Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing

Title:
Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing
Authors:
Scoville, Delia J.; Uhm, Tae Kyu Brian; Shallcross, Jamie A.; Whelan, Rebecca J. ( 0000-0002-9293-1528 )
Abstract:
CA125 is a mucin glycoprotein whose concentration in serum correlates with a woman’s risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. Using fluorescence anisotropy and affinity probe capillary electrophoresis, the binding affinities of four aptamer candidates were evaluated. Two aptamers, CA125_1 and CA125_12, both without primers, were found to bind to clinically relevant concentrations of the protein target. Binding was differently influenced by the presence of Mg 2+ ions, being required for binding of CA125_1 and abrogating binding of CA125_12. In conclusion, One-Pot SELEX was found to be a promising selection method that yielded DNA aptamers to a clinically important protein target.
Citation:
Scoville, Delia J., Tae Kyu Brian Uhm, Jamie A. Shallcross, and Rebecca J. Whelan. 2017. "Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing." Journal of Nucleic Acids: 1-9.
Publisher:
Hindawi Publishing Corporation
DATE ISSUED:
2017-02-09
Department:
Chemistry and Biochemistry
Type:
Article
PUBLISHED VERSION:
10.1155/2017/9879135
Additional Links:
https://www.hindawi.com/journals/jna/2017/9879135/
PERMANENT LINK:
http://hdl.handle.net/11282/620532

Full metadata record

DC FieldValue Language
dc.contributor.authorScoville, Delia J.en
dc.contributor.authorUhm, Tae Kyu Brianen
dc.contributor.authorShallcross, Jamie A.en
dc.contributor.authorWhelan, Rebecca J.en
dc.date.accessioned2017-09-25T15:23:05Z-
dc.date.available2017-09-25T15:23:05Z-
dc.date.issued2017-02-09-
dc.identifier.citationScoville, Delia J., Tae Kyu Brian Uhm, Jamie A. Shallcross, and Rebecca J. Whelan. 2017. "Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing." Journal of Nucleic Acids: 1-9.en
dc.identifier.issn2090-0201-
dc.identifier.urihttp://hdl.handle.net/11282/620532-
dc.description.abstractCA125 is a mucin glycoprotein whose concentration in serum correlates with a woman’s risk of developing ovarian cancer and also indicates response to therapy in diagnosed patients. Accurate detection of this large, complex protein in patient samples is of great clinical relevance. We suggest that powerful new diagnostic tools may be enabled by the development of nucleic acid aptamers with affinity for CA125. Here, we report on our use of One-Pot SELEX to isolate single-stranded DNA aptamers with affinity for CA125, followed by high-throughput sequencing of the selected oligonucleotides. This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. Using fluorescence anisotropy and affinity probe capillary electrophoresis, the binding affinities of four aptamer candidates were evaluated. Two aptamers, CA125_1 and CA125_12, both without primers, were found to bind to clinically relevant concentrations of the protein target. Binding was differently influenced by the presence of Mg 2+ ions, being required for binding of CA125_1 and abrogating binding of CA125_12. In conclusion, One-Pot SELEX was found to be a promising selection method that yielded DNA aptamers to a clinically important protein target.en
dc.language.isoen_USen
dc.publisherHindawi Publishing Corporationen
dc.identifier.doi10.1155/2017/9879135-
dc.relation.urlhttps://www.hindawi.com/journals/jna/2017/9879135/en
dc.subject.departmentChemistry and Biochemistryen_US
dc.titleSelection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencingen_US
dc.typeArticleen
dc.identifier.journalJournal of Nucleic Acidsen
dc.subject.keywordIn-vitro selectionen_US
dc.subject.keywordExponential enrichmenten_US
dc.subject.keywordSystematic evolutionen_US
dc.subject.keywordHigh-affinityen_US
dc.subject.keywordPelvic massen_US
dc.subject.keywordLigandsen_US
dc.subject.keywordCA-125en_US
dc.subject.keywordPolymeraseen_US
dc.subject.keywordCarcinomaen_US
dc.rightsArchived with thanks to Journal of Nucleic Acidsen
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