Sequence-Specific Preconcentration of a Mutation Prone KRAS Fragment from Plasma using Ion-tagged Oligonucleotides Coupled to qPCR Compatible Magnetic Ionic Liquid Solvents

dc.contributor.author Emaus, Miranda
dc.contributor.author Anderson, Jared
dc.contributor.author Varona, Marcelino
dc.contributor.author Anderson, Jared
dc.contributor.department Chemistry
dc.date 2019-06-03T15:22:12.000
dc.date.accessioned 2020-06-30T01:16:47Z
dc.date.available 2020-06-30T01:16:47Z
dc.date.copyright Tue Jan 01 00:00:00 UTC 2019
dc.date.embargo 2020-04-09
dc.date.issued 2019-01-01
dc.description.abstract <p><p id="x-x-abspara0010">Circulating tumor DNA (ctDNA) is a source of mutant DNA found in plasma and holds great promise in guiding cancer diagnostics, prognostics, and treatment. However, ctDNA fragments are challenging to detect in plasma due to their low abundance compared to wild-type DNA. In this study, a series of ion-tagged oligonucleotides (ITO) were synthesized using thiol-ene click chemistry and designed to selectively anneal target DNA. The ITO-DNA duplex was subsequently captured using a hydrophobic magnetic ionic liquid (MIL) as a liquid support. Extracted target DNA was quantified by adding the DNA-enriched MIL to the quantitative polymerase chain reaction (qPCR) buffer to streamline the extraction procedure. Clinically relevant concentrations of the mutation prone <em>KRAS</em>fragment, which has been linked to colorectal, lung, and bladder cancer, were preconcentrated using the ITO-MIL strategy allowing for enrichment factors as high as 19.49 ± 1.44 from pure water and 4.02 ± 0.50 from 10-fold diluted plasma after a 1 min extraction. Preconcentration could only be achieved when adding the ITO probe to the sample validating the selectivity of the ITO in the capture process. In addition, the amplification efficiency of qPCR was not affected when performing extractions from a diluted-plasma matrix demonstrating that the ITO-MIL approach coupled to direct-qPCR can be used to quantitate DNA from complex matrices. In comparison, commercially available steptavidin-coated magnetic beads were observed to lose selectivity when performing extractions from a 10-fold diluted plasma matrix. The selectivity of the ITO-MIL method, coupled with the ability to rapidly preconcentrate clinically relevant concentrations of target DNA from 10-fold diluted plasma, suggests that this method has the potential to be applied towards the extraction of ctDNA fragments from clinical samples.</p>
dc.description.comments <p>This is a manuscript of an article published as Emaus, Miranda N., Marcelino Varona, and Jared L. Anderson. "Sequence-Specific Preconcentration of a Mutation Prone KRAS Fragment from Plasma using Ion-tagged Oligonucleotides Coupled to qPCR Compatible Magnetic Ionic Liquid Solvents." <em>Analytica Chimica Acta</em> (2019). DOI: <a href="http://dx.doi.org/10.1016/j.aca.2019.04.005" target="_blank">10.1016/j.aca.2019.04.005</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/chem_pubs/1121/
dc.identifier.articleid 2124
dc.identifier.contextkey 14267077
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath chem_pubs/1121
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/14425
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/chem_pubs/1121/2019_AndersonJared_SequenceSpecific.pdf|||Fri Jan 14 18:45:16 UTC 2022
dc.source.uri 10.1016/j.aca.2019.04.005
dc.subject.disciplines Analytical Chemistry
dc.subject.keywords DNA extraction
dc.subject.keywords cell-free DNA
dc.subject.keywords PCR
dc.subject.keywords ionic liquid
dc.subject.keywords magnetic separation
dc.title Sequence-Specific Preconcentration of a Mutation Prone KRAS Fragment from Plasma using Ion-tagged Oligonucleotides Coupled to qPCR Compatible Magnetic Ionic Liquid Solvents
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 9618e7bf-b6eb-4753-affc-fca4bcc405cb
relation.isOrgUnitOfPublication 42864f6e-7a3d-4be3-8b5a-0ae3c3830a11
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