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Characterization of the binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the fluorescent properties of YO and YOYO complexed with the polynucleotides and double-stranded DNA.
Biopolymers. 1995 Aug; 36(2):153-67.B

Abstract

The interaction between the fluorescent dye YO (oxazole yellow) and the alternating polynucleotides [poly(dA-dT)]2 [the duplex of alternating poly(dA-dT)] and [poly(dG-dC)]2 [the duplex of alternating poly(dG-dC)] has been studied with optical spectroscopic techniques including absorbance, flow linear dichroism, CD, and fluorescence measurements. The principal features of the spectra are very similar for the two polynucleotide solutions, showing that YO binds quite similarly to AT and GC base pairs. From a strongly negative reduced linear dichroism (LDr) in the dye absorption band, an induced negative CD, and transfer of energy from the bases to bound YO, we conclude that at low mixing ratios YO is intercalated in both [poly(dA-dT)]2 and [poly(dG-dC)]2. At higher mixing ratios an external binding mode starts to contribute, evidenced from the appearance of an exciton CD. The conclusion that YO binds in a similar way to AT and GC base pairs should be valid also for the dimer YOYO since its YO units have been found to bind to double-stranded (dsDNA) in the same way as the YO monomer. The fluorescence properties of YO and YOYO complexed with DNA or the polynucleotides have been characterized by studying the dependence of fluorescence intensity on temperature, mixing ratio, and ionic strength. The fluorescence intensity and fluorescence lifetime of YO-DNA decrease strongly with increasing mixing ratio, whereas the fluorescence intensity of YOYO-DNA shows a weaker dependence, indicating that the quantum yield depends on the distance between the YO chromophores on the DNA chain. Further, the fluorescence intensity of YO depends on the base sequence; the quantum yield and fluorescence lifetime for YO complexed with [poly(dG-dC)]2 are about twice as large as for YO complexed with [poly(dA-dT)]2. Measurements of excitation spectra at different mixing ratios and different emission wavelengths indicate that the fluorescence of the externally bound chromophores is negligible compared to the intercalated ones.

Authors+Show Affiliations

Department of Physical Chemistry, Chalmers University of Technology, Göteborg, Sweden.No affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

7492743

Citation

Larsson, A, et al. "Characterization of the Binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the Fluorescent Properties of YO and YOYO Complexed With the Polynucleotides and Double-stranded DNA." Biopolymers, vol. 36, no. 2, 1995, pp. 153-67.
Larsson A, Carlsson C, Jonsson M. Characterization of the binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the fluorescent properties of YO and YOYO complexed with the polynucleotides and double-stranded DNA. Biopolymers. 1995;36(2):153-67.
Larsson, A., Carlsson, C., & Jonsson, M. (1995). Characterization of the binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the fluorescent properties of YO and YOYO complexed with the polynucleotides and double-stranded DNA. Biopolymers, 36(2), 153-67.
Larsson A, Carlsson C, Jonsson M. Characterization of the Binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the Fluorescent Properties of YO and YOYO Complexed With the Polynucleotides and Double-stranded DNA. Biopolymers. 1995;36(2):153-67. PubMed PMID: 7492743.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Characterization of the binding of YO to [poly(dA-dT)]2 and [poly(dG-dC)]2, and of the fluorescent properties of YO and YOYO complexed with the polynucleotides and double-stranded DNA. AU - Larsson,A, AU - Carlsson,C, AU - Jonsson,M, PY - 1995/8/1/pubmed PY - 1995/8/1/medline PY - 1995/8/1/entrez SP - 153 EP - 67 JF - Biopolymers JO - Biopolymers VL - 36 IS - 2 N2 - The interaction between the fluorescent dye YO (oxazole yellow) and the alternating polynucleotides [poly(dA-dT)]2 [the duplex of alternating poly(dA-dT)] and [poly(dG-dC)]2 [the duplex of alternating poly(dG-dC)] has been studied with optical spectroscopic techniques including absorbance, flow linear dichroism, CD, and fluorescence measurements. The principal features of the spectra are very similar for the two polynucleotide solutions, showing that YO binds quite similarly to AT and GC base pairs. From a strongly negative reduced linear dichroism (LDr) in the dye absorption band, an induced negative CD, and transfer of energy from the bases to bound YO, we conclude that at low mixing ratios YO is intercalated in both [poly(dA-dT)]2 and [poly(dG-dC)]2. At higher mixing ratios an external binding mode starts to contribute, evidenced from the appearance of an exciton CD. The conclusion that YO binds in a similar way to AT and GC base pairs should be valid also for the dimer YOYO since its YO units have been found to bind to double-stranded (dsDNA) in the same way as the YO monomer. The fluorescence properties of YO and YOYO complexed with DNA or the polynucleotides have been characterized by studying the dependence of fluorescence intensity on temperature, mixing ratio, and ionic strength. The fluorescence intensity and fluorescence lifetime of YO-DNA decrease strongly with increasing mixing ratio, whereas the fluorescence intensity of YOYO-DNA shows a weaker dependence, indicating that the quantum yield depends on the distance between the YO chromophores on the DNA chain. Further, the fluorescence intensity of YO depends on the base sequence; the quantum yield and fluorescence lifetime for YO complexed with [poly(dG-dC)]2 are about twice as large as for YO complexed with [poly(dA-dT)]2. Measurements of excitation spectra at different mixing ratios and different emission wavelengths indicate that the fluorescence of the externally bound chromophores is negligible compared to the intercalated ones. SN - 0006-3525 UR - https://www.unboundmedicine.com/medline/citation/7492743/Characterization_of_the_binding_of_YO_to_[poly_dA_dT_]2_and_[poly_dG_dC_]2_and_of_the_fluorescent_properties_of_YO_and_YOYO_complexed_with_the_polynucleotides_and_double_stranded_DNA_ L2 - https://doi.org/10.1002/bip.360360205 DB - PRIME DP - Unbound Medicine ER -