Determination of binding affinities of triplex forming oligonucleotides using a fluorescent intercalator displacement (FID) assay

https://doi.org/10.1016/j.bmcl.2003.07.005Get rights and content

Abstract

The binding affinities of several triplex forming oligonucleotides were determined using a fluorescent intercalator displacement (FID) assay.

The binding affinities of several triplex forming oligonucleotides were determined using a fluorescent intercalator displacement (FID) assay.

  1. Download : Download high-res image (137KB)
  2. Download : Download full-size image

Section snippets

Results and Discussion

Below, we report the binding affinities of several triplex forming oligonucleotides with homopurine homopyrimidine hairpins consisting of either a pure T·AT and C+·GC triad (hairpins 1 and 2, 9-mer TFOs) or incorporating both T·AT and C+·GC triads (hairpins 3 and 4, 13-mer TFOs) (Fig. 3).

The results are summarized in Table 1. In each case of triplex formation, a well defined titration curve was observed exhibiting the expected 1:1 stoichiometry of binding and providing association constants

Acknowledgements

We gratefully acknowledge the financial support of NIH (CA 41986, CA 78045) and the Skaggs Institute for Chemical Biology. W.C.T. is a Skaggs Fellow and recipient of an ACS Medicinal Chemistry Division Graduate Fellowship sponsored by Wyeth Ayerst (2002–2003).

References (19)

  • M. Rougée et al.

    Biochemistry

    (1992)
    J.-L. Mergny et al.

    Biochemistry

    (1991)
    R.W. Roberts et al.

    Proc. Natl. Acad. Sci. U.S.A.

    (1991)
    J. Völker et al.

    J. Mol. Biol.

    (1993)
  • S. Reither et al.

    BMC Biochem.

    (2002)
  • Y.-W. Ham et al.

    Bioorg. Med. Chem. Lett.

    (2003)
  • G. Felsenfeld et al.

    J. Am. Chem. Soc.

    (1957)
  • H.E. Moser et al.

    Science

    (1987)
    S.F. Singleton et al.

    J. Am. Chem. Soc.

    (1992)
    L.J. Maher et al.

    Science

    (1989)
    D. Pei et al.

    Proc. Natl. Acad. Sci. U.S.A.

    (1990)
  • K.M. Vasquez et al.

    Trends Biochem. Sci.

    (1998)
    M.P. Knauert et al.

    Hum. Mol. Genet.

    (2001)
  • M. Cooney et al.

    Science

    (1988)
    L.J. Maher et al.

    Biochemistry

    (1992)
    G. Duval-Valentin et al.

    Proc. Natl. Acad. Sci. U.S.A.

    (1992)
  • K.M. Vasquez et al.

    Rev. Biophys.

    (2002)
    I. Radhakrishnan et al.

    Biochemistry

    (1994)
    Y.-K. Cheng et al.

    Prog. Biophys. Mol. Biol.

    (1992)
    R. Haner et al.

    Biochemistry

    (1990)
  • G.E. Plum et al.

    Proc. Natl. Acad. Sci. U.S.A.

    (1990)
    G.E. Plum et al.

    J. Mol. Biol.

    (1995)
    N. Sugimoto et al.

    Bull. Chem. Soc. Jpn.

    (1992)
There are more references available in the full text version of this article.

Cited by (16)

  • CSI-FID: High throughput label-free detection of DNA binding molecules

    2009, Bioorganic and Medicinal Chemistry Letters
View all citing articles on Scopus
View full text