Lopez, S. G., Ruedas-Rama, M. J., Casares, S., Alvarez-Pez, J. M. and Orte, A. (2012) Bulk and single-molecule fluorescence studies of the saturation of the DNA double helix using YOYO-3 intercalator dye. Journal of Physical Chemistry B, 116(38), pp. 11561-11569. (doi: 10.1021/jp303438d) (PMID:22947035)
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Abstract
We report a thorough photophysical characterization of the interactions between double-stranded DNA (dsDNA) and the trimethine cyanine homodimer dye YOYO-3. The fluorescence emission of this dye is enhanced by intercalation within the DNA double helix. We have explored the saturation of the dsDNA by bound YOYO-3 at the single-molecule level by studying the single-pair Förster resonance energy transfer (FRET) from an energy donor, Alexa Fluor 488, tagged at the 5′ end of the double helix and the energy acceptor, YOYO-3, bound to the same DNA molecule. The spontaneous binding of YOYO-3 gives rise to an effective distribution of different FRET efficiencies and, therefore, donor–acceptor (D–A) distances. These distributions reveal the existence of multiple states of YOYO-3. Steady-state and time-resolved fluorescence and circular dichroism confirmed the presence of a DNA-bound aggregate of YOYO-3, conspicuous at high dye/base pair ratios. The spectral features of the aggregate suggest that it may have the structure of a parallel H-aggregate.
| Item Type: | Articles |
|---|---|
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Lopez, Dr Sergio |
| Authors: | Lopez, S. G., Ruedas-Rama, M. J., Casares, S., Alvarez-Pez, J. M., and Orte, A. |
| College/School: | College of Science and Engineering > School of Chemistry |
| Journal Name: | Journal of Physical Chemistry B |
| Publisher: | American Chemical Society |
| ISSN: | 1520-6106 |
| ISSN (Online): | 1520-5207 |
| Published Online: | 04 September 2012 |
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