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    Orientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer

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    Wilson_2005_Orientational Dynamics and Dye-DNA Interactions.pdf (327.6Kb)
    Issue Date
    2005-05
    Author
    Wilson, George S.
    Unruh, Jay R.
    Gokulrangan, Giridharan
    Lushington, Gerald H.
    Johnson, Carey K.
    Publisher
    Biophysical Society
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
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    Abstract
    We report the picosecond and nanosecond timescale rotational dynamics of a dye-labeled DNA oligonucleotide or ‘‘aptamer’’ designed to bind specifically to immunoglobulin E. Rotational dynamics in combination with fluorescence lifetime measurements provide information about dye-DNA interactions. Comparison of Texas Red (TR), fluorescein, and tetramethylrhodamine (TAMRA)-labeled aptamers reveals surprising differences with significant implications for biophysical studies employing such conjugates. Time-resolved anisotropy studies demonstrate that the TR- and TAMRA-aptamer anisotropy decays are dominated by the overall rotation of the aptamer, whereas the fluorescein-aptamer anisotropy decay displays a subnanosecond rotational correlation time much shorter than that expected for the overall rotation of the aptamer. Docking and molecular dynamics simulations suggest that the low mobility of TR is a result of binding in the groove of the DNA helix. Additionally, associated anisotropy analysis of the TAMRA-aptamer reveals both quenched and unquenched states that experience significant coupling to the DNA motion. Therefore, quenching of TAMRA by guanosine must depend on the configuration of the dye bound to the DNA. The strong coupling of TR to the rotational dynamics of the DNA aptamer, together with the absence of quenching of its fluorescence by DNA, makes it a good probe of DNA orientational dynamics. The understanding of the nature of dye-DNA interactions provides the basis for the development of bioconjugates optimized for specific biophysical measurements and is important for the sensitivity of anisotropy-based DNA-protein interaction studies employing such conjugates.
    URI
    http://hdl.handle.net/1808/8414
    DOI
    https://doi.org/10.1529/biophysj.104.054148
    Collections
    • Chemistry Scholarly Works [610]
    Citation
    J.R. Unruh, G. Gokulrangan, G.H. Lushington, C.K. Johnson, and G.S. Wilson, Orientational Dynamics and Dye-DNA Interactions in a DNA Aptamer, Biophysical Journal. 88, 3455-3465 (2005). http://dx.doi.org/10.1529/biophysj.104.054148

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    Lawrence, KS 66045
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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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