title: Dynamics in the DNA recognition by DAPI: exploration of the various binding modes.
abstract: Two distinct modes of interaction of the fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), depending on the sequence of DNA, have been reported in the literature. In the present study, the dynamics of solvation has been utilized to explore the binding interaction of DAPI to DNA oligomers of different sequences. Picosecond-resolved fluorescence and polarization-gated anisotropy have been used to characterize the binding of DAPI to the different oligomers. In the double-stranded dodecamer of sequence CGCGAATTCGCG (oligo1), the solvation relaxation dynamics of the probe reveals time constants of 0.130 ns (75%) and 2.35 ns (25%). Independent exploration of the minor-groove environment of oligo1 using another well-known minor-groove binder Hoechst 33258 (H258) shows similar timescales, further confirming minor-groove binding of DAPI to oligo1. In the double-stranded dodecamer (oligo2) having the sequence GCGCGCGCGCGC, where intercalation has been reported in the literature, no solvation is observed in our experimental window. DAPI bound to oligo2 shows quenching of fluorescence compared to that of DAPI in a buffer. The quenching of fluorescence of DAPI intercalated in DNA is also borne out by the appearance of a fast component of 30 ps in the fluorescence lifetime, revealing electron transfer to DAPI from GC base pairs, between which it intercalates. In addition to this, the excited-state lifetime of the probe in the DAPI-DNA complex also shows a time constant similar to that of the dye in a buffer, indicating that the excited-state photoprocesses associated with the free dye is also operative in this binding mode, consistent with the binding geometry of the DAPI in the DNA. The dynamics of DAPI in calf thymus DNA having a random sequence of base pairs is similar to that associated with the DNA minor groove. Our studies clearly explore the structure-dynamics correlation of the DAPI-DNA complex in the two distinct modes of interaction of DAPI with DNA.
authors.affiliation: Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India.
authors.forename: Debapriya
authors.initials: D
authors.lastname: Banerjee
authors.forename: Samir Kumar
authors.initials: SK
authors.lastname: Pal
mesh_terms: D000225:Adenine / Q000737:chemistry; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D006690:Bisbenzimidazole / Q000737:chemistry*; D002021:Buffers; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry; D007211:Indoles / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013941:Thymine / Q000737:chemistry; D013997:Time Factors
chemical_list: D002021:Buffers; D005456:Fluorescent Dyes; D007211:Indoles; D007364:Intercalating Agents; D009841:Oligonucleotides; D012997:Solvents; C007293:DAPI; D006147:Guanine; D003596:Cytosine; D004247:DNA; D000225:Adenine; D006690:Bisbenzimidazole; D013941:Thymine