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dc.contributor.authorWilson, George S.
dc.contributor.authorUnruh, Jay R.
dc.contributor.authorGokulrangan, Giridharan
dc.contributor.authorLushington, Gerald H.
dc.contributor.authorJohnson, Carey K.
dc.date.accessioned2011-11-18T19:57:58Z
dc.date.available2011-11-18T19:57:58Z
dc.date.issued2005-05
dc.identifier.citationJ.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
dc.identifier.urihttp://hdl.handle.net/1808/8414
dc.description.abstractWe 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.
dc.description.sponsorshipDynamic Aspects of Chemical Biology Training Grant (National Institutes of Health 5 T32 GM08545-09), Support from the Petroleum Research Fund, administered by the American Chemical Society.
dc.language.isoen_US
dc.publisherBiophysical Society
dc.titleOrientational Dynamics and Dye-DNA Interactions in a Dye-Labeled DNA Aptamer
dc.typeArticle
kusw.kuauthorWilson, George S.
kusw.kuauthorJohnson, Carey K.
kusw.kudepartmentChemistry
dc.identifier.doi10.1529/biophysj.104.054148
dc.identifier.orcidhttps://orcid.org/0000-0003-3077-4990
kusw.oaversionScholarly/refereed, publisher version
kusw.oapolicyThis item does not meet KU Open Access policy criteria.
dc.rights.accessrightsopenAccess


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