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Stacking-induced fluorescence increase reveals allosteric interactions through DNA.

ABSTRACT: From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dynamics of a DNA hairpin down to the single-molecule level. We also show that varying the position of a single abasic site up to 20 base pairs away modulates the dye-DNA interaction, indicative of through-backbone allosteric interactions. The phenomenon of stacking-induced fluorescence increase (SIFI) should find widespread use in the study of the structure, dynamics and reactivity of nucleic acids.

SUBMITTER: Morten MJ

PROVIDER: S-EPMC6265455 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Stacking-induced fluorescence increase reveals allosteric interactions through DNA.

Morten Michael J MJ Lopez Sergio G SG Steinmark I Emilie IE Rafferty Aidan A Magennis Steven W SW

Nucleic acids research 20181101 21

From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently attached Cy3 dye undergoes strong enhancement of fluorescence intensity and lifetime when stacked in a nick, gap or overhang region in duplex DNA. This is used to probe hybridization dy ...[more]

PMID: 30277520

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