Optical determination of the electronic coupling and intercalation geometry of thiazole orange homodimer in DNA
Name
Bathe-CunninghamPD-JChemPhys-2017.pdf
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Author(s)
Cunningham, Paul D.
Díaz, Sebastián A.
Medintz, Igor L.
Melinger, Joseph S.
Bricker, William P
Bathe, Mark
Date Issued
August 2017
Journal
The Journal of Chemical Physics
Publisher
American Institute of Physics (AIP)
Citation
Cunningham, Paul D., William P. Bricker, Sebastián A. Díaz, Igor L. Medintz, Mark Bathe, and Joseph S. Melinger. “Optical Determination of the Electronic Coupling and Intercalation Geometry of Thiazole Orange Homodimer in DNA.” The Journal of Chemical Physics 147, no. 5 (August 7, 2017): 055101. © 2018 AIP Publishing LLC
Version
Final published version
Abstract
Sequence-selective bis-intercalating dyes exhibit large increases in fluorescence in the presence of specific DNA sequences. This property makes this class of fluorophore of particular importance to biosensing and super-resolution imaging. Here we report ultrafast transient anisotropy measurements of resonance energy transfer (RET) between thiazole orange (TO) molecules in a complex formed between the homodimer TOTO and double-stranded (ds) DNA. Biexponential homo-RET dynamics suggest two subpopulations within the ensemble: 80% intercalated and 20% non-intercalated. Based on the application of the transition density cube method to describe the electronic coupling and Monte Carlo simulations of the TOTO/dsDNA geometry, the dihedral angle between intercalated TO molecules is estimated to be 81° ± 5°, corresponding to a coupling strength of 45 ± 22 cm[superscript −1]. Dye intercalation with this geometry is found to occur independently of the underlying DNA sequence, despite the known preference of TOTO for the nucleobase sequence CTAG. The non-intercalated subpopulation is inferred to have a mean inter-dye separation distance of 19 Å, corresponding to coupling strengths between 0 and 25 cm[superscript −1]. This information is important to enable the rational design of energy transfer systems that utilize TOTO as a relay dye. The approach used here is generally applicable to determining the electronic coupling strength and intercalation configuration of other dimeric bis-intercalators.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
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DOI of Published Version
https://doi.org/10.1063/1.4995431
