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Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA

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Abstract

The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.

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Funding

This work was funded by the Natural Sciences and Engineering Research Council of Canada, and National Research Council of Canada.

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Authors and Affiliations

  1. Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, L2S 3A1, Canada

    Hayley-Ann Bennett, Alyssa McAdorey & Hongbin Yan

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  1. Hayley-Ann Bennett
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  2. Alyssa McAdorey
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  3. Hongbin Yan
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Contributions

HB: writing – original draft, methodology, investigation, formal analysis. AM: review & editing, methodology. HY: Conceptualization, supervision, formal analysis, writing, review & editing.

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Correspondence to Hongbin Yan.

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Bennett, HA., McAdorey, A. & Yan, H. Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA. J Fluoresc 34, 1193–1205 (2024). https://doi.org/10.1007/s10895-023-03343-8

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