Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nuclelic acids

Asif Iqbal, Sinan Arslan, Burak Okumus, Timothy J. Wilson, Gerard Giraud, David G. Norman, Taekjip Ha, David M. J. Lilley (Lead / Corresponding author)

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    225 Citations (Scopus)

    Abstract

    We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Forster transfer obeys the orientation dependence as expected for a dipole-dipole interaction.

    Original languageEnglish
    Pages (from-to)11176-11181
    Number of pages6
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume105
    Issue number32
    DOIs
    Publication statusPublished - 12 Aug 2008

    Keywords

    • cyanine fluorophores
    • FRET
    • kappa squared
    • single-molecule FRET
    • DNA
    • RIBOZYME
    • HYBRID
    • TOOL

    Cite this

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    title = "Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nuclelic acids",
    abstract = "We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Forster transfer obeys the orientation dependence as expected for a dipole-dipole interaction.",
    keywords = "cyanine fluorophores, FRET, kappa squared, single-molecule FRET, DNA, RIBOZYME, HYBRID, TOOL",
    author = "Asif Iqbal and Sinan Arslan and Burak Okumus and Wilson, {Timothy J.} and Gerard Giraud and Norman, {David G.} and Taekjip Ha and Lilley, {David M. J.}",
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    TY - JOUR

    T1 - Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nuclelic acids

    AU - Iqbal, Asif

    AU - Arslan, Sinan

    AU - Okumus, Burak

    AU - Wilson, Timothy J.

    AU - Giraud, Gerard

    AU - Norman, David G.

    AU - Ha, Taekjip

    AU - Lilley, David M. J.

    PY - 2008/8/12

    Y1 - 2008/8/12

    N2 - We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Forster transfer obeys the orientation dependence as expected for a dipole-dipole interaction.

    AB - We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5' ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Forster transfer obeys the orientation dependence as expected for a dipole-dipole interaction.

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    KW - kappa squared

    KW - single-molecule FRET

    KW - DNA

    KW - RIBOZYME

    KW - HYBRID

    KW - TOOL

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    JO - Proceedings of the National Academy of Sciences

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