroscopy and thermogravimetric analyses were used to characterise the available functional groups and thermo-molecular stability of the immobilised polymer generated with Schiff-base activation and immobilisation scheme. The initial degradation temperature of the polymethacrylate stationary support increased with each step of the Schiff-base process: poly(Ethylene glycol Dimethacrylate-co-Glycidyl methacrylate) or poly(EDMA-co-GMA) [196.0 °C (±1.8)]; poly(EDMA-co-GMA)-Ethylenediamine [235.9 °C (±6.1)]; poly(EDMA-co-GMA)-Ethylenediamine-Glutaraldehyde [255.4 °C (±2.7)]; and aptamer-modified monolith [273.7 °C (±2.5)]. These initial temperature increments reflected in the associated endothermic energies were determined with differential scanning calorimetry. The aptameric ligand density obtained after immobilisation was 480 pmol/μL. Increase in pH and ionic concentration affected the surface charge distribution and the binding characteristics of the aptamer-modified disk-monoliths, resulting in the optimum binding pH and ionic concentration of 8.0 and 5 mM Mg2+, respectively. These results are critical in understanding and setting parametric constraints indispensable to develop and enhance the performance of aptasensors.
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Affiliation(s)
- Caleb Acquah
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia.,School of Nutrition Science, Faculty of Health Science, University of Ottawa, K1N 6N5, Ontario, Canada
| | - Yi Wei Chan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Sharadwata Pan
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, 85354, Germany
| | - Lau Sie Yon
- Department of Chemical Engineering, Curtin University, Sarawak, 98009, Malaysia
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia
| | - Haobo Guo
- Department of Computer Science and Engineering, University of Tennessee, Chattanooga, TN, 37403, United States.,SimCenter, University of Tennessee, Chattanooga, TN, 37403, United States
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, TN, 37403, United States.
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16
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Young BE, Kundu N, Sczepanski JT. Mirror-Image Oligonucleotides: History and Emerging Applications. Chemistry 2019; 25:7981-7990. [PMID: 30913332 PMCID: PMC6615976 DOI: 10.1002/chem.201900149] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 01/13/2023]
Abstract
As chiral molecules, naturally occurring d-oligonucleotides have enantiomers, l-DNA and l-RNA, which are comprised of l-(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d-counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l-oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d-oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d- and l-oligonucleotides to form contiguous Watson-Crick base pairs with each other has ultimately led to the perception that l-oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l-oligonucleotides, while overcoming (and even exploiting) their inability to Watson-Crick base pair with the natural polymer. Herein, a brief history of l-oligonucleotide research is presented and emerging l-oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.
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Affiliation(s)
- Brian E. Young
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jonathan T. Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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17
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Lyu Y, Teng IT, Zhang L, Guo Y, Cai R, Zhang X, Qiu L, Tan W. Comprehensive Regression Model for Dissociation Equilibria of Cell-Specific Aptamers. Anal Chem 2018; 90:10487-10493. [PMID: 30039967 PMCID: PMC6522138 DOI: 10.1021/acs.analchem.8b02484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A comprehensive nonlinear regression model for dissociation equilibria of cell-specific aptamers is proposed by considering the effect of receptor expression level. Benefiting from the global regression of simultaneous equations, the fitted parameters reach a very significant level, indicating the statistical validity of this updated model. According to the fitting results, we found that dissociation constants fitted using the previous model are obviously larger than the updated values, which can be explained by the effect of receptor number on curve fitting. In addition, equivalent receptor density can be estimated using the updated model, which may lead to some new judgments about reported results of cell-SELEX.
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Affiliation(s)
- Yifan Lyu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - I-Ting Teng
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yian Guo
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Ren Cai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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18
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Farzin L, Shamsipur M, Samandari L, Sheibani S. Advances in the design of nanomaterial-based electrochemical affinity and enzymatic biosensors for metabolic biomarkers: A review. Mikrochim Acta 2018; 185:276. [PMID: 29721621 DOI: 10.1007/s00604-018-2820-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/24/2018] [Indexed: 10/17/2022]
Abstract
This review (with 340 refs) focuses on methods for specific and sensitive detection of metabolites for diagnostic purposes, with particular emphasis on electrochemical nanomaterial-based sensors. It also covers novel candidate metabolites as potential biomarkers for diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis. Following an introduction into the field of metabolic biomarkers, a first major section classifies electrochemical biosensors according to the bioreceptor type (enzymatic, immuno, apta and peptide based sensors). A next section covers applications of nanomaterials in electrochemical biosensing (with subsections on the classification of nanomaterials, electrochemical approaches for signal generation and amplification using nanomaterials, and on nanomaterials as tags). A next large sections treats candidate metabolic biomarkers for diagnosis of diseases (in the context with metabolomics), with subsections on biomarkers for neurodegenerative diseases, autism spectrum disorder and hepatitis. The Conclusion addresses current challenges and future perspectives. Graphical abstract This review focuses on the recent developments in electrochemical biosensors based on the use of nanomaterials for the detection of metabolic biomarkers. It covers the critical metabolites for some diseases such as neurodegenerative diseases, autism spectrum disorder and hepatitis.
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Affiliation(s)
- Leila Farzin
- Radiation Application Research School, Nuclear Science and Technology Research Institute, P.O. Box 11365-3486, Tehran, Iran.
| | - Mojtaba Shamsipur
- Department of Chemistry, Razi University, P.O. Box 67149-67346, Kermanshah, Iran
| | - Leila Samandari
- Department of Chemistry, Razi University, P.O. Box 67149-67346, Kermanshah, Iran
| | - Shahab Sheibani
- Radiation Application Research School, Nuclear Science and Technology Research Institute, P.O. Box 11365-3486, Tehran, Iran
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19
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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.
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Affiliation(s)
- Chenhua Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA.
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20
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Yu X, Song H, Huang J, Chen Y, Dai M, Lin X, Xie Z. An aptamer@AuNP-modified POSS–polyethylenimine hybrid affinity monolith with a high aptamer coverage density for sensitive and selective recognition of ochratoxin A. J Mater Chem B 2018; 6:1965-1972. [DOI: 10.1039/c7tb03319b] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new POSS-based aptamer affinity hybrid monolith, Apt@AuNPs@POSS–PEI, with a well-controlled 3D skeletal structure and a high aptamer coverage density of up to 1413 pmol μL−1 has been facilely fabricated.
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Affiliation(s)
- Xia Yu
- Institute of Food Safety and Environment Monitoring
- Fuzhou University
- Fuzhou
- China
| | - Hongliang Song
- Institute of Food Safety and Environment Monitoring
- Fuzhou University
- Fuzhou
- China
| | - Jing Huang
- Institute of Food Safety and Environment Monitoring
- Fuzhou University
- Fuzhou
- China
| | - Yongxuan Chen
- Fujian Inspection and Research Institute for product quality
- Fuzhou
- China
| | - Ming Dai
- Fujian Inspection and Research Institute for product quality
- Fuzhou
- China
| | - Xucong Lin
- Institute of Food Safety and Environment Monitoring
- Fuzhou University
- Fuzhou
- China
| | - Zenghong Xie
- Institute of Food Safety and Environment Monitoring
- Fuzhou University
- Fuzhou
- China
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21
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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.
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22
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Zhang Z, Oni O, Liu J. New insights into a classic aptamer: binding sites, cooperativity and more sensitive adenosine detection. Nucleic Acids Res 2017; 45:7593-7601. [PMID: 28591844 PMCID: PMC5737652 DOI: 10.1093/nar/gkx517] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 06/01/2017] [Indexed: 11/27/2022] Open
Abstract
The DNA aptamer for adenosine (also for AMP and ATP) is a highly conserved sequence that has recurred in a few selections. It it a widely used model aptamer for biosensor development, and its nuclear magnetic resonance structure shows that each aptamer binds two AMP molecules. In this work, each binding site was individually removed by rational sequence design, while the remaining site still retained a similar binding affinity and specificity as confirmed by isothermal titration calorimetry. The thermodynamic parameters of binding are presented, and its biochemical implications are discussed. The number of binding sites can also be increased, and up to four sites are introduced in a single DNA sequence. Finally, the different sequences are made into fluorescent biosensors based on the structure-switching signaling aptamer design. The one-site aptamer has 3.8-fold higher sensitivity at lower adenosine concentration with a limit of detection of 9.1 μM adenosine, but weaker fluorescence signal at higher adenosine concentrations, consistent with a moderate cooperativity in the original aptamer. This work has offered insights into a classic aptamer for the relationship between the number of binding sites and sensitivity, and a shorter aptamer for improved biosensor design.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Olatunji Oni
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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23
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24
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Li Y, Sun L, Zhao Q. Competitive fluorescence anisotropy/polarization assay for ATP using aptamer as affinity ligand and dye-labeled ATP as fluorescence tracer. Talanta 2017; 174:7-13. [PMID: 28738645 DOI: 10.1016/j.talanta.2017.05.077] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/18/2017] [Accepted: 05/26/2017] [Indexed: 12/26/2022]
Abstract
We developed an aptamer-based competitive fluorescence anisotropy (FA)/fluorescence polarization (FP) assay for adenosine triphosphate (ATP). Different from the traditional fluorescence polarization immunoassays for small molecules, here DNA aptamer against ATP was used as affinity ligand, and tetramethylrhodamine (TMR) labeled ATP served as fluorescent tracer. The binding between TMR-labeled ATP and aptamer gave large FA due to molecular volume increase and restricted rotation of the dye-labeled ATP. When ATP was added in solution, ATP competitively displaced the TMR-labeled ATP from aptamer affinity complex, causing decrease of FA of TMR-labeled ATP. The buffer containing MgCl2 and incubation at low temperature were preferred for large FA change in the FA assay. The FA change was further enhanced in this competitive FA assay by increasing the molecular weight of aptamer through extension of aptamer sequences or conjugating streptavidin protein on aptamer. This method allowed for the detection of ATP in the range from 0.5μM to 1mM, generating the maximum FA change about 0.187 (corresponding maximum FP change about 0.242). The detection of ATP spiked in diluted urine or serum sample was achieved, showing capability for analysis in complex sample matrix. This assay also enabled the detection of the analogues of ATP, e.g. adenosine, adenosine monophosphate (AMP), and adenosine diphosphate (ADP) with similar sensitivity. This aptamer-based competitive FA assay takes advantages of aptamer in ease of synthesis, good thermal stability, and facile modulating the molecular mass of aptamer.
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Affiliation(s)
- Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linlin Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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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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26
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Hu T, Wen W, Zhang X, Wang S. Nicking endonuclease-assisted recycling of target-aptamer complex for sensitive electrochemical detection of adenosine triphosphate. Analyst 2017; 141:1506-11. [PMID: 26815141 DOI: 10.1039/c5an02484f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An electrochemical biosensor was developed for the detection of adenosine triphosphate (ATP) based on target-induced conformation switching and nicking endonuclease (NEase)-assisted signal amplification. The electrochemical biosensor was constructed by base pairing and target recognition. After capture DNA hybridized with the gold electrode, a significant current of Methylene Blue (MB) was obtained by differential pulse voltammetry. In the presence of ATP, the hairpin DNA formed a G-quadruplex structure due to the specific recognition between hairpin DNA and ATP. Then the exposed part of the target-aptamer complex hybridized with the 3'-terminus of capture DNA to form a specific nicking site for Nb.BbvCI, which led to NEase-assisted target-aptamer complex recycling. The released target-aptamer complex hybridized with the remaining capture DNA. Nb.BbvCI-assisted target-aptamer complex recycling caused the continuous cleavage of capture DNA with MB at its 5'-terminus, resulting in release of a certain amount of DNA fragment labeled with MB. Then the current value decreased significantly. The reduced current showed a linear range from 10 nM to 1 μM with a limit of detection as low as 3.4 nM. Furthermore, the proposed strategy can be used for the detection of similar substances.
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Affiliation(s)
- Tianxing Hu
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Wei Wen
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules & College of Chemistry and Chemical Engineering, Hubei University, Wuhan 430062, PR China.
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27
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Yang J, Zhu J, Pei R, Oliver JA, Landry DW, Stojanovic MN, Lin Q. Integrated Microfluidic Aptasensor for Mass Spectrometric Detection of Vasopressin in Human Plasma Ultrafiltrate. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2016; 8:5190-5196. [PMID: 28090219 PMCID: PMC5228624 DOI: 10.1039/c5ay02979a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a microfluidic aptamer-based biosensor for detection of low-molecular-weight biomarkers in patient samples. Using a microfluidic device that integrates aptamer-based specific analyte extraction, isocratic elution, and detection by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, we demonstrate rapid, sensitive and label-free detection of arginine vasopressin (AVP) in human plasma ultrafiltrate. AVP molecules in complex matrices are specifically captured by an aptamer that is immobilized on microbeads via affinity binding in a microchamber. After the removal of unbound, contaminating molecules through washing, aptamer-AVP complexes are thermally disrupted via on-chip temperature control. Released AVP molecules are eluted with purified water and transferred to a separate microchamber, and deposited onto a single spot on a MALDI plate via repeated, piezoelectrically actuated ejection, which enriches AVP molecules over the spot area. This integrated on-chip sample processing enables the quantitative detection of low-abundance AVP by MALDI-TOF mass spectrometry in a rapid and label-free manner. Our experimental results show the detection of AVP in human plasma ultrafiltrate as low as physiologically relevant picomolar concentrations via aptamer-based selective preconcentration, demonstrating the potential of our approach as a rapid (~ 1hr), sensitive clinical AVP assay.
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Affiliation(s)
- J. Yang
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, United States
| | - J. Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, United States
| | - R. Pei
- Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - J. A. Oliver
- Department of Medicine, Columbia University, New York, NY 10032, United States
| | - D. W. Landry
- Department of Medicine, Columbia University, New York, NY 10032, United States
| | - M. N. Stojanovic
- Department of Medicine, Columbia University, New York, NY 10032, United States
| | - Q. Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, United States
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28
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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]
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29
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Zhang H, Zhou L, Zhu Z, Yang C. Recent Progress in Aptamer-Based Functional Probes for Bioanalysis and Biomedicine. Chemistry 2016; 22:9886-900. [PMID: 27243551 DOI: 10.1002/chem.201503543] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/16/2016] [Indexed: 01/01/2023]
Abstract
Nucleic acid aptamers are short synthetic DNA or RNA sequences that can bind to a wide range of targets with high affinity and specificity. In recent years, aptamers have attracted increasing research interest due to their unique features of high binding affinity and specificity, small size, excellent chemical stability, easy chemical synthesis, facile modification, and minimal immunogenicity. These properties make aptamers ideal recognition ligands for bioanalysis, disease diagnosis, and cancer therapy. This review highlights the recent progress in aptamer selection and the latest applications of aptamer-based functional probes in the fields of bioanalysis and biomedicine.
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Affiliation(s)
- Huimin Zhang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Leiji Zhou
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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30
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Groher F, Suess B. In vitro selection of antibiotic-binding aptamers. Methods 2016; 106:42-50. [PMID: 27223401 DOI: 10.1016/j.ymeth.2016.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/10/2016] [Accepted: 05/15/2016] [Indexed: 01/06/2023] Open
Abstract
Despite its wide applicability the selection of small molecule-binding RNA aptamers with high affinity binding and specificity is still challenging. We will present here a protocol which allows the in vitro selection of antibiotic-binding aptamers which turned out to be important building blocks for the design process of synthetic riboswitches. The presented methods will be compared with alternative in vitro selection protocols. A detailed note section will point out useful tips and pitfalls.
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Affiliation(s)
- Florian Groher
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany.
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31
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Tan SY, Acquah C, Sidhu A, Ongkudon CM, Yon LS, Danquah MK. SELEX Modifications and Bioanalytical Techniques for Aptamer-Target Binding Characterization. Crit Rev Anal Chem 2016; 46:521-37. [PMID: 26980177 DOI: 10.1080/10408347.2016.1157014] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The quest to improve the detection of biomolecules and cells in health and life sciences has led to the discovery and characterization of various affinity bioprobes. Libraries of synthetic oligonucleotides (ssDNA/ssRNA) with randomized sequences are employed during Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select highly specific affinity probes called aptamers. With much focus on the generation of aptamers for a variety of target molecules, conventional SELEX protocols have been modified to develop new and improved SELEX protocols yielding highly specific and stable aptamers. Various techniques have been used to analyze the binding interactions between aptamers and their cognate molecules with associated merits and limitations. This article comprehensively reviews research advancements in the generation of aptamers, analyses physicochemical conditions affecting their binding characteristics to cellular and biomolecular targets, and discusses various field applications of aptameric binding. Biophysical techniques employed in the characterization of the molecular and binding features of aptamers to their cognate targets are also discussed.
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Affiliation(s)
- Sze Y Tan
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Caleb Acquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Amandeep Sidhu
- b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia.,c Faculty of Health Sciences , Curtin University , Perth , Australia
| | - Clarence M Ongkudon
- d Biotechnology Research Institute , University Malaysia Sabah , Kota Kinabalu , Sabah , Malaysia
| | - L S Yon
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia
| | - Michael K Danquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
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32
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Acquah C, Moy CKS, Danquah MK, Ongkudon CM. Development and characteristics of polymer monoliths for advanced LC bioscreening applications: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1015-1016:121-134. [PMID: 26919447 DOI: 10.1016/j.jchromb.2016.02.016] [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: 12/14/2015] [Revised: 02/13/2016] [Accepted: 02/13/2016] [Indexed: 01/05/2023]
Abstract
Biomedical research advances over the past two decades in bioseparation science and engineering have led to the development of new adsorbent systems called monoliths, mostly as stationary supports for liquid chromatography (LC) applications. They are acknowledged to offer better mass transfer hydrodynamics than their particulate counterparts. Also, their architectural and morphological traits can be tailored in situ to meet the hydrodynamic size of molecules which include proteins, pDNA, cells and viral targets. This has enabled their development for a plethora of enhanced bioscreening applications including biosensing, biomolecular purification, concentration and separation, achieved through the introduction of specific functional moieties or ligands (such as triethylamine, N,N-dimethyl-N-dodecylamine, antibodies, enzymes and aptamers) into the molecular architecture of monoliths. Notwithstanding, the application of monoliths presents major material and bioprocess challenges. The relationship between in-process polymerisation characteristics and the physicochemical properties of monolith is critical to optimise chromatographic performance. There is also a need to develop theoretical models for non-invasive analyses and predictions. This review article therefore discusses in-process analytical conditions, functionalisation chemistries and ligands relevant to establish the characteristics of monoliths in order to facilitate a wide range of enhanced bioscreening applications. It gives emphasis to the development of functional polymethacrylate monoliths for microfluidic and preparative scale bio-applications.
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Affiliation(s)
- Caleb Acquah
- Curtin Sarawak Research Institute, Curtin University, Sarawak 98009, Malaysia; Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia
| | - Charles K S Moy
- Department of Civil Engineering, Xi'an Jiaotong-Liverpool University, Jiangsu 215123, China
| | - Michael K Danquah
- Curtin Sarawak Research Institute, Curtin University, Sarawak 98009, Malaysia; Department of Chemical Engineering, Curtin University, Sarawak 98009, Malaysia.
| | - Clarence M Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
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33
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Zhao JC, Zhu QY, Zhao LY, Lian HZ, Chen HY. Preparation of an aptamer based organic–inorganic hybrid monolithic column with gold nanoparticles as an intermediary for the enrichment of proteins. Analyst 2016; 141:4961-7. [DOI: 10.1039/c6an00957c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gold nanoparticles are used as an intermediary in a sandwich structure for the preparation of an aptamer-based organic–inorganic hybrid affinity monolithic column.
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Affiliation(s)
- Jin-cheng Zhao
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210023
| | - Qing-yun Zhu
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210023
| | - Ling-yu Zhao
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210023
| | - Hong-zhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210023
| | - Hong-yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science
- Collaborative Innovation Center of Chemistry for Life Sciences
- School of Chemistry & Chemical Engineering and Center of Materials Analysis
- Nanjing University
- Nanjing 210023
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34
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McKeague M, McConnell EM, Cruz-Toledo J, Bernard ED, Pach A, Mastronardi E, Zhang X, Beking M, Francis T, Giamberardino A, Cabecinha A, Ruscito A, Aranda-Rodriguez R, Dumontier M, DeRosa MC. Analysis of In Vitro Aptamer Selection Parameters. J Mol Evol 2015; 81:150-61. [PMID: 26530075 DOI: 10.1007/s00239-015-9708-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Nucleic acid aptamers are novel molecular recognition tools that offer many advantages compared to their antibody and peptide-based counterparts. However, challenges associated with in vitro selection, characterization, and validation have limited their wide-spread use in the fields of diagnostics and therapeutics. Here, we extracted detailed information about aptamer selection experiments housed in the Aptamer Base, spanning over two decades, to perform the first parameter analysis of conditions used to identify and isolate aptamers de novo. We used information from 492 published SELEX experiments and studied the relationships between the nucleic acid library, target choice, selection methods, experimental conditions, and the affinity of the resulting aptamer candidates. Our findings highlight that the choice of target and selection template made the largest and most significant impact on the success of a de novo aptamer selection. Our results further emphasize the need for improved documentation and more thorough experimentation of SELEX criteria to determine their correlation with SELEX success.
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Affiliation(s)
- Maureen McKeague
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Erin M McConnell
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Jose Cruz-Toledo
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Elyse D Bernard
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Amanda Pach
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Emily Mastronardi
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Xueru Zhang
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Michael Beking
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Tariq Francis
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Amanda Giamberardino
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ashley Cabecinha
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Annamaria Ruscito
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Rocio Aranda-Rodriguez
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture, Ottawa, ON, K1A 0K9, Canada
| | - Michel Dumontier
- Biology Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada. .,Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
| | - Maria C DeRosa
- Chemistry Department, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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35
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Acquah C, Danquah MK, Agyei D, Moy CKS, Sidhu A, Ongkudon CM. Deploying aptameric sensing technology for rapid pandemic monitoring. Crit Rev Biotechnol 2015; 36:1010-1022. [PMID: 26381238 DOI: 10.3109/07388551.2015.1083940] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genome of virulent strains may possess the ability to mutate by means of antigenic shift and/or antigenic drift as well as being resistant to antibiotics with time. The outbreak and spread of these virulent diseases including avian influenza (H1N1), severe acute respiratory syndrome (SARS-Corona virus), cholera (Vibrio cholera), tuberculosis (Mycobacterium tuberculosis), Ebola hemorrhagic fever (Ebola Virus) and AIDS (HIV-1) necessitate urgent attention to develop diagnostic protocols and assays for rapid detection and screening. Rapid and accurate detection of first cases with certainty will contribute significantly in preventing disease transmission and escalation to pandemic levels. As a result, there is a need to develop technologies that can meet the heavy demand of an all-embedded, inexpensive, specific and fast biosensing for the detection and screening of pathogens in active or latent forms to offer quick diagnosis and early treatments in order to avoid disease aggravation and unnecessary late treatment costs. Nucleic acid aptamers are short, single-stranded RNA or DNA sequences that can selectively bind to specific cellular and biomolecular targets. Aptamers, as new-age bioaffinity probes, have the necessary biophysical characteristics for improved pathogen detection. This article seeks to review global pandemic situations in relation to advances in pathogen detection systems. It particularly discusses aptameric biosensing and establishes application opportunities for effective pandemic monitoring. Insights into the application of continuous polymeric supports as the synthetic base for aptamer coupling to provide the needed convective mass transport for rapid screening is also presented.
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Affiliation(s)
- Caleb Acquah
- a Curtin Sarawak Research Institute, Curtin University , Sarawak 98009 , Malaysia.,b Department of Chemical Engineering , Curtin University , Sarawak 98009 , Malaysia
| | - Michael K Danquah
- b Department of Chemical Engineering , Curtin University , Sarawak 98009 , Malaysia
| | - Dominic Agyei
- c Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences Deakin University , Geelong-Waurn Ponds , Australia
| | - Charles K S Moy
- d Faculty of Engineering and Science , Curtin University , Sarawak 98009 , Malaysia
| | - Amandeep Sidhu
- a Curtin Sarawak Research Institute, Curtin University , Sarawak 98009 , Malaysia.,e Faculty of Health Sciences , Curtin University , Perth 6102 , Australia , and
| | - Clarence M Ongkudon
- f Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu , Sabah, 88400 , Malaysia
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36
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Zhu L, Liu Y, Yang P, Liu B. Label-free Aptasensor based on Electrodeposition of Gold Nanoparticles on Graphene and Its Application in the Quantification of Adenosine Triphosphate. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.04.100] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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37
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Shcherbinin DS, Gnedenko OV, Khmeleva SA, Usanov SA, Gilep AA, Yantsevich AV, Shkel TV, Yushkevich IV, Radko SP, Ivanov AS, Veselovsky AV, Archakov AI. Computer-aided design of aptamers for cytochrome p450. J Struct Biol 2015; 191:112-9. [PMID: 26166326 DOI: 10.1016/j.jsb.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
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Affiliation(s)
- Dmitrii S Shcherbinin
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
| | - Oksana V Gnedenko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Sergey A Usanov
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Aliaksei V Yantsevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Tatsiana V Shkel
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Ivan V Yushkevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Alexis S Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | | | - Alexander I Archakov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
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Aptamer-based organic-silica hybrid affinity monolith prepared via “thiol-ene” click reaction for extraction of thrombin. Talanta 2015; 138:52-58. [DOI: 10.1016/j.talanta.2015.02.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/31/2015] [Accepted: 02/04/2015] [Indexed: 12/27/2022]
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39
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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]
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40
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Zhao Q, Lv Q, Wang H. Aptamer fluorescence anisotropy sensors for adenosine triphosphate by comprehensive screening tetramethylrhodamine labeled nucleotides. Biosens Bioelectron 2015; 70:188-93. [PMID: 25814408 DOI: 10.1016/j.bios.2015.03.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/13/2015] [Accepted: 03/15/2015] [Indexed: 02/02/2023]
Abstract
We previously reported a fluorescence anisotropy (FA) approach for small molecules using tetramethylrhodamine (TMR) labeled aptamer. It relies on target-binding induced change of intramolecular interaction between TMR and guanine (G) base. TMR-labeling sites are crucial for this approach. Only terminal ends and thymine (T) bases could be tested for TMR labeling in our previous work, possibly causing limitation in analysis of different targets with this FA strategy. Here, taking the analysis of adenosine triphosphate (ATP) as an example, we demonstrated a success of conjugating TMR on other bases of aptamer adenine (A) or cytosine (C) bases and an achievement of full mapping various labeling sites of aptamers. We successfully constructed aptamer fluorescence anisotropy (FA) sensors for adenosine triphosphate (ATP). We conjugated single TMR on adenine (A), cytosine (C), or thymine (T) bases or terminals of a 25-mer aptamer against ATP and tested FA responses of 14 TMR-labeled aptamer to ATP. The aptamers having TMR labeled on the 16th base C or 23rd base A were screened out and exhibited significant FA-decreasing or FA-increasing responses upon ATP, respectively. These two favorable TMR-labeled aptamers enabled direct FA sensing ATP with a detection limit of 1 µM and the analysis of ATP in diluted serum. The comprehensive screening various TMR labeling sites of aptamers facilitates the successful construction of FA sensors using TMR-labeled aptamers. It will expand application of TMR-G interaction based aptamer FA strategy to a variety of targets.
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Affiliation(s)
- Qiang Zhao
- Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, PR China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
| | - Qin Lv
- Institute of Environmental Science, College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, PR China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
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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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42
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Zhang L, Liu H, Shao Y, Lin C, Jia H, Chen G, Yang D, Wang Y. Selective lighting up of epiberberine alkaloid fluorescence by fluorophore-switching aptamer and stoichiometric targeting of human telomeric DNA G-quadruplex multimer. Anal Chem 2015; 87:730-7. [PMID: 25429435 PMCID: PMC5515279 DOI: 10.1021/ac503730j] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aptamers, that exist naturally in living cells as functional elements and can switch nonfluorescent natural targets to fluorophores, are very useful in developing highly sensitive and selective biosensors and screening functional agents. This work demonstrates that human telomeric G-quadruplex (HTG) can serve as a potential fluorophore-switching aptamer (FSA) to target a natural isoquinoline alkaloid. We found that, among the G-quadruplexes studied here and the various structurally similar alkaloids including epiberberine (EPI), berberine (BER), palmatine (PAL), jatrorrhizine (JAT), coptisine (COP), worenine (WOR), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT), only the HTG DNA, especially with a 5'-TA-3' residue at the 5' end of the G-quadruplex tetrad (5'-TAG3(TTAG3)3-3', TA[Q]) as the minimal sequence, is the most efficient FSA to selectively light up the EPI fluorescence. Compared to the 5' end flanking sequences, the 3' end flanking sequences of the tetrad contribute significantly less to the recognition of EPI. The binding affinity of EPI to TA[Q] (K(d) = 37 nM) is at least 20 times tighter than those of the other alkaloids. The steady-state absorption, steady-state/time-resolved fluorescence, and NMR studies demonstrate that EPI most likely interact with the 5' end flanking sequence substructure beyond the core [Q] and the G-quadruplex tetrad in a much more specific manner than the other alkaloids. The highly selective and tight binding of EPI with the FSA and significantly enhanced fluorescence suggest the potential development of a selective EPI sensor (detection limit of 10 nM). More importantly, EPI, as the brightest FSA emitter among the alkaloids, can also serve as an efficient conformation probe for HTG DNA and discriminate the DNA G-quadruplex from the RNA counterpart. Furthermore, EPI can bind stoichiometrically to each G-quadruplex unit of long HTG DNA multimer with the most significant fluorescence enhancement, which has not been achieved by the previously reported probes. Our work suggests the potential use of EPI as a bioimaging probe and a therapeutic DNA binder.
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Affiliation(s)
- Lihua Zhang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Hua Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Clement Lin
- College of Pharmacy, BIO5 Institute, Arizona Cancer Center, Department of Chemistry, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Danzhou Yang
- College of Pharmacy, BIO5 Institute, Arizona Cancer Center, Department of Chemistry, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
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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.
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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
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A novel affinity disks for bovine serum albumin purification. Appl Biochem Biotechnol 2014; 175:454-68. [PMID: 25308615 DOI: 10.1007/s12010-014-1273-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
Abstract
The adsorption characteristics of bovine serum albumin (BSA) onto the supermacroporous poly(hydroxyethylmethacrylate)-Reactive Green 19 [p(HEMA)-RG] cryogel disks have been investigated in this paper. p(HEMA) cryogel disks were prepared by radical polymerization initiated by N,N,N',N'-tetramethylene diamine (TEMED) and ammonium persulfate (APS) pair in an ice bath. Reactive Green (RG) 19 was covalently attached to the p(HEMA) cryogel disks. These disks were used in BSA adsorption studies to interrogate the effects of pH, initial protein concentration, ionic strength, and temperature. BSA adsorption capacity of the p(HEMA)-RG cryogel disk was significantly improved after the incorporation of RG. Adsorption capacity reached a plateau value at about 0.8 mg/mL at pH 4.0. The amount of adsorbed BSA decreased from 37.7 to 13.9 mg/g with increasing NaCl concentration. The enthalpy of BSA adsorption onto the p(HEMA)-RG cryogel disk was calculated as -58.4 kJ/mol. The adsorption equilibrium isotherm was fitted well by the Freundlich model. BSA was desorbed from cryogel disks (over 90 %) using 0.5 M NaSCN, and the purity of desorbed BSA was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The experimental results showed that the p(HEMA)-RG cryogel disks have potential for the quick protein separation and purification process.
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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.
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Seidel SAI, Markwardt NA, Lanzmich SA, Braun D. Thermophoresis in nanoliter droplets to quantify aptamer binding. Angew Chem Int Ed Engl 2014; 53:7948-51. [PMID: 24895233 DOI: 10.1002/anie.201402514] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/11/2014] [Indexed: 11/08/2022]
Abstract
Biomolecule interactions are central to pharmacology and diagnostics. These interactions can be quantified by thermophoresis, the directed molecule movement along a temperature gradient. It is sensitive to binding induced changes in size, charge, or conformation. Established capillary measurements require at least 0.5 μL per sample. We cut down sample consumption by a factor of 50, using 10 nL droplets produced with acoustic droplet robotics (Labcyte). Droplets were stabilized in an oil-surfactant mix and locally heated with an IR laser. Temperature increase, Marangoni flow, and concentration distribution were analyzed by fluorescence microscopy and numerical simulation. In 10 nL droplets, we quantified AMP-aptamer affinity, cooperativity, and buffer dependence. Miniaturization and the 1536-well plate format make the method high-throughput and automation friendly. This promotes innovative applications for diagnostic assays in human serum or label-free drug discovery screening.
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Affiliation(s)
- Susanne A I Seidel
- Systems Biophysics, Physics Department, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-University Munich, Amalienstrasse 54, 80799 Munich (Germany) http://www.biosystems.physik.lmu.de
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Li S, Chen D, Zhou Q, Wang W, Gao L, Jiang J, Liang H, Liu Y, Liang G, Cui H. A general chemiluminescence strategy for measuring aptamer-target binding and target concentration. Anal Chem 2014; 86:5559-66. [PMID: 24828232 DOI: 10.1021/ac501061c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although much effort has been made for studies on aptamer-target interactions due to promising applications of aptamers in biomedical and analytical fields, measurement of the aptamer-target binding constant and binding site still remains challenging. Herein, we report a sensitive label-free chemiluminescence (CL) strategy to determine the target concentration and, more importantly, to measure the target-aptamer binding constant and binding site. This approach is suitable for multiple types of targets, including small molecules, peptides, and proteins that can enhance the CL initiated by N-(aminobutyl)-N-ethylisoluminol functionalized gold colloids, making the present method a general platform to investigate aptamer-target interactions. This approach can achieve extremely high sensitivity with nanogram samples for measuring the target-aptamer binding constant. And the measurement could be rapidly performed using a simple and low-cost CL system. It provides an effective tool for studying the binding of biologically important molecules to nucleic acids and the selection of aptamers. Besides, we have also discovered that the 14-mer aptamer fragment itself split from the ATP-binding aptamer could selectively capture ATP. The binding constant, site, and conformation between ATP and the 14-mer aptamer fragment were obtained using such a novel CL strategy and molecular dynamic simulation.
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Affiliation(s)
- Shiyuan Li
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry, University of Science and Technology of China , Hefei, Anhui 230026, P. R. China
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Song W, Zhang Q, Xie X, Zhang S. Fluorescence aptameric sensor for isothermal circular strand-displacement polymerization amplification detection of adenosine triphosphate. Biosens Bioelectron 2014; 61:51-6. [PMID: 24851721 DOI: 10.1016/j.bios.2014.04.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/08/2014] [Accepted: 04/19/2014] [Indexed: 01/18/2023]
Abstract
In this work, isothermal circular strand-displacement polymerization amplification assay is developed for highly specific and sensitive detection of adenosine triphosphate (ATP). The amplification process consists of circular common target molecule-displacement polymerization (CCDP) and circular nucleic acid strand-displacement polymerization (CNDP). In the presence of ATP, the complementary strand was released from the aptamer by the target recognition of ATP, and catalyzed the subsequent cycle reaction. With the polymerase and primer, the displaced target triggers the process of CCDP. With the involvement of nicking endonuclease, the released complementary strand triggers the CNDP. Combined CCDP with CNDP, the exponentially produced fluorescence probes are obtained, achieving a detection limit of ATP as low as 2.6 × 10(-10)M. Moreover, the proposed strategy exhibits an excellent specificity and is successfully applied in real sample assay which demonstrates potential application in practical samples.
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Affiliation(s)
- Weiling Song
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qiao Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xuxu Xie
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology of Tumor Markers, Linyi University, Linyi 276005, PR China.
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Abstract
Isolating a particular strand of DNA from a double stranded DNA duplex is an important step in aptamer generation as well as many other biotechnology applications. Here we describe a microfluidic, flow-through, dialysis device for isolating single-stranded DNA (ssDNA) from double-stranded DNA (dsDNA). The device consists of two channels fabricated in polydimethylsiloxane (PDMS) separated by a track etched polycarbonate membrane (800 nm pore size). To isolate ssDNA, dual-biotin labelled dsDNA was immobilized onto streptavidin-coated polystyrene beads. Alkaline treatment was used to denature dsDNA, releasing the non-biotinylated ssDNA. In the flow-through dialysis device the liberated ssDNA was able to cross the membrane and was collected in an outlet channel. The complementary sequence bound to the bead was unable to cross the membrane and was directed to a waste channel. The effect of NaOH concentration and flow rate on purity and yield were compared. >95% ssDNA purity was achieved at 25 mM NaOH. However, lower flow rates were necessary to achieve ssDNA yields approaching the 50% theoretical maximum of the concurrent-flow device. Under optimized conditions the microfluidic isolation achieved even higher purity ssDNA than analogous manual procedures.
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Affiliation(s)
- Yixiao Sheng
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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