title: The fluorophore 4',6-diamidino-2-phenylindole (DAPI) induces DNA folding in long double-stranded DNA.
abstract: DAPI (4',6-diamidino-2-phenylindole) is a widely used fluorescent dye, whose complicated binding features to DNAs and RNAs have been the object of debates and are still not fully understood. In this study, different approaches were employed, including binding equilibrium measurements (spectrofluorometry), melting experiments (spectrophotometry), viscometric measurements, circular dichroism, and T-jump kinetic analyses; all data concur in shedding light on the complex mechanistic aspects of the binding mode of DAPI to natural DNA. Conditions are found that induce the mode of the DAPI/DNA interaction to change from groove binding to intercalation. Moreover, it is observed, for the first time, that DAPI is able to induce the formation of a rather compact polymer-dye adduct under particular conditions. The results suggest that this form is a folded or coiled DNA structure stabilized by DAPI dye bridges.
authors.affiliation: Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento 35, 56126 Pisa, Italy.
authors.forename: Maria Rosa
authors.initials: MR
authors.lastname: Beccia
authors.forename: Tarita
authors.initials: T
authors.lastname: Biver
authors.forename: Alberto
authors.initials: A
authors.lastname: Pardini
authors.forename: Jacopo
authors.initials: J
authors.lastname: Spinelli
authors.forename: Fernando
authors.initials: F
authors.lastname: Secco
authors.forename: Marcella
authors.initials: M
authors.lastname: Venturini
authors.forename: Natalia
authors.initials: N
authors.lastname: Busto Vázquez
authors.forename: Maria Pilar
authors.initials: MP
authors.lastname: Lopez Cornejo
authors.forename: Victoria Isabel
authors.initials: VI
authors.lastname: Martin Herrera
authors.forename: Rafael
authors.initials: R
authors.lastname: Prado Gotor
mesh_terms: D002942:Circular Dichroism; D004396:Coloring Agents / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry; D007211:Indoles / Q000737:chemistry*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D044366:Transition Temperature
chemical_list: D004396:Coloring Agents; D005456:Fluorescent Dyes; D007211:Indoles; D011108:Polymers; C007293:DAPI; D012313:RNA; D004247:DNA