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Bakhshandeh F, Zheng H, Barra NG, Sadeghzadeh S, Ausri I, Sen P, Keyvani F, Rahman F, Quadrilatero J, Liu J, Schertzer JD, Soleymani L, Poudineh M. Wearable Aptalyzer Integrates Microneedle and Electrochemical Sensing for In Vivo Monitoring of Glucose and Lactate in Live Animals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2313743. [PMID: 38752744 DOI: 10.1002/adma.202313743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/13/2024] [Indexed: 06/19/2024]
Abstract
Continuous monitoring of clinically relevant biomarkers within the interstitial fluid (ISF) using microneedle (MN)-based assays, has the potential to transform healthcare. This study introduces the Wearable Aptalyzer, an integrated system fabricated by combining biocompatible hydrogel MN arrays for ISF extraction with an electrochemical aptamer-based biosensor for in situ monitoring of blood analytes. The use of aptamers enables continuous monitoring of a wide range of analytes, beyond what is possible with enzymatic monitoring. The Wearable Aptalyzer is used for real-time and multiplexed monitoring of glucose and lactate in ISF. Validation experiments using live mice and rat models of type 1 diabetes demonstrate strong correlation between the measurements collected from the Wearable Aptalyzer in ISF and those obtained from gold-standard techniques for blood glucose and lactate, for each analyte alone and in combination. The Wearable Aptalyzer effectively addresses the limitations inherent in enzymatic detection methods as well as solid MN biosensors and the need for reliable and multiplexed bioanalytical monitoring in vivo.
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Affiliation(s)
- Fatemeh Bakhshandeh
- Department of Engineering Physics, McMaster University Hamilton, Hamilton, L8S 4L8, Ontario, Canada
| | - Hanjia Zheng
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Nicole G Barra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8S 4L8, Ontario, Canada
| | - Sadegh Sadeghzadeh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Irfani Ausri
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Payel Sen
- Department of Engineering Physics, McMaster University Hamilton, Hamilton, L8S 4L8, Ontario, Canada
| | - Fatemeh Keyvani
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Fasih Rahman
- Department of Kinesiology and Health Science, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Joe Quadrilatero
- Department of Kinesiology and Health Science, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, University of Waterloo, Waterloo, N2L 3G1, Canada
| | - Jonathan D Schertzer
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8S 4L8, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, L8S 4L8, Ontario, Canada
- Centre for Metabolism, Obesity and Diabetes Research, McMaster University, Hamilton, L8S 4L8, Ontario, Canada
| | - Leyla Soleymani
- Department of Engineering Physics, McMaster University Hamilton, Hamilton, L8S 4L8, Ontario, Canada
- School of Biomedical Engineering, McMaster University, Hamilton, L8S 4L8, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, L8S 4L8, Ontario, Canada
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, N2L 3G1, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, N2L 3W4, ON, Canada
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2
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Bržezická T, Kohútová L, Glatz Z. Atypical applications of transverse diffusion of laminar flow profiles methodology for in-capillary reactions in capillary electrophoresis. J Sep Sci 2024; 47:e2400157. [PMID: 38982555 DOI: 10.1002/jssc.202400157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Capillary electrophoresis (CE) is a powerful separation technique offering quick and efficient analyses in various fields of bioanalytical chemistry. It is characterized by many well-known advantages, but one, which is perhaps the most important for this application field, is somewhat overlooked. It is the possibility to perform chemical and biochemical reactions at the nL scale inside the separation capillary. There are two basic formats applicable for this purpose, heterogeneous and homogeneous. In the former, one reactant is immobilized onto a particle or monolithic support or directly on the capillary wall, and the other is injected. In the latter, the reactant mixing inside a capillary is based on electromigration or diffusion. One of the diffusion-based methodologies, termed Transverse Diffusion of Laminar Flow Profiles, is the subject of this review. Since most studies utilizing in-capillary reactions in CE focus on enzymes, which are being continuously and exhaustively reviewed, this review covers the atypical applications of this methodology, but still in the bioanalytical field. As can be seen from the demonstrated applications, they are not limited to reactions, but can also be utilized for other biochemical systems.
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Affiliation(s)
- Taťána Bržezická
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lenka Kohútová
- 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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3
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Walter J, Eludin Z, Drabovich AP. Redefining serological diagnostics with immunoaffinity proteomics. Clin Proteomics 2023; 20:42. [PMID: 37821808 PMCID: PMC10568870 DOI: 10.1186/s12014-023-09431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lack of universal reference standards, potential cross-reactivity, and challenges with multiplexing the complete panel of human immunoglobulin isotypes and subclasses. Redesign of conventional serological tests to include multiplex quantification of immunoglobulin isotypes and subclasses, utilize universal reference standards, and minimize cross-reactivity and non-specific binding will facilitate the development of assays with higher diagnostic specificity. Improved serological assays with higher diagnostic specificity will enable screenings of asymptomatic populations and may provide earlier detection of infectious diseases, autoimmune disorders, and cancer. In this review, we present the major clinical needs for serological diagnostics, overview conventional immunoassay detection techniques, present the emerging immunoassay detection technologies, and discuss in detail the advantages and limitations of mass spectrometry and immunoaffinity proteomics for serological diagnostics. Finally, we explore the design of novel immunoaffinity-proteomic assays to evaluate cell-mediated immunity and advance the sequencing of clinically relevant immunoglobulins.
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Affiliation(s)
- Jonathan Walter
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zicki Eludin
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
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4
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Wang TY, Rukundo JL, Le ATH, Ivanov NA, Le Blanc JCY, Gorin BI, Krylov SN. Transient Incomplete Separation of Species with Close Diffusivity to Study the Stability of Affinity Complexes. Anal Chem 2022; 94:15415-15422. [DOI: 10.1021/acs.analchem.2c03313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Ye Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | - Jean-Luc Rukundo
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | - An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | - Nikita A. Ivanov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
| | | | - Boris I. Gorin
- Eurofins CDMO Alphora, 2395 Speakman Drive #2001, Mississauga, OntarioL5K 1B3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, OntarioM3J 1P3, Canada
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5
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Onaş AM, Dascălu C, Raicopol MD, Pilan L. Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets. BIOSENSORS 2022; 12:816. [PMID: 36290952 PMCID: PMC9599214 DOI: 10.3390/bios12100816] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.
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Affiliation(s)
- Andra Mihaela Onaş
- Advanced Polymer Materials Group, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Constanţa Dascălu
- Faculty of Applied Sciences, University ‘Politehnica’ of Bucharest, 313 Splaiul Independenţei, District 6, 060042 Bucharest, Romania
| | - Matei D. Raicopol
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
| | - Luisa Pilan
- Faculty of Chemical Engineering and Biotechnologies, University ‘Politehnica’ of Bucharest, 1-7 Gheorghe Polizu, District 1, 011061 Bucharest, Romania
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6
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Fu Z, Rais Y, Dara D, Jackson D, Drabovich AP. Rational Design and Development of SARS-CoV-2 Serological Diagnostics by Immunoprecipitation-Targeted Proteomics. Anal Chem 2022; 94:12990-12999. [PMID: 36095284 PMCID: PMC9523617 DOI: 10.1021/acs.analchem.2c01325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Current design of serological tests utilizes conservative
immunoassay
approaches and is focused on fast and convenient assay development,
throughput, straightforward measurements, and affordability. Limitations
of common serological assays include semiquantitative measurements,
cross-reactivity, lack of reference standards, and no differentiation
between human immunoglobulin subclasses. In this study, we suggested
that a combination of immunoaffinity enrichments with targeted proteomics
would enable rational design and development of serological assays
of infectious diseases, such as COVID-19. Immunoprecipitation-targeted
proteomic assays allowed for sensitive and specific measurements of
NCAP_SARS2 protein with a limit of detection of 313 pg/mL in serum
and enabled differential quantification of anti-SARS-CoV-2 antibody
isotypes (IgG, IgA, IgM, IgD, and IgE) and individual subclasses (IgG1-4
and IgA1-2) in plasma and saliva. Simultaneous evaluation of the numerous
antigen–antibody subclass combinations revealed a receptor-binding
domain (RBD)-IgG1 as a combination with the highest diagnostic performance.
Further validation revealed that anti-RBD IgG1, IgG3, IgM, and IgA1
levels were significantly elevated in convalescent plasma, while IgG2,
IgG4, and IgA2 were not informative. Anti-RBD IgG1 levels in convalescent
(2138 ng/mL) vs negative (95 ng/mL) plasma revealed 385 ng/mL as a
cutoff to detect COVID-19 convalescent plasma. Immunoprecipitation-targeted
proteomic assays will facilitate improvement and standardization of
the existing serological tests, enable rational design of novel tests,
and offer tools for the comprehensive investigation of immunoglobulin
subclass cooperation in immune response.
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Affiliation(s)
- Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Delaram Dara
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Dana Jackson
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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7
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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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8
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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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Hartati YW, Komala DR, Hendrati D, Gaffar S, Hardianto A, Sofiatin Y, Bahti HH. An aptasensor using ceria electrodeposited-screen-printed carbon electrode for detection of epithelial sodium channel protein as a hypertension biomarker. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202040. [PMID: 33972878 PMCID: PMC8074578 DOI: 10.1098/rsos.202040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/20/2021] [Indexed: 06/02/2023]
Abstract
Epithelial sodium channel (ENaC) is a transmembrane protein that has an essential role in maintaining the levels of sodium in blood plasma. A person with a family history of hypertension has a high enough amount of ENaC protein in the kidneys or other organs, so that the ENaC protein acts as a marker that a person is susceptible to hypertension. An aptasensor involves aptamers, which are oligonucleotides that function similar to antibodies, as sensing elements. An electrochemical aptasensor for the detection of ENaC was developed using a screen-printed carbon electrode (SPCE) which was modified by electrodeposition of cerium oxide (CeO2). The aptamer immobilization was via the streptavidin-biotin system. The measurement of changes in current of the active redox [Fe(CN)6]3-/4- was carried out by differential pulse voltammetry. The surfaces of SPCE and SPCE/CeO2 were characterized using scanning electron microscopy, voltammetry and electrochemical impedance spectroscopy. The Box-Behnken experimental optimization design revealed the streptavidin incubation time, aptamer incubation time and streptavidin concentrations were 30 min, 30 min and 10.8 µg ml-1, respectively. Various concentrations of ENaC were used to obtain the linearity range of 0.05-3.0 ng ml-1, and the limits of detection and quantification were 0.012 ng ml-1 and 0.038 ng ml-1, respectively. This aptasensor method has the potential to measure the ENaC protein levels in urine samples as well as to be a point-of-care device.
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Affiliation(s)
- Yeni Wahyuni Hartati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Dina Ratna Komala
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Diana Hendrati
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Shabarni Gaffar
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Ari Hardianto
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
| | - Yulia Sofiatin
- Department of Public Health, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Husein Hernandi Bahti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia
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10
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Hoshino H, Kasahara Y, Kuwahara M, Obika S. DNA Polymerase Variants with High Processivity and Accuracy for Encoding and Decoding Locked Nucleic Acid Sequences. J Am Chem Soc 2020; 142:21530-21537. [PMID: 33306372 DOI: 10.1021/jacs.0c10902] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Xenobiotic nucleic acids (XNAs) are chemically modified nucleic acid analogues with potential applications in nucleic acid-based therapeutics including nucleic acid aptamers, ribozymes, small interfering RNAs, and antisense oligonucleotides. We have developed a promising XNA for therapeutic uses, 2',4'-bridged nucleic acid (2',4'-BNA), also known as locked nucleic acid (LNA). Unlike the rational design of small interfering and antisense oligonucleotides, the development of LNA aptamers and catalysts requires genetically engineered polymerases that enable the synthesis of LNA from DNA and the converse reverse transcription. However, no LNA decoders or encoders with sufficient performance have been developed. In this study, we developed variants of KOD DNA polymerase, a family B DNA polymerase derived from Thermococcus kodakarensis KOD1, which are effective LNA decoders and encoders, via structural analyses. KOD DGLNK (KOD: N210D/Y409G/A485L/D614N/E664K) enabled LNA synthesis from DNA (DNA → LNA), and KOD DLK (KOD: N210D/A485L/E664K) enabled LNA reverse transcription to DNA (LNA → DNA). Both variants exhibited greatly improved efficiency and accuracy. Notably, we synthesized LNAs longer than one kilobase using KOD DGLNK. We also showed that these variants can accept 2'-O-methyl (2'-OMe), a common modification for therapeutic uses. Here, we also show that LNA and 2'-OMe mix aptamer can be practically obtained via SELEX. The variants can be used as powerful tools for creating XNA aptamers and catalysts to completely eliminate the natural species, DNA and RNA.
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Affiliation(s)
- Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Diagnostic and Therapeutic Value of Aptamers in Envenomation Cases. Int J Mol Sci 2020; 21:ijms21103565. [PMID: 32443562 PMCID: PMC7278915 DOI: 10.3390/ijms21103565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
It is now more than a century since Albert Calmette from the Institut Pasteur changed the world of envenomation by demonstrating that antibodies raised against animal venoms have the ability to treat human victims of previously fatal bites or stings. Moreover, the research initiated at that time effectively launched the discipline of toxicology, first leading to the search for toxic venom components, followed by the demonstration of venoms that also contained compounds of therapeutic value. Interest from pharmaceutical companies to treat envenomation is, however, declining, mainly for economic reasons, and hence, the World Health Organization has reclassified this public health issue to be a highest priority concern. While the production, storage, and safety of antivenom sera suffer from major inconveniences, alternative chemical and technological approaches to the problem of envenomation need to be considered that bypass the use of antibodies for toxin neutralization. Herein, we review an emerging strategy that relies on the use of aptamers and discuss how close—or otherwise—we are to finding a viable alternative to the use of antibodies for the therapy of human envenomation.
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12
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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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13
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High-efficiency selection of aptamers for bovine lactoferrin by capillary electrophoresis and its aptasensor application in milk powder. Talanta 2019; 205:120088. [PMID: 31450439 DOI: 10.1016/j.talanta.2019.06.088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/14/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023]
Abstract
Capillary electrophoresis-based systematic evolution of ligands by exponential enrichment (CE-SELEX) is a high-efficient technique for aptamers selection, and has been evolved into many modes. In this study, we obtained the aptamer against bovine lactoferrin (BLF) with high affinity (dissociation constant, Kd = 20.74 ± 6.89 nM) and good specificity (>1000 folds) using single step CE-SELEX (ssCE-SELEX) mode. In the selection process, ssCE demonstrated high-efficiency selection with bulk Kd reaching at 0.19 ± 0.04 μM by only two rounds, as compared to capillary zone electrophoresis (CZE) mode with Kd of 0.39 ± 0.03 μM. Next-generation sequencing (NGS) was performed by two methods of high output (Hiseq) and medium output (Miseq) with different sequencing depths, and their same results of high-frequency sequences confirmed the reliability of the obtained sequences. Through affinity analysis, the primer region and single base mutation (SBM) were observed to affect the sequence structure and to result in affinity change. Besides, molecular dynamics (MD) simulation was performed to validate the binding affinity of the candidates with BLF by analyzing binding sites, interaction forces, and binding free energy. Moreover, BLF detection in milk powder matrices was completed successfully with the optimized CE-aptasensor. The signal response was in a good linear relationship (R2 = 0.9930) with 4-128 nM of BLF and the detection limit was 1 nM. The obtained results of BLF in four milk powder samples were in an acceptable agreement with the labeled concentrations. This study presented a completed CE based process including aptamers selection, affinity characterization, and detection application, which also validated the high-efficiency selection of ssCE-SELEX mode.
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14
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Le ATH, Krylova SM, Krylov SN. Determination of the Equilibrium Constant and Rate Constant of Protein-Oligonucleotide Complex Dissociation under the Conditions of Ideal-Filter Capillary Electrophoresis. Anal Chem 2019; 91:8532-8539. [PMID: 31136154 DOI: 10.1021/acs.analchem.9b01801] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ideal-filter capillary electrophoresis (IFCE) allows selection of protein binders from oligonucleotide libraries in a single step of partitioning in which protein-bound and unbound oligonucleotides move in the opposite directions. In IFCE, the unbound oligonucleotide does not reach the detector, imposing a problem for finding the equilibrium constant ( Kd) and rate constant ( koff) of protein-oligonucleotide complex dissociation. We report a double-passage approach that allows finding Kd and koff under the IFCE conditions, i.e. near-physiological pH and ionic strength. First, a plug of the protein-oligonucleotide equilibrium mixture passes to the detector in a pressure-driven flow, allowing for both the complex and free oligonucleotide to be detected as a single first peak. Second, the pressure is turned off and the voltage is applied to reverse the migration of only the complex which is detected as the second peak. The experiment is repeated with a lower voltage consequently resulting in longer travel time of the complex to the detector, greater extent of complex dissociation, and the decreased area of the second peak. Finally, the peak areas are used to calculate the values of Kd and koff. Here we explain theoretical and practical aspects of the double-passage approach, prove its validity quantitatively, and, demonstrate its application to determine Kd and koff for an affinity complex between a protein and its DNA aptamer. The double-passage approach for finding Kd and koff of protein-oligonucleotide complexes under the IFCE conditions is a perfect complement for IFCE-based selection of protein binders from oligonucleotide libraries.
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Affiliation(s)
- An T H Le
- 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
| | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions , York University , Toronto , Ontario M3J 1P3 , Canada
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15
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Gu L, Yan W, Wu H, Fan S, Ren W, Wang S, Lyu M, Liu J. Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum. Anal Chem 2019; 91:7887-7893. [DOI: 10.1021/acs.analchem.9b01707] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - Wei Ren
- Key Laboratory of Marine Biology, Nanjing Agricultural University, Nanjing, Jiangsu 210000, P. R. China
| | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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16
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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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17
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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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18
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Tanaka K, Kasahara Y, Miyamoto Y, Okuda T, Kasai T, Onodera K, Kuwahara M, Oka M, Yoneda Y, Obika S. Development of oligonucleotide-based antagonists of Ebola virus protein 24 inhibiting its interaction with karyopherin alpha 1. Org Biomol Chem 2019; 16:4456-4463. [PMID: 29850750 DOI: 10.1039/c8ob00706c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The investigation of protein-protein interactions (PPIs) and the preparation of antagonists are important for determining whether certain proteins are suitable medical targets. In the present study, we used the capillary electrophoresis-systematic evolution of ligands by exponential enrichment to generate natural and artificial nucleic acid aptamers targeting Ebola virus protein 24 (eVP24), demonstrating that artificial aptamers, synthesised utilising a uridine analogue with an adenine residue at its C5 position, exhibited activities exceeding those of natural ones. To confirm the functionality of the as-prepared aptamers, their abilities to inhibit the PPIs of eVP24 were determined by capillary electrophoresis and bio-layer interferometry, and the obtained results unambiguously demonstrated that these aptamers interacted with the functional site of eVP24 and were thus good antagonists.
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Affiliation(s)
- Keisuke Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
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19
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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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20
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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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21
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Zhu C, Wang X, Li L, Hao C, Hu Y, Rizvi AS, Qu F. Online reaction based single-step CE for Protein-ssDNA complex obtainment to assist aptamer selection. Biochem Biophys Res Commun 2018; 506:169-175. [PMID: 30340834 DOI: 10.1016/j.bbrc.2018.08.189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/07/2023]
Abstract
CE application in aptamer selection (CE-SELEX) shows more advantages than other selection methods. In this study, an online reaction based single-step CE (ssCE) mode was employed for fast obtaining protein-ssDNA complex. Using human thrombin (H-Thr) and its aptamer Apt29 as models, we accomplished the procedures of mixing, reaction, separation, detection and complex collection in single step online process, which took about 10 min to obtain the H-Thr/Apt29 complex. Important factors, affecting the aptamer and H-Thr interaction (buffer, ratio of aptamer and H-Thr amount), and complex separation and collection (voltage and temperature) were discussed. Later, the online reaction of H-Thr with an 80 nt ssDNA library was realized under optimized conditions, and the H-Thr/ssDNA complex was collected and subjected to PCR. By analyzing the PCR product through capillary gel electrophoresis, the resulting approximative 80 nt DNA length validated the ssDNA sequence in complex. To confirm the availability of ssCE mode, two ssDNA libraries with different lengths (56 nt and 82 nt ssDNA) and three proteins (platelet derived growth factor, PDGF-BB; lactoferrin protein, LF; and single-strand DNA binding protein, SSB) were utilized. Their complex peaks were also observed in electropherograms as expected. Additionally, the online incubation of ssDNA and H-Thr was achieved by stopping the separation voltage for some time when ssDNA passed the H-Thr zone. Our results show the ssCE mode has apparent merits of saving time and sample cost for aptamer selection against protein targets.
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Affiliation(s)
- Chao Zhu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Xiaoqian Wang
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Linsen Li
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Chenxu Hao
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Youhao Hu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Aysha Sarfraz Rizvi
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Feng Qu
- The School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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22
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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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23
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Yan Z, Wang J. Quantifying the Kinetic Residence Time as a Potential Complement to Affinity for the Aptamer Selection. J Phys Chem B 2018; 122:8380-8385. [PMID: 30114357 DOI: 10.1021/acs.jpcb.8b06418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aptamers have been widely developed for biotechnological and therapeutic applications in recent years. Increasing evidence shows that the quality of the aptamer is determined not only by the thermodynamic stability but also by the kinetic residence time when binding with its target. However, both experimental and computational selection methods of aptamers concentrate solely on the binding affinity optimization. Here, we propose a computational method for the quantification of the residence time by describing the kinetics on the underlying funneled binding energy landscape of aptamer-target complex as a diffusion process. The quantified residence time is examined to have the capacity to discriminate native aptamer-target complexes against non-native ones. It is found that the residence time is correlated with the binding affinity but with significant dispersion, suggesting that the residence time can be a potential complement in selecting the aptamer. On the basis of the results, a two-dimensional selection method with both the thermodynamic binding affinity and the residence time as kinetic specificity is suggested for diverse applications of aptamers. This alters conventional aptamer selection methods by considering the kinetic residence time in addition to the affinity.
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Affiliation(s)
- Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun , Jilin 130022 , P. R. China.,Department of Chemistry & Physics , State University of New York at Stony Brook , Stony Brook , New York 11794-3400 , United States
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24
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Kochmann S, Le ATH, Hili R, Krylov SN. Predicting efficiency of NECEEM‐based partitioning of protein binders from nonbinders in DNA‐encoded libraries. Electrophoresis 2018; 39:2991-2996. [DOI: 10.1002/elps.201800270] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sven Kochmann
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
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25
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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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26
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Morihiro K, Kasahara Y, Obika S. Biological applications of xeno nucleic acids. MOLECULAR BIOSYSTEMS 2017; 13:235-245. [PMID: 27827481 DOI: 10.1039/c6mb00538a] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Xeno nucleic acids (XNAs) are a group of chemically modified nucleic acid analogues that have been applied to various biological technologies such as antisense oligonucleotides, siRNAs and aptamers.
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Affiliation(s)
- Kunihiko Morihiro
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan and Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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27
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Volk DE, Lokesh GLR. Development of Phosphorothioate DNA and DNA Thioaptamers. Biomedicines 2017; 5:E41. [PMID: 28703779 PMCID: PMC5618299 DOI: 10.3390/biomedicines5030041] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/03/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers are short RNA- or DNA-based affinity reagents typically selected from combinatorial libraries to bind to a specific target such as a protein, a small molecule, whole cells or even animals. Aptamers have utility in the development of diagnostic, imaging and therapeutic applications due to their size, physico-chemical nature and ease of synthesis and modification to suit the application. A variety of oligonucleotide modifications have been used to enhance the stability of aptamers from nuclease degradation in vivo. The non-bridging oxygen atoms of the phosphodiester backbones of RNA and DNA aptamers can be substituted with one or two sulfur atoms, resulting in thioaptamers with phosphorothioate or phosphorodithioate linkages, respectively. Such thioaptamers are known to have increased binding affinity towards their target, as well as enhanced resistance to nuclease degradation. In this review, we discuss the development of phosphorothioate chemistry and thioaptamers, with a brief review of selection methods.
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Affiliation(s)
- David E Volk
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Ganesh L R Lokesh
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
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28
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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29
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Li HH, Wen CY, Hong CY, Lai JC. Evaluation of aptamer specificity with or without primers using clinical samples for C-reactive protein by magnetic-assisted rapid aptamer selection. RSC Adv 2017. [DOI: 10.1039/c7ra07249j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aptamers with primer binding sites are necessary for the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process.
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Affiliation(s)
- Huan-Hao Li
- Department of Mechanical Engineering
- Hong Kong Polytechnic University
- Hong Kong Special Administrative Region
- Hong Kong
| | - Chih-Yung Wen
- Department of Mechanical Engineering
- Hong Kong Polytechnic University
- Hong Kong Special Administrative Region
- Hong Kong
| | - Chin-Yih Hong
- Graduate Institute of Biomedical Engineering
- National Chung Hsing University
- Taichung
- Taiwan
| | - Ji-Ching Lai
- Institute of Electro-optical Science and Technology
- National Taiwan Normal University
- Taipei
- Taiwan
- Research Assistant Center
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30
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Ouyang W, Ko SH, Wu D, Wang AY, Barone PW, Hancock WS, Han J. Microfluidic Platform for Assessment of Therapeutic Proteins Using Molecular Charge Modulation Enhanced Electrokinetic Concentration Assays. Anal Chem 2016; 88:9669-9677. [PMID: 27624735 DOI: 10.1021/acs.analchem.6b02517] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Therapeutic proteins (TPs) are critical in modern medicine, yet shortage of TPs in disaster situations and remote areas remains a worldwide challenge. Manufacturing and real-time release of TPs on demand at the point-of-care is considered the key to this issue, which requires reliable and rapid analytics techniques for quality assurance. Herein we report a microfluidic platform that could be implemented in-line and at the point-of-care for real-time decision-making about the quality of a TP. The in vivo efficacy and duration of efficacy of TPs were assessed by the equilibrium and kinetics of TP and TP receptor (TPR) binding, using electrokinetic concentration (EC) and molecular charge modulation (MCM). EC can simultaneously concentrate and separate bound and unbound species in an assay based on electrical mobility, allowing for the quantification of binding. MCM enables the application of EC to arbitrary TPs by enhancing the mobility differences between TPs, TPRs, and TP-TPR complexes. This technology is homogeneous and overcomes many practical challenges of conventional heterogeneous assays. We developed various formats of assays for equilibrium and kinetic analysis and rapid determination of degradation of TPs, obtaining results comparable to state-of-the-art technologies with significantly less time (<1 h) and simpler setup. Finally, we demonstrated that the results of MCM-EC based assays correlated well with those from mass spectrometry and cell-based assay, which are the industrial standards for quality testing of TPs.
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Affiliation(s)
| | | | - Di Wu
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Annie Yu Wang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | | | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
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31
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Kanoatov M, Mehrabanfar S, Krylov SN. Systematic Approach to Optimization of Experimental Conditions in Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures. Anal Chem 2016; 88:9300-8. [DOI: 10.1021/acs.analchem.6b02882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mirzo Kanoatov
- Department of Chemistry and
Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sina Mehrabanfar
- 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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32
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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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33
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Lou B, Chen E, Zhao X, Qu F, Yan J. The application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution. J Chromatogr A 2016; 1437:203-209. [PMID: 26877178 DOI: 10.1016/j.chroma.2016.01.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 01/06/2016] [Accepted: 01/27/2016] [Indexed: 01/16/2023]
Abstract
Whole-cell SELEX faces more difficulties than SELEX against purified molecules target. In this work, we demonstrate the application of capillary electrophoresis for assisting whole-cell aptamers selection by characterizing complete ssDNA distribution. We chose three cancer cell lines U251, Hela and PC3 as target, FAM labeled Sgc8c (a 41mer aptamer) and FAM labeled 41mer random ssDNA library as ssDNA model. CE conditions of running buffer and capillary length and inner diameter as well as UV and LIF detection were optimized. The distribution percentage of Sgc8c and ssDNA library against U251, Hela and PC3 was demonstrated, the relative peak area of their complex is 8.94%, 1.05% and 0.44% for Sgc8c and 9.03%, 1.04% and 0.12% for ssDNA library respectively. Under the chosen experimental conditions, binding ability comparison of three cell lines was U251>Hela>PC3, which was validated by laser confocol microscope. For each cell, distribution percentage of ssDNA library was compared with that of Sgc8c. Finally, whole-cell complex of U251-Sgc8c was confirmed by increase incubation time and fraction CE analysis.
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Affiliation(s)
- Beilei Lou
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Erning Chen
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Centre for Physical and Chemical Analysis, Beijing 100089, China
| | - Xinying Zhao
- Beijing Centre for Physical and Chemical Analysis, Beijing 100089, China
| | - Feng Qu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Jieying Yan
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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34
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Dong L, Tan Q, Ye W, Liu D, Chen H, Hu H, Wen D, Liu Y, Cao Y, Kang J, Fan J, Guo W, Wu W. Screening and Identifying a Novel ssDNA Aptamer against Alpha-fetoprotein Using CE-SELEX. Sci Rep 2015; 5:15552. [PMID: 26497223 PMCID: PMC4620443 DOI: 10.1038/srep15552] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Alpha-fetoprotein (AFP) is a liver cancer associated protein and has long been utilized as a serum tumor biomarker of disease progression. AFP is usually detected in HCC patients by an antibody based system. Recently, however, aptamers generated from systematic evolution of ligands by exponential enrichment (SELEX) were reported to have an alternative potential in targeted imaging, diagnosis and therapy. In this study, AFP-bound ssDNA aptamers were screened and identified using capillary electrophoresis (CE) SELEX technology. After cloning, sequencing and motif analysis, we successfully confirmed an aptamer, named AP273, specifically targeting AFP. The aptamer could be used as a probe in AFP immunofluorescence imaging in HepG2, one AFP positive cancer cell line, but not in A549, an AFP negative cancer cell line. More interesting, the aptamer efficiently inhibited the migration and invasion of HCC cells after in vivo transfection. Motif analysis revealed that AP273 had several stable secondary motifs in its structure. Our results indicate that CE-SELEX technology is an efficient method to screen specific protein-bound ssDNA, and AP273 could be used as an agent in AFP-based staining, diagnosis and therapy, although more works are still needed.
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Affiliation(s)
- Lili Dong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Qiwen Tan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Ye
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongli Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Haifeng Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongwei Hu
- Shanghai Aijin Biochemical Science &Technology Co. Ltd., Shanghai 200336, China
| | - Duo Wen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Yang Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Ya Cao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Key Laboratory of Chinese Ministry of Education, Changsha 410078, China
| | - Jingwu Kang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.,Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Weizhong Wu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
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35
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Hilton JP, Olsen T, Kim J, Zhu J, Nguyen T, Barbu M, Pei R, Stojanovic M, Lin Q. Isolation of thermally sensitive protein-binding oligonucleotides on a microchip. MICROFLUIDICS AND NANOFLUIDICS 2015; 19:795-804. [PMID: 31223297 PMCID: PMC6586242 DOI: 10.1007/s10404-015-1604-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/24/2015] [Indexed: 06/07/2023]
Abstract
This paper presents a microfluidic chip capable of isolating thermally sensitive protein-binding aptamer candidates. The chip makes use of bead-immobilized target molecules and DNA (deoxyribonucleic acid) sequences to enable a simplified chip design, in which affinity selection and PCR (polymerase chain reaction) amplification of target-binding sequences occur in temperature-controlled microchambers. Using pressure-driven flow, buffer containing single-stranded DNA molecules with randomized sequences is cycled through a series of affinity selection and PCR amplification steps on microbeads. Successive introduction of the sample to each chamber effects a process of competition whereby DNA strands with weak binding strength to target molecules are rejected in favor of strongly binding sequences. Using bead-based PCR, the amplification step was miniaturized and integrated with affinity selection, resulting in significant reductions in process time and reagent use. As a demonstration, temperature-dependent selection and amplification of single-stranded oligonucleotides that bind to human Immuno-globulin E (IgE) was performed in 4 h, a 20-fold reduction in process time as compared to conventional methods that would require approximately a week. Fluorescent binding assays then demonstrated that the desired temperature specificity was imparted to the aptamer candidates within just one round of selection, and within two rounds the aptamer candidates exhibited enhanced affinity toward IgE.
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Affiliation(s)
- John P. Hilton
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Timothy Olsen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Jinho Kim
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Mihaela Barbu
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Renjun Pei
- Suzhou Institute of Nano‑Tech and Nano‑Bionics, Chinese Academy of Sciences, Suzhou 215123, Jiangsu, China
| | - Milan Stojanovic
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
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36
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Zheng X, Bi C, Li Z, Podariu M, Hage DS. Analytical methods for kinetic studies of biological interactions: A review. J Pharm Biomed Anal 2015; 113:163-80. [PMID: 25700721 PMCID: PMC4516701 DOI: 10.1016/j.jpba.2015.01.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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37
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Tang T, Deng J, Zhang M, Shi G, Zhou T. Quantum dot-DNA aptamer conjugates coupled with capillary electrophoresis: A universal strategy for ratiometric detection of organophosphorus pesticides. Talanta 2015; 146:55-61. [PMID: 26695234 DOI: 10.1016/j.talanta.2015.08.023] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/29/2022]
Abstract
Based on the highly sensitivity and stable-fluorescence of water-soluble CdTe/CdS core-shell quantum dots (QDs) with broad-specificity DNA aptamers, a novel ratiometric detection strategy was proposed for the sensitive detection of organophosphorus pesticides by capillary electrophoresis with laser-induced fluorescence (CE-LIF). The as-prepared QDs were first conjugated with the amino-modified oligonucleotide (AMO) by amidation reaction, which is partial complementary to the DNA aptamer of organophosphorus pesticides. Then QD-labeled AMO (QD-AMO) was incubated with the DNA aptamer to form QD-AMO-aptamer duplex. When the target organophosphorus pesticides were added, they could specifically bind the DNA aptamer, leading to the cleavage of QD-AMO-aptamer duplex, accompany with the release of QD-AMO. As a result, the ratio of peak height between QD-AMO and QD-AMO-aptamer duplex changed in the detection process of CE-LIF. This strategy was subsequently applied for the detection of phorate, profenofos, isocarbophos, and omethoate with the detection limits of 0.20, 0.10, 0.17, and 0.23μM, respectively. This is the first report about using QDs as the signal indicators for organophosphorus pesticides detection based on broad-specificity DNA aptamers by CE-LIF, thus contributing to extend the scope of application of QDs in different fields. The proposed method has great potential to be a universal strategy for rapid detection of aptamer-specific small molecule targets by simply changing the types of aptamer sequences.
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Affiliation(s)
- Tingting Tang
- School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jingjing Deng
- School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241 PR China.
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241 PR China
| | - Tianshu Zhou
- School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, PR China.
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38
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Whitty EG, Maniego AR, Bentwitch SA, Guillaneuf Y, Jones MR, Gaborieau M, Castignolles P. Cellular Response to Linear and Branched Poly(acrylic acid). Macromol Biosci 2015; 15:1724-34. [PMID: 26257305 DOI: 10.1002/mabi.201500153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/29/2015] [Indexed: 12/14/2022]
Abstract
Poly(acrylic acid-co-sodium acrylate) (PNaA) is a pH-responsive polymer with potential in anticancer drug delivery. The cytotoxicity and intracellular effects of 3-arm star, hyperbranched and linear PNaA were investigated with L1210 progenitor leukemia cells and L6 myoblast cells. Free solution capillary electrophoresis demonstrated interactions of PNaA with serum proteins. In a 72 h MTT assay most PNaAs exhibited a IC50 between 7 and 14 mmol L(-1), showing that precipitation may be a sufficient purification for PNaA dilute solutions. Dialyzed 3-arm star and hyperbranched PNaA caused an increase in L6 cell viability, challenging the suitability of MTT as cytotoxicity assay for PNaA. Fluorescent confocal microscopy revealed merging of cellular lipids after exposure to PNaA, likely caused by serum starvation.
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Affiliation(s)
- Elizabeth G Whitty
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Alison R Maniego
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Sharon A Bentwitch
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Yohann Guillaneuf
- CNRS, Institut de Chimie Radicalaire, Aix-Marseille Université, UMR 7273, 13397, Marseille, France
| | - Mark R Jones
- University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Marianne Gaborieau
- University of Western Sydney, Molecular Medicine Research Group, Locked Bag 1797, Penrith, New South Wales, 2751, Australia. .,University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia. .,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia.
| | - Patrice Castignolles
- University of Western Sydney, Australian Centre for Research on Separation Science (ACROSS), Locked Bag 1797, Penrith, New South Wales, 2751, Australia.,University of Western Sydney, School of Science and Health, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
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39
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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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40
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Kanoatov M, Galievsky VA, Krylova SM, Cherney LT, Jankowski HK, Krylov SN. Using nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) for simultaneous determination of concentration and equilibrium constant. Anal Chem 2015; 87:3099-106. [PMID: 25668425 DOI: 10.1021/acs.analchem.5b00171] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a versatile tool for studying affinity binding. Here we describe a NECEEM-based approach for simultaneous determination of both the equilibrium constant, K(d), and the unknown concentration of a binder that we call a target, T. In essence, NECEEM is used to measure the unbound equilibrium fraction, R, for the binder with a known concentration that we call a ligand, L. The first set of experiments is performed at varying concentrations of T, prepared by serial dilution of the stock solution, but at a constant concentration of L, which is as low as its reliable quantitation allows. The value of R is plotted as a function of the dilution coefficient, and dilution corresponding to R = 0.5 is determined. This dilution of T is used in the second set of experiments in which the concentration of T is fixed but the concentration of L is varied. The experimental dependence of R on the concentration of L is fitted with a function describing their theoretical dependence. Both K(d) and the concentration of T are used as fitting parameters, and their sought values are determined as the ones that generate the best fit. We have fully validated this approach in silico by using computer-simulated NECEEM electropherograms and then applied it to experimental determination of the unknown concentration of MutS protein and K(d) of its interactions with a DNA aptamer. The general approach described here is applicable not only to NECEEM but also to any other method that can determine a fraction of unbound molecules at equilibrium.
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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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41
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Riley KR, Gagliano J, Xiao J, Libby K, Saito S, Yu G, Cubicciotti R, Macosko J, Colyer CL, Guthold M, Bonin K. Combining capillary electrophoresis and next-generation sequencing for aptamer selection. Anal Bioanal Chem 2015; 407:1527-32. [PMID: 25579462 PMCID: PMC4329186 DOI: 10.1007/s00216-014-8427-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 12/11/2014] [Accepted: 12/18/2014] [Indexed: 11/26/2022]
Abstract
Next-generation sequencing (NGS) machines can sequence millions of DNA strands in a single run, such as oligonucleotide (oligo) libraries comprising millions to trillions of discrete oligo sequences. Capillary electrophoresis is an attractive technique to select tight binding oligos or "aptamers" because it requires minimal sample volumes (e.g., 100 nL) and offers a solution-phase selection environment through which enrichment of target-binding oligos can be determined quantitatively. We describe here experiments using capillary transient isotachophoresis (ctITP)-based nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) as a method for selecting aptamers from a randomized library containing a known (29mer) thrombin-binding aptamer. Our capillary electrophoresis (CE)-selected samples were sequenced by the Ion Torrent Personal Genome Machine (PGM) and analyzed for selection efficiency. We show that a single round of CE selection can enrich a randomer synthetic DNA oligo mixture for thrombin-binding activity from 0.4% aptamer content before selection to >15% aptamer content.
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Affiliation(s)
- Kathryn R. Riley
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109 USA
| | - Jason Gagliano
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109 USA
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109 USA
| | - Kara Libby
- NanoMedica LLC, Winston-Salem, NC 27101 USA
| | - Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570 Japan
| | - Guo Yu
- NanoMedica LLC, Winston-Salem, NC 27101 USA
| | | | - Jed Macosko
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109 USA
| | - Christa L. Colyer
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109 USA
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109 USA
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109 USA
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42
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Wu X, Chen J, Wu M, Zhao JX. Aptamers: active targeting ligands for cancer diagnosis and therapy. Theranostics 2015; 5:322-44. [PMID: 25699094 PMCID: PMC4329498 DOI: 10.7150/thno.10257] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 10/22/2014] [Indexed: 02/07/2023] Open
Abstract
Aptamers, including DNA, RNA and peptide aptamers, are a group of promising recognition units that can specifically bind to target molecules and cells. Due to their excellent specificity and high affinity to targets, aptamers have attracted great attention in various fields in which selective recognition units are required. They have been used in biosensing, drug delivery, disease diagnosis and therapy (especially for cancer treatment). In this review, we summarized recent applications of DNA and RNA aptamers in cancer theranostics. The specific binding ability of aptamers to cancer-related markers and cancer cells ensured their high performance for early diagnosis of cancer. Meanwhile, the efficient targeting ability of aptamers to cancer cells and tissues provided a promising way to deliver imaging agents and drugs for cancer imaging and therapy. Furthermore, with the development of nanoscience and nanotechnology, the conjugation of aptamers with functional nanomaterials paved an exciting way for the fabrication of theranostic agents for different types of cancers, which might be a powerful tool for cancer treatment.
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Affiliation(s)
- Xu Wu
- 1. Department of Chemistry, School of Arts and Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Jiao Chen
- 1. Department of Chemistry, School of Arts and Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Min Wu
- 2. Department of Basic Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, USA
| | - Julia Xiaojun Zhao
- 1. Department of Chemistry, School of Arts and Sciences, University of North Dakota, Grand Forks, ND, USA
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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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Hagiwara K, Fujita H, Kasahara Y, Irisawa Y, Obika S, Kuwahara M. In vitro selection of DNA-based aptamers that exhibit RNA-like conformations using a chimeric oligonucleotide library that contains two different xeno-nucleic acids. MOLECULAR BIOSYSTEMS 2014; 11:71-6. [PMID: 25325213 DOI: 10.1039/c4mb00436a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We successfully generated chimeric DNA aptamers that contained six nucleoside analogs of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) in the primer region and multiple guanosine analogs of 2'-deoxy-2'-fluoro-ribonucleic acid (FNA) in the non-primer region using capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX). Active species enrichment became saturated only after five selection rounds, and we obtained DNA-based xeno-nucleic acid (XNA) aptamers that had high binding affinities for the target human thrombin, with dissociation constant (Kd) values of ≥10 nanomolar. Based on sequence and circular dichroism (CD) analyses, these XNA aptamers exhibited RNA-like conformations, which could cause DNA-based strands to adopt structurally diverse conformations.
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Affiliation(s)
- Kenta Hagiwara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan.
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Li Q, Zhao X, Liu H, Qu F. Low pH capillary electrophoresis application to improve capillary electrophoresis-systematic evolution of ligands by exponential enrichment. J Chromatogr A 2014; 1364:289-94. [PMID: 25193175 DOI: 10.1016/j.chroma.2014.08.073] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/24/2022]
Abstract
In this work, a novel low pH CE-SELEX (LpH-CE-SELEX) as a CE-SELEX variant is proposed. Transferring (Trf), bovine serum albumin (BSA) and cytochrome c (Cyt c) as model protein are incubated with a FAM labeled ssDNA library, respectively. Incubation mixture is separated in low pH CE (pH 2.6), where positively charged protein, protein-ssDNA complex and negatively charged ssDNA library migrate oppositely without EOF driven. Analysis of protein-ssDNA complex under positive voltage and unbound ssDNA library under negative voltage by CE-UV are applied for interactive evaluation. By increasing injection time, larger amount protein-ssDNA complex can be collected conveniently at the cathode end whereas ssDNA migrates to anode. Finally, stability of protein-ssDNA complex in low pH CE separation is discussed.
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Affiliation(s)
- Qian Li
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xinying Zhao
- Beijing Centre for Physical and Chemical Analysis, Beijing 100089, China
| | - Hongyang Liu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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Lin H, Zhang W, Jia S, Guan Z, Yang CJ, Zhu Z. Microfluidic approaches to rapid and efficient aptamer selection. BIOMICROFLUIDICS 2014; 8:041501. [PMID: 25379085 PMCID: PMC4189129 DOI: 10.1063/1.4890542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/07/2014] [Indexed: 05/04/2023]
Abstract
With their advantages as molecular recognition elements, aptamers have been extensively studied and used for bioanalytical and biomedical applications. However, the process of enrichment and screening of aptamers remains a bottleneck for aptamer development. Recently, microfluidic methods have been increasingly used for rapid and efficient aptamer selection, showing their remarkable advantages over conventional methods. This review briefly introduces aptamers and their advantages. The conventional process of generating aptamers is discussed, followed by the analysis of the key obstacles to efficient aptamer selection. Microfluidic methods for highly efficient enrichment and screening of aptamers are reviewed in detail.
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Affiliation(s)
- Hui Lin
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Weiting Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Shasha Jia
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhichao Guan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Chaoyong James Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, People's Republic of China
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Kuwahara M, Obika S. In vitro selection of BNA (LNA) aptamers. ARTIFICIAL DNA, PNA & XNA 2014; 4:39-48. [PMID: 24044051 DOI: 10.4161/adna.25786] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/17/2013] [Indexed: 01/03/2023]
Abstract
Recently, we achieved the first in vitro selection of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5'-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5'-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses.
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Science and Technology; Gunma University; Gunma, Japan
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Lou X, Zhao T, Liu R, Ma J, Xiao Y. Self-Assembled DNA Monolayer Buffered Dynamic Ranges of Mercuric Electrochemical Sensor. Anal Chem 2013; 85:7574-80. [DOI: 10.1021/ac401680c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan
North Road 105, Beijing 100048, China
| | - Tao Zhao
- Department of Chemistry, Capital Normal University, Xisanhuan
North Road 105, Beijing 100048, China
| | - Ran Liu
- Department of Chemistry, Capital Normal University, Xisanhuan
North Road 105, Beijing 100048, China
| | - Jie Ma
- Department of Chemistry, Capital Normal University, Xisanhuan
North Road 105, Beijing 100048, China
| | - Yi Xiao
- Department of Chemistry
and Biochemistry, Florida International University, Miami, FL 33199, United States
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49
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Affiliation(s)
- Kasper K Karlsen
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense M, Denmark
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50
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Kasahara Y, Irisawa Y, Fujita H, Yahara A, Ozaki H, Obika S, Kuwahara M. Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer. Anal Chem 2013; 85:4961-7. [PMID: 23662585 DOI: 10.1021/ac400058z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemically modified DNA aptamers specific to human α-thrombin were obtained from oligodeoxyribonucleotide (ODN) libraries by using a capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) method. These libraries contained 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the primer region and/or C5-modified thymidine bearing N(6)-ethyladenine (t) in the nonprimer region. Modified DNA aptamers showed high binding affinities to the target, with dissociation constants (Kd) values in the range of subnanomolar to several ten nanomolar levels. The introduction of base modification significantly suppressed the frequency of G-quadruplex motifs, which are often seen in thrombin-binding DNA aptamers. The resulting alternatives contained the 10-mer consensus sequence t5Gt2G2, which is frequently found in modified DNA aptamers with subnanomolar protein binding affinities. Furthermore, some base- and sugar-modified DNA aptamers with the 12-mer consensus sequence t2G2tC(A/G)A2G2t displayed binding activities that were dependent on the presence of B/L nucleotides in the primer region. Such aptamers were interestingly not recovered from a natural DNA library or from DNA libraries modified with either B/L nucleotides or t's. This emerging characteristic binding property will enable the creation of a direct selection methodology for DNA-based molecular switches that are triggered by chemical conversion of B/L nucleotides introduced to constant sequence regions in ODN libraries.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
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