Electronic DNA detection and diagnostics

Arpita De

    Research output: ThesisPhD Thesis - Research UT, graduation UT

    141 Downloads (Pure)

    Abstract

    The Nanopill project is an ambitious undertaking with the objective to develop an early-warning cancer diagnostic pill that is ingested by the patient. The Nanopill collects intestinal fluid as the pill travels down the intestinal tract, and tests for the presence of a free floating hyper-methylated DNA (hm-DNA) with a gene sequence specific for colorectal cancer. Since the development of the entire Nanopill system is beyond the scope of a single doctoral thesis, this thesis focused on the development and realization of an automated microscale bioassay for the capture and enrichment of the hm-DNA colorectal cancer marker and the subsequent detection of the specific DNA sequence using all-electronic silicon nanowire (Si-NW) biosensors without the use of amplification. Free-floating hm-DNA is present in very low concentrations in biological samples, such as stool, sputum, urine, blood, and gastrointestinal fluid. A capture and pre-concentraion of hm-DNA would be used, prior to detection on Si-NWs. The pre-concentration system has been designed and implemented using a pillar-based glass-silicon microfluidic chip for the solid-phase extraction of hm-DNA with methyl binding domain (MBD) protein that specifically captures double-stranded hm-DNA in the CpG island hyper-methylation context. The MBD extraction microchip is designed for the capture and elution of hm-DNA with quantities less than 1 ng ml-1 and was able to demonstrate 28× concentration factor of the input concentration.
    Original languageEnglish
    QualificationDoctor of Philosophy
    Awarding Institution
    • University of Twente
    Supervisors/Advisors
    • van den Berg, Albert , Supervisor
    • Carlen, Edwin, Advisor
    Thesis sponsors
    Award date30 Aug 2013
    Place of PublicationZutphen
    Publisher
    Print ISBNs978-90-365-0263-4
    DOIs
    Publication statusPublished - 30 Aug 2013

    Fingerprint

    DNA
    Silicon
    CpG Islands
    Methylation
    Fluids
    Bioassay
    DNA sequences
    Microfluidics
    Biosensors
    Nanowires
    Amplification
    Blood
    Genes
    Glass
    Proteins

    Keywords

    • EWI-23681
    • IR-86969
    • METIS-297242

    Cite this

    De, Arpita. / Electronic DNA detection and diagnostics. Zutphen : Wohrmann Print Service, 2013. 155 p.
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    abstract = "The Nanopill project is an ambitious undertaking with the objective to develop an early-warning cancer diagnostic pill that is ingested by the patient. The Nanopill collects intestinal fluid as the pill travels down the intestinal tract, and tests for the presence of a free floating hyper-methylated DNA (hm-DNA) with a gene sequence specific for colorectal cancer. Since the development of the entire Nanopill system is beyond the scope of a single doctoral thesis, this thesis focused on the development and realization of an automated microscale bioassay for the capture and enrichment of the hm-DNA colorectal cancer marker and the subsequent detection of the specific DNA sequence using all-electronic silicon nanowire (Si-NW) biosensors without the use of amplification. Free-floating hm-DNA is present in very low concentrations in biological samples, such as stool, sputum, urine, blood, and gastrointestinal fluid. A capture and pre-concentraion of hm-DNA would be used, prior to detection on Si-NWs. The pre-concentration system has been designed and implemented using a pillar-based glass-silicon microfluidic chip for the solid-phase extraction of hm-DNA with methyl binding domain (MBD) protein that specifically captures double-stranded hm-DNA in the CpG island hyper-methylation context. The MBD extraction microchip is designed for the capture and elution of hm-DNA with quantities less than 1 ng ml-1 and was able to demonstrate 28× concentration factor of the input concentration.",
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    De, A 2013, 'Electronic DNA detection and diagnostics', Doctor of Philosophy, University of Twente, Zutphen. https://doi.org/10.3990/1.9789036502634

    Electronic DNA detection and diagnostics. / De, Arpita.

    Zutphen : Wohrmann Print Service, 2013. 155 p.

    Research output: ThesisPhD Thesis - Research UT, graduation UT

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    De A. Electronic DNA detection and diagnostics. Zutphen: Wohrmann Print Service, 2013. 155 p. https://doi.org/10.3990/1.9789036502634