Theoretical Study on the Selective Fluorescence of PicoGreen: Binding Models and Photophysical Properties

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  • Masaki Okoshi
    Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University
  • Patchreenart Saparpakorn
    Department of Chemistry, Faculty of Science, Kasetsart University
  • Yuta Takada
    Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University
  • Supa Hannongbua
    Department of Chemistry, Faculty of Science, Kasetsart University
  • Hiromi Nakai
    Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University

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<jats:title>Abstract</jats:title> <jats:p>PicoGreen (PG) is used as a probe to selectively quantitate double-stranded (ds-) DNA because it shows unique fluorescence enhancement when complexed with DNA. By binding to ds- and single-stranded (ss-) DNA, the quantum yields of PG–DNA complexes become remarkably larger than that of a free molecule. In the present theoretical study, the fluorescence enhancement mechanism of PG–DNA complexes was investigated using molecular docking simulations and ab initio quantum chemical methods. The binding energies between PG and ds-DNA were calculated to be larger than those in the case of PG and ss-DNA owing to the existence of an extra π–π stacking interaction. Nonradiative deactivation paths through conical intersections between the ground and the first excited states were obtained for a free PG molecule, while steric repulsions between PG and DNA hindered such deactivation processes in the case of PG–DNA complexes.</jats:p>

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