Hybridization characteristics of biomolecular adaptors, covalent DNA streptavidin conjugates

CM Niemeyer*, W Burger, RMJ Hoedemakers

*Corresponding author for this work

    Research output: Contribution to journalArticleAcademicpeer-review

    49 Citations (Scopus)

    Abstract

    Semisynthetic, covalent streptavidin-DNA adducts are versatile molecular connectors for the fabrication of both nano-and microstructured protein arrays by use of DNA hybridization. In this study, the hybridization characteristics of six adduct species, each containing a different DNA sequence of 21 or 24 bases, have been compared. First, the adducts were conjugated to biotinylated alkaline phosphatase, and their binding to immobilized oligomer complements of similar lengths was quantified in a microplate assay. The binding efficiency observed varied to a great extent with the specific sequence of the oligonucleotide attached, and could not be predicted from affiliated thermodynamic data of duplex stability. To further elucidate the hybridization properties, the hybridization rate constants of association and dissociation (k(assn) and k(dissn)) have been determined for both unconjugated oligonucleotides and protein adducts, using a surface plasmon resonance biosensor. The k(assn) values observed for the oligonucleotides are in the range of 9 x 10(3) to 2 x 10(5) M-1 s(-1) and correlate with structural properties of the probe strands. Up to 3-fold decreased k(assn) values were obtained for the corresponding protein adducts. Likewise, values were observed for k(dissn) ranging from 1.4 x 10(-4) to 1.9 x 10(-5) s(-1) for the oligonucleotides. The dissociation of the analogous protein conjugates was reduced by up to 5-fold. The extent of this decrease correlates with the formation of homodimeric or intramolecular aggregation of probe strands. A mechanistic model for explaining these data is based on attractive intramolecular interaction between the nucleic acid and protein moiety.

    Original languageEnglish
    Pages (from-to)168-175
    Number of pages8
    JournalBIOCONJUGATE CHEMISTRY
    Volume9
    Issue number2
    Publication statusPublished - 1998

    Keywords

    • RESONANCE ENERGY-TRANSFER
    • DUPLEX STABILITY
    • OLIGONUCLEOTIDE
    • KINETICS
    • ARRAYS
    • MOLECULES
    • SEQUENCE

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