Oxazole yellow dye interactions with short DNA oligomers of homogeneous base composition and their hybrids

Biospectroscopy
L D SimonL B McGown

Abstract

Interactions between short single-stranded DNA oligomers of homogeneous base composition and the fluorescent probes oxazole yellow (YO) and its homodimer YOYO are described. The oligomers included 15-mers and 30-mers of polydA, polydT, polydG, and polydC. Interactions between the dyes and DNA hybrids formed from complementary homogeneous strands of equal length were also investigated. No interactions were observed between the dyes and the monomeric monophosphate nucleosides A, G, T, or C. The dyes were found to interact much more strongly with the purine oligomers polydA and polydG than with the pyrimidine oligomers polydT and polydC. PolydA of both lengths has strong interactions with YOYO, whereas the polydG 30-mer interacts strongly with monomeric YO. The 15-mers of polydG and polydC of both lengths show little interaction with either dye. Interactions of the dyes with the polydA/polydT and polydG/polydC hybrids tend to be dominated by interactions with polydA and polydG, respectively. Although dye interactions generally were facilitated by hybridization, particularly for polydA/polydT, the interactions were similar to those with the single strands and different from those that have been observed in long double-stranded DNA.

Citations

Apr 18, 1998·Biospectroscopy·K H AbramoL B McGown
Feb 21, 2009·Angewandte Chemie·Sina Berndl, Hans-Achim Wagenknecht
Aug 13, 2011·Organic & Biomolecular Chemistry·Shuji IkedaAkimitsu Okamoto
Jul 9, 2013·Journal of Biomolecular Structure & Dynamics·Shohini Ghosh DattaBhaskar Datta
Jan 17, 2016·Chemistry : a European Journal·Sina BerndlHans-Achim Wagenknecht
Mar 16, 2013·Chemical Record : an Official Publication of the Chemical Society of Japan ... [et Al.]·Gosuke Hayashi, Akimitsu Okamoto
Jun 11, 2011·Chemical Society Reviews·Akimitsu Okamoto
Mar 2, 2006·Journal of the American Chemical Society·Venugopal KarunakaranOliver Seitz
Jun 8, 2006·Journal of the American Chemical Society·Alexandre FürstenbergEric Vauthey

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