Peptide Nucleic Acid (PNA)-DNA duplexes: comparison of hybridization affinity between vertically and horizontally tethered PNA probes

Arpita De, Serhiy Souchelnytskyi, Albert van den Berg, Edwin Carlen

    Research output: Contribution to journalArticleAcademicpeer-review

    13 Citations (Scopus)

    Abstract

    We compare the PNA-DNA duplex hybridization characteristics of vertically tethered and new horizontally tethered PNA probes on solid surfaces. The horizontal 15-mer PNA probe has been synthesized with linker molecules attached at three locations (gamma-points) positioned along the PNA backbone that provides covalent attachment of the probe with the backbone aligned parallel to the surface, which is important for DNA hybridization assays that use electric field effect sensors for detection. A radioactive labeled assay and real-time surface plasmon resonance (SPR) biosensor are used to assess the probe surface density, nonspecific binding, and DNA hybridization affinity, respectively, of the new PNA probe configuration. The estimated equilibrium dissociation constants of the horizontally tethered duplex and the vertically tethered duplex are of the same order of magnitude (K-D approximate to 5 nM), which indicates a sufficient hybridization affinity for many electronic biosensors, that benefit from the horizontal alignment, which minimizes the effects of counterion screening.
    Original languageEnglish
    Pages (from-to)4607-4612
    Number of pages6
    JournalACS applied materials & interfaces
    Volume5
    Issue number11
    DOIs
    Publication statusPublished - 12 Jun 2013

    Keywords

    • PNA
    • Surface hybridization
    • Counterion screening
    • γ-PNA
    • Chiral backbone

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