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Wang TY, Ji H, Everton D, Le ATH, Krylova SM, Fournier R, Krylov SN. Fundamental Determinants of the Accuracy of Equilibrium Constants for Affinity Complexes. Anal Chem 2023; 95:15826-15832. [PMID: 37831482 DOI: 10.1021/acs.analchem.3c03557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The equilibrium constant of a chemical reaction is arguably the key thermodynamic parameter in chemistry; we naturally expect that equilibrium constants are determined accurately. The majority of equilibrium constants determined today are those of binding reactions that form affinity complexes, such as protein-protein, protein-DNA, and protein-small molecule. There is growing awareness that the determination of equilibrium constants for highly stable affinity complexes may be very inaccurate. However, fundamental (i.e., method-independent) determinants of accuracy are poorly understood. Here, we present a study that explicitly shows what the accuracy of equilibrium constants of affinity complexes depends on. This study reveals the critical importance of the choice of concentration of interacting components and creates a theoretical foundation for improving the accuracy of the equilibrium constants. The predicted influence of concentrations on accuracy was confirmed experimentally. The results of this fundamental study provide instructive guidance for experimentalists independently on the method they use.
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Affiliation(s)
- Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Hongchen Ji
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Daniel Everton
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - René Fournier
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
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2
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Le ATH, Wang TY, Krylova SM, Beloborodov SS, Krylov SN. Quantitative Characterization of Partitioning in Selection of DNA Aptamers for Protein Targets by Capillary Electrophoresis. Anal Chem 2022; 94:2578-2588. [DOI: 10.1021/acs.analchem.1c04560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M. Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Stanislav S. Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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Nevídalová H, Michalcová L, Glatz Z. Capillary electrophoresis-based immunoassay and aptamer assay: A review. Electrophoresis 2020; 41:414-433. [PMID: 31975407 DOI: 10.1002/elps.201900426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 12/31/2022]
Abstract
Over the last two decades, the group of techniques called affinity probe CE has been widely used for the detection and the determination of several types of biomolecules with high sensitivity. These techniques combine the low sample consumption and high separation power of CE with the selectivity of the probe to the target molecule. The assays can be defined according to the type of probe used: CE immunoassays, with an antibody as the probe, or aptamer-based CE, with an aptamer as the probe. Immunoassays are generally divided into homogeneous and heterogeneous groups, and homogeneous variant can be further performed in competitive or noncompetitive formats. Interacting partners are free in solution at homogeneous assay, as opposed to heterogeneous analyses, where one of them is immobilized onto a solid support. Highly sensitive fluorescence, chemiluminescence or electrochemical detections were typically used in this type of study. The use of the aptamers as probes has several advantages over antibodies such as shorter generation time, higher thermal stability, lower price, and lower variability. The aptamer-based CE technique was in practice utilized for the determination of proteins in biological fluids and environmentally or clinically important small molecules. Both techniques were also transferred to microchip. This review is focused on theoretical principles of these techniques and a summary of their applications in research.
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Affiliation(s)
- Hana Nevídalová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Michalcová
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zdeněk Glatz
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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Zhu C, Yang G, Ghulam M, Li L, Qu F. Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers. Biotechnol Adv 2019; 37:107432. [PMID: 31437572 DOI: 10.1016/j.biotechadv.2019.107432] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/24/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023]
Abstract
Aptamers have drawn considerable attention as newly emerging molecular recognition elements in clinical diagnostics, drug delivery, therapeutics, environmental monitoring, and food safety analyses. As the in vitro screening antibody analogs, aptamers are enabled to recognize various types of targets with high affinity and specificity like or even superior to antibodies. However, the restrictions and inefficiency of selection have been hampering their wider application. Among various modified systematic evolution of ligands by exponential enrichment (SELEX) methods, capillary electrophoresis (CE)-SELEX holds multiple functions and advantages with the powerful qualitative and quantitative analysis capabilities, less consumption of sample and analytical reagent, natural binding environment, higher screening efficiency, and availability in multiple modes. This review summarizes the key developments in the area of CE-SELEX by leading research groups, including our teams' ten years of research and experience to help researchers fully understand and utilize CE-SELEX. Aptamers' history, applications, as well as the SELEX developments, have been briefly described; the advantages of CE-SELEX are highlighted compared with the conventional SELEX methods. Further, we describe some essential CE-SELEX models and provide an overview of the CE-SELEX, including the targets and ssDNA library, every technical point in the selection process, and post-SELEX protocol. We expect this review will inspire more researchers to have insight into the screening problems from CE-SELEX viewpoint and will help to improve the selection efficiency and probability of success to meet the growing needs of aptamers' discovery in bioanalytical and medical fields.
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Affiliation(s)
- Chao Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Murtaza Ghulam
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing 100081, China.
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6
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Le ATH, Krylova SM, Krylov SN. Ideal-filter capillary electrophoresis: A highly efficient partitioning method for selection of protein binders from oligonucleotide libraries. Electrophoresis 2019; 40:2553-2564. [PMID: 31069842 DOI: 10.1002/elps.201900028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/16/2019] [Accepted: 05/02/2019] [Indexed: 12/22/2022]
Abstract
Selection of affinity ligands for protein targets from oligonucleotide libraries currently involves multiple rounds of alternating steps of partitioning of protein-bound oligonucleotides (binders) from protein-unbound oligonucleotides (nonbinders). We have recently introduced ideal-filter capillary electrophoresis (IFCE) for binder selection in a single step of partitioning. In IFCE, protein-binder complexes and nonbinders move inside the capillary in the opposite directions, and the efficiency of their partitioning reaches 109 , i.e., only one of a billion molecules of nonbinders leaks through IFCE while all binders pass through. The condition of IFCE can be satisfied when the magnitude of the mobility of EOF is smaller than that of the protein-binder complexes and larger than that of nonbinders. The efficiency of partitioning in IFCE is 10 million times higher than those of solid-phase-based methods of partitioning typically used in selection of affinity ligands for protein targets from oligonucleotide libraries. Here, we provide additional details on our justification for IFCE development. We elaborate on electrophoretic aspects of the method and define the theoretical range of EOF mobilities that support IFCE. Based on these theoretical results, we identify an experimental range of background electrolyte's ionic strength that supports IFCE. We also extend our interpretation of the results and discuss in-depth IFCE's prospective in practical applications and fundamental studies.
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Affiliation(s)
- An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
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Online reaction based single-step capillary electrophoresis-systematic evolution of ligands by exponential enrichment for ssDNA aptamers selection. Anal Chim Acta 2019; 1070:112-122. [PMID: 31103164 DOI: 10.1016/j.aca.2019.04.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/19/2019] [Accepted: 04/15/2019] [Indexed: 12/29/2022]
Abstract
Capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) has proven to be an effective technique for aptamers selection. In this study, we present an online reaction based convenient single-step CE-SELEX (ssCE-SELEX) mode with human thrombin (H-Thr) as a model target. The selection progress was monitored through bulk Kd analysis, which showed more than a 1000-fold improvement over the initial library after two rounds of selection. Three selected candidate sequences presented high binding affinities against H-Thr with nanomolar (nM) Kd determined by nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM, 56.4-177.1 nM) and CE based non-linear fitting (CE-NLF, 98.2-199.7 nM). They also exhibited high specificities towards H-Thr compared with bovine thrombin, IgG, lysozyme, and lactoferrin. Meanwhile, the Kd results by isothermal titration calorimetry (ITC) confirmed the effective CE in measuring the aptamer affinity. In addition, three candidates were applied as aptasensors in the AuNPs based colorimetric assay, which showed visible color change and good linear relationships (R2 > 0.93) with H-Thr concentration. Furthermore, molecular dynamics (MD) simulation was performed to validate the binding of the three candidates with H-Thr by binding sites and binding free energy. The ssCE-SELEX method avoids off-line incubation, saves time and sample, and may provide a universal and convenient method for aptamers selection.
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8
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Le ATH, Krylova SM, Kanoatov M, Desai S, Krylov SN. Ideal-Filter Capillary Electrophoresis (IFCE) Facilitates the One-Step Selection of Aptamers. Angew Chem Int Ed Engl 2019; 58:2739-2743. [PMID: 30577082 DOI: 10.1002/anie.201812974] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/14/2018] [Indexed: 11/06/2022]
Abstract
Selection of aptamers from oligonucleotide libraries currently requires multiple rounds of alternating steps of partitioning of binders from nonbinders and enzymatic amplification of all collected oligonucleotides. Herein, we report a highly practical solution for reliable one-step selection of aptamers. We introduce partitioning by ideal-filter capillary electrophoresis (IFCE) in which binders and nonbinders move in the opposite directions. The efficiency of IFCE-based partitioning reaches 109 , which is ten million times higher than that of typical solid-phase partitioning methods. One step of IFCE-based partitioning is sufficient for the selection of a high-affinity aptamer pool for a protein target. Partitioning by IFCE promises to become an indispensable tool for fast and robust selection of binders from different types of oligonucleotide libraries.
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Affiliation(s)
- An T H Le
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Svetlana M Krylova
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Mirzo Kanoatov
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Shrey Desai
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Sergey N Krylov
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
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9
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Le ATH, Krylova SM, Kanoatov M, Desai S, Krylov SN. Ideal‐Filter Capillary Electrophoresis (IFCE) Facilitates the One‐Step Selection of Aptamers. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- An T. H. Le
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Svetlana M. Krylova
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Mirzo Kanoatov
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Shrey Desai
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
| | - Sergey N. Krylov
- Centre for Research on Biomolecular InteractionsYork University Toronto Ontario M3J 1P3 Canada
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10
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Niu Y, Wan A, Lin Z, Lu X, Wan G. N 6-Methyladenosine modification: a novel pharmacological target for anti-cancer drug development. Acta Pharm Sin B 2018; 8:833-843. [PMID: 30505654 PMCID: PMC6251950 DOI: 10.1016/j.apsb.2018.06.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 12/11/2022] Open
Abstract
N6-Methyladenosine (m6A) modification is the most pervasive modification of human mRNA molecules. It is reversible via regulation of m6A modification methyltransferase, demethylase and proteins that preferentially recognize m6A modification as “writers”, “erasers” and “readers”, respectively. Altered expression levels of the m6A modification key regulators substantially affect their function, leading to significant phenotype changes in the cell and organism. Recent studies have proved that the m6A modification plays significant roles in regulation of metabolism, stem cell self-renewal, and metastasis in a variety of human cancers. In this review, we describe the potential roles of m6A modification in human cancers and summarize their underlying molecular mechanisms. Moreover, we will highlight potential therapeutic approaches by targeting the key m6A modification regulators for cancer drug development.
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11
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Beloborodov SS, Bao J, Krylova SM, Shala-Lawrence A, Johnson PE, Krylov SN. Aptamer facilitated purification of functional proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1073:201-206. [PMID: 29287247 DOI: 10.1016/j.jchromb.2017.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/15/2017] [Accepted: 12/15/2017] [Indexed: 12/13/2022]
Abstract
DNA aptamers are attractive capture probes for affinity chromatography since, in contrast to antibodies, they can be chemically synthesized and, in contrast to tag-specific capture probes (such as Nickel-NTA or Glutathione), they can be used for purification of proteins free of genetic modifications (such as His or GST tags). Despite these attractive features of aptamers as capture probes, there are only a few reports on aptamer-based protein purification and none of them includes a test of the purified protein's activity, thus, leaving discouraging doubts about method's ability to purify proteins in their active state. The goal of this work was to prove that aptamers could facilitate isolation of active proteins. We refined a complete aptamer-based affinity purification procedure, which takes 4 h to complete. We further applied this procedure to purify two recombinant proteins, MutS and AlkB, from bacterial cell culture: 0.21 mg of 85%-pure AlkB from 4 mL of culture and 0.24 mg of 82%-pure MutS from 0.5 mL of culture. Finally, we proved protein activity by two capillary electrophoresis based assays: an enzymatic assay for AlkB and a DNA-binding assay for MutS. We suggest that in combination with aptamer selection for non-purified protein targets in crude cell lysate, aptamer-based purification provides a means of fast isolation of tag-free recombinant proteins in their native state without the use of antibodies.
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Affiliation(s)
- Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jiayin Bao
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Agnesa Shala-Lawrence
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada.
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12
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McKeague M. Aptamers for DNA Damage and Repair. Int J Mol Sci 2017; 18:ijms18102212. [PMID: 29065503 PMCID: PMC5666892 DOI: 10.3390/ijms18102212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
DNA is damaged on a daily basis, which can lead to heritable mutations and the activation of proto-oncogenes. Therefore, DNA damage and repair are critical risk factors in cancer, aging and disease, and are the underlying bases of most frontline cancer therapies. Much of our current understanding of the mechanisms that maintain DNA integrity has been obtained using antibody-based assays. The oligonucleotide equivalents of antibodies, known as aptamers, have emerged as potential molecular recognition rivals. Aptamers possess several ideal properties including chemical stability, in vitro selection and lack of batch-to-batch variability. These properties have motivated the incorporation of aptamers into a wide variety of analytical, diagnostic, research and therapeutic applications. However, their use in DNA repair studies and DNA damage therapies is surprisingly un-tapped. This review presents an overview of the progress in selecting and applying aptamers for DNA damage and repair research.
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Affiliation(s)
- Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland.
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13
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Beloborodov SS, Panferov VG, Safenkova IV, Krylova SM, Dzantiev BB, Krylov SN. Unexpected Electrophoretic Behavior of Complexes between Rod-like Virions and Bivalent Antibodies. Anal Chem 2016; 88:11908-11912. [PMID: 27934118 DOI: 10.1021/acs.analchem.6b03779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report on the unexpected electrophoretic behavior of complexes between rod-like virus particles (virions) and bivalent antibodies. The multiple complexes formed by the virions and antibodies migrated with electrophoretic mobilities of much greater absolute values than those of the unbound virions or antibodies while typically complexes have mobilities intermediate to those of their components. We hypothesized that the mobilities of unusually high absolute values are caused by the cross-linking of virions by bivalent antibodies into aggregates with prominent side-to-side binding. Theoretically, the mobility of such aggregates should be proportional to the square root of the number of cross-linked virions. The formation of virion aggregates with prominent side-to-side binding was confirmed by atomic force microscopy. The dependence of the aggregate mobility on the number of cross-linked virions can be used to estimate this number.
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Affiliation(s)
- Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
| | - Vasily G Panferov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences , Moscow 119071, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences , Moscow 119071, Russia
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences , Moscow 119071, Russia
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
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Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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15
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Yufa R, Krylova SM, Bruce C, Bagg EA, Schofield CJ, Krylov SN. Emulsion PCR significantly improves nonequilibrium capillary electrophoresis of equilibrium mixtures-based aptamer selection: allowing for efficient and rapid selection of aptamer to unmodified ABH2 protein. Anal Chem 2014; 87:1411-9. [PMID: 25495441 DOI: 10.1021/ac5044187] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), a homogeneous approach to select DNA aptamers, is among the most efficient partitioning techniques. In contrast with surface-based systematic evolution of ligands by exponential enrichment (SELEX) approaches, the ability of NECEEM to select aptamers to unmodified proteins in solution is preferable for identifying aptamers for eventual in vivo use. The high stringency and low sample volumes of NECEEM, although generally beneficial, can result in binding of very few aptamers, requiring highly efficient amplification to propagate them. When amplified with standard PCR, detectable library enrichment can fail due to the fast conversion of the aptamers into byproducts and preferential amplification of nonbinders. As an alternative, we proposed the use of emulsion PCR (ePCR), which is known to reduce byproduct formation, as a PCR mode for coupling with NECEEM partitioning. For the first time, we tested the advantages of ePCR in NECEEM-based aptamer selection to a medically relevant DNA repair enzyme, ABH2. We report that the combination of ePCR with NECEEM allowed for the selection of aptamers in the first three rounds of SELEX, while SELEX with conventional PCR failed in a number of attempts. Selected aptamers to an unmodified ABH2 protein have potential use in diagnostics and as leads for anticancer cotherapies, used as enhancements of alkylating agents in chemotherapy.
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Affiliation(s)
- Roman Yufa
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University , Toronto, Ontario M3J 1P3, Canada
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16
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Ye Fu
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
| | - Chuan He
- Department of Chemistry and
Institute for Biophysical Dynamics, The
University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United
States
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17
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Affiliation(s)
- Guanqun Zheng
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago , 929 East 57th Street, Chicago, Illinois 60637, United States
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Prediction of aptamer-target interacting pairs with pseudo-amino acid composition. PLoS One 2014; 9:e86729. [PMID: 24466214 PMCID: PMC3899287 DOI: 10.1371/journal.pone.0086729] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/15/2013] [Indexed: 11/19/2022] Open
Abstract
Aptamers are oligonucleic acid or peptide molecules that bind to specific target molecules. As a novel and powerful class of ligands, aptamers are thought to have excellent potential for applications in the fields of biosensing, diagnostics and therapeutics. In this study, a new method for predicting aptamer-target interacting pairs was proposed by integrating features derived from both aptamers and their targets. Features of nucleotide composition and traditional amino acid composition as well as pseudo amino acid were utilized to represent aptamers and targets, respectively. The predictor was constructed based on Random Forest and the optimal features were selected by using the maximum relevance minimum redundancy (mRMR) method and the incremental feature selection (IFS) method. As a result, 81.34% accuracy and 0.4612 MCC were obtained for the training dataset, and 77.41% accuracy and 0.3717 MCC were achieved for the testing dataset. An optimal feature set of 220 features were selected, which were considered as the ones that contributed significantly to the interacting aptamer-target pair predictions. Analysis of the optimal feature set indicated several important factors in determining aptamer-target interactions. It is anticipated that our prediction method may become a useful tool for identifying aptamer-target pairs and the features selected and analyzed in this study may provide useful insights into the mechanism of interactions between aptamers and targets.
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Liyanage R, Krylova SM, Krylov SN. Minimizing adsorption of histidine-tagged proteins for the study of protein–deoxyribonucleic acid interactions by kinetic capillary electrophoresis. J Chromatogr A 2013; 1322:90-6. [DOI: 10.1016/j.chroma.2013.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 01/24/2023]
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Krylova SM, Koshkin V, Bagg E, Schofield CJ, Krylov SN. Mechanistic studies on the application of DNA aptamers as inhibitors of 2-oxoglutarate-dependent oxygenases. J Med Chem 2012; 55:3546-52. [PMID: 22471443 PMCID: PMC4681096 DOI: 10.1021/jm300243h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli (E. coli) AlkB protein and its functional human homologues belong to a subfamily of 2-oxoglutarate (2OG) dependent oxygenases (2OG oxygenases for simplicity) that enable the repair of cytotoxic methylation damage in nucleic acids and that catalyze t-RNA oxidations. DNA alkylation is a major mechanism of action for cytotoxic anticancer drugs. Thus, the inhibition of oxidative demethylation, catalyzed by these enzymes, has the potential to improve the efficacy of chemotherapies. Here we report that oligonucleotide aptamers constitute a new class of potent inhibitors of 2OG oxygenases. DNA aptamers can selectively bind to AlkB, with nanomolar affinity, and efficiently inhibit catalysis. The mechanism of inhibition was studied by capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. Inhibition constants of the aptamers were determined and shown to correlate well with K(d) values. The results of kinetic analyses imply that the aptamers bind AlkB away from the active site. Our findings should stimulate the development of oligonucleotide aptamers for human homologues of AlkB and further their study as potential enhancers of chemotherapy efficiency.
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Affiliation(s)
- Svetlana M. Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Vasilij Koshkin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Eleanor Bagg
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
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Woon ECY, Demetriades M, Bagg EAL, Aik W, Krylova SM, Ma JHY, Chan M, Walport LJ, Wegman DW, Dack KN, McDonough MA, Krylov SN, Schofield CJ. Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic acid demethylase. J Med Chem 2012; 55:2173-84. [PMID: 22263962 DOI: 10.1021/jm201417e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Oxoglutarate-dependent nucleic acid demethylases are of biological interest because of their roles in nucleic acid repair and modification. Although some of these enzymes are linked to physiology, their regulatory roles are unclear. Hence, there is a desire to develop selective inhibitors for them; we report studies on AlkB, which reveal it as being amenable to selective inhibition by small molecules. Dynamic combinatorial chemistry linked to mass spectrometric analyses (DCMS) led to the identification of lead compounds, one of which was analyzed by crystallography. Subsequent structure-guided studies led to the identification of inhibitors of improved potency, some of which were shown to be selective over two other 2OG oxygenases. The work further validates the use of the DCMS method and will help to enable the development of inhibitors of nucleic acid modifying 2OG oxygenases both for use as functional probes and, in the longer term, for potential therapeutic use.
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Affiliation(s)
- Esther C Y Woon
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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Yao J, Sun Y, Yang M, Duan Y. Chemistry, physics and biology of graphene-based nanomaterials: new horizons for sensing, imaging and medicine. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c2jm31632c] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Affiliation(s)
- Matthew Geiger
- University of Minnesota, Department of Chemistry, 207
Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Amy L. Hogerton
- University of Minnesota, Department of Chemistry, 207
Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Michael T. Bowser
- University of Minnesota, Department of Chemistry, 207
Pleasant Street South East, Minneapolis, Minnesota 55455, United States
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Cherney LT, Kanoatov M, Krylov SN. Method for Determination of Peak Areas in Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures. Anal Chem 2011; 83:8617-22. [DOI: 10.1021/ac2027113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Leonid T. Cherney
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Mirzo Kanoatov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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Kanoatov M, Krylov SN. DNA adsorption to the reservoir walls causing irreproducibility in studies of protein-DNA interactions by methods of kinetic capillary electrophoresis. Anal Chem 2011; 83:8041-5. [PMID: 21923122 DOI: 10.1021/ac202048y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methods of kinetic capillary electrophoresis (KCE) facilitate kinetic studies of protein-DNA interactions and highly efficient selection of DNA aptamers for protein targets. Here, we report a previously unnoticed source of error that affects the precision and accuracy of KCE-based measurements. The error manifests itself in cases that require the use of low concentrations of DNA. In such measurements, the reproducibility of the signal generated by the same fluorescently labeled DNA sample can have a relative standard deviation (RSD) as high as 40%. We have investigated the cause of the irreproducibility and found that it is attributed to DNA adsorption to the surface of the sample vials, in which protein-DNA mixtures are prepared prior to a KCE experiment. The use of commercially available "high DNA recovery" sample vials does not resolve the problem. We have found that the problem can be significantly alleviated by the passivation of the vial surface with blocking agents, such as masking DNA or bovine serum albumin (BSA). The described adsorption of DNA to the surface of sample vials may also be important in other procedures that deal with low DNA concentrations, such as aptamer selection and quantitative PCR.
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Affiliation(s)
- Mirzo Kanoatov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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Krylova SM, Dove PM, Kanoatov M, Krylov SN. Slow-dissociation and slow-recombination assumptions in nonequilibrium capillary electrophoresis of equilibrium mixtures. Anal Chem 2011; 83:7582-5. [PMID: 21853979 DOI: 10.1021/ac2018876] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a kinetic affinity method with both analytical and preparative applications. NECEEM requires that the dissociation of the complexes be negligible in its first phase and the recombination of the dissociated complexes be negligible in its second phase. Here, we introduce a method, which facilitates easy examination of whether or not these requirements are satisfied. We derived expressions for two parameters, termed the slow-dissociation parameter (SDP) and slow-recombination parameter (SRP), which can be used to assess the assumptions. Both parameters should be much less than 1 for the assumptions to be satisfied. We calculated the two parameters for new and previously published NECEEM experiments and found that the assumptions were satisfied in all of them. Finally, we discuss changes to NECEEM conditions that should be done if the assumptions are found not to be satisfied. The SDP/SRP assessment helps to easily validate the results of NECEEM-based analyses and thus makes the NECEEM method more robust.
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Affiliation(s)
- Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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de Jong S, Krylov SN. Protein labeling enhances aptamer selection by methods of kinetic capillary electrophoresis. Anal Chem 2011; 83:6330-5. [PMID: 21728308 DOI: 10.1021/ac201242r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methods of kinetic capillary electrophoresis (KCE) facilitate highly efficient selection of DNA aptamers for protein targets. The inability to detect native proteins at low concentrations in capillary electrophoresis creates, however, a significant obstacle for many important protein targets. Here we suggest that protein labeling with new Chromeo dyes can help to overcome this obstacle. By labeling a number of proteins with Chromeo P503, we show that the labeling procedure enables accurate detection of proteins in CE without significantly affecting their electrophoretic mobility or their ability to bind DNA. Moreover, Chromeo P503 does not appear to label the amino-groups of buffer components to a significant extent, making the labeling procedure compatible with a large number of selection and run buffers. Fluorescent labeling of protein targets with Chromeo dyes empowers selection of aptamers by KCE methods and promises to increase the rate at which aptamers for new targets are being developed and introduced in various applications.
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