Event Title

Optimization of Magnetic Fluidic SELEX to Select Aptamers for Ovarian Cancer Biomarker HE4

Location

King Building 237

Document Type

Presentation

Start Date

4-27-2018 5:30 PM

End Date

4-27-2018 6:50 PM

Abstract

Ovarian cancer is among the most difficult to detect and deadly cancers, bringing about the need for more sensitive tools in clinical diagnosis. High-affinity nucleic acid aptamers demonstrate many advantages over traditional diagnostic antibodies. In order to select aptamers for the ovarian cancer biomarker HE4, we have optimized magnetic-fluidic SELEX as well as implemented a bioinformatic pipeline to aid in the refinement of the resultant sequence data. As suggested by its name, magnetic-fluidic SELEX makes use of Ni-NTA magnetic agarose beads complexed with the tagged protein of interest, HE4-6-His, aided by a fluidics platform to fix and separate strongly binding potential aptamers from weakly binding potential aptamers. In addition, we improved processing between SELEX rounds by optimizing asymmetric PCR and gel extraction. We used this system for five rounds of SELEX, after which each candidate pool was sequenced on an Illumina HiSeq; resulting sequence data were processed using the Galaxy bioinformatics platform. We found that the population of DNA has been substantially altered during SELEX, with some evidence that select candidates may show affinity for HE4. We expect to continue to use Galaxy alongside capillary electrophoresis and fluorescence anisotropy to analyze the binding capabilities of top aptamer candidates.

Keywords:

analytical chemistry, cancer, biochemistry, bioinformatics

Notes

Session VII, Panel 19 - Physical | Science
Moderator: Dan Stinebring, Francis D. Federighi Professor of Physics

Major

Biochemistry; Biology

Advisor(s)

Manish Mehta, Chemistry and Biochemistry
Yolanda Cruz, Biology

Project Mentor(s)

Rebecca Whelan, Chemistry and Biochemistry

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Apr 27th, 5:30 PM Apr 27th, 6:50 PM

Optimization of Magnetic Fluidic SELEX to Select Aptamers for Ovarian Cancer Biomarker HE4

King Building 237

Ovarian cancer is among the most difficult to detect and deadly cancers, bringing about the need for more sensitive tools in clinical diagnosis. High-affinity nucleic acid aptamers demonstrate many advantages over traditional diagnostic antibodies. In order to select aptamers for the ovarian cancer biomarker HE4, we have optimized magnetic-fluidic SELEX as well as implemented a bioinformatic pipeline to aid in the refinement of the resultant sequence data. As suggested by its name, magnetic-fluidic SELEX makes use of Ni-NTA magnetic agarose beads complexed with the tagged protein of interest, HE4-6-His, aided by a fluidics platform to fix and separate strongly binding potential aptamers from weakly binding potential aptamers. In addition, we improved processing between SELEX rounds by optimizing asymmetric PCR and gel extraction. We used this system for five rounds of SELEX, after which each candidate pool was sequenced on an Illumina HiSeq; resulting sequence data were processed using the Galaxy bioinformatics platform. We found that the population of DNA has been substantially altered during SELEX, with some evidence that select candidates may show affinity for HE4. We expect to continue to use Galaxy alongside capillary electrophoresis and fluorescence anisotropy to analyze the binding capabilities of top aptamer candidates.