title: Investigation of DNA binding modes for a symmetrical cyanine dye trication: effect of DNA sequence and structure.
abstract: The DNA binding behavior of a tricationic cyanine dye (DiSC3+(5)) was studied using the [Poly(dA-dT)]2, [Poly(dI-dC)]2 and Poly(dA) x Poly(dT) duplex sequences and the Poly(dA) x 2Poly(dT) triplex. Optical spectroscopy and viscometry results indicate that the dye binds to the triplex structure by intercalation, to the nonalternating Poly(dA) x Poly(dT) duplex through minor groove binding and to the alternating [Poly(dA-dT)]2 duplex by a combination of two binding modes: intercalation at low concentration and dimerization within the minor groove at higher concentration. Dimerization occurs at lower dye concentrations for the [Poly(dI-dC)]2 sequence, consistent with our previous investigations on an analogous monocationic cyanine dye. [Seifert, J.L., et al. (1999) J. Am. Chem. Soc. 121, 2987-2995] These studies illustrate the diversity of DNA binding modes that are available to a given ligand structure.
authors.affiliation: Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213-3890, USA.
authors.forename: R
authors.initials: R
authors.lastname: Cao
authors.forename: C F
authors.initials: CF
authors.lastname: Venezia
authors.forename: B A
authors.initials: BA
authors.lastname: Armitage
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D052160:Benzothiazoles; D002232:Carbocyanines / Q000737:chemistry / Q000378:metabolism*; D002412:Cations / Q000737:chemistry / Q000378:metabolism; D002942:Circular Dichroism; D004396:Coloring Agents / Q000737:chemistry / Q000378:metabolism*; D019281:Dimerization; D007364:Intercalating Agents / Q000737:chemistry / Q000378:metabolism*; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011061:Poly A / Q000737:chemistry / Q000378:metabolism; D011071:Poly T / Q000737:chemistry / Q000378:metabolism; D011067:Poly dA-dT / Q000737:chemistry / Q000378:metabolism*; D011089:Polydeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D013696:Temperature; D014783:Viscosity
chemical_list: D052160:Benzothiazoles; D002232:Carbocyanines; D002412:Cations; D004396:Coloring Agents; D007364:Intercalating Agents; D011089:Polydeoxyribonucleotides; D011061:Poly A; D011071:Poly T; C015465:poly(dA); C031156:poly d(I-C); D011067:Poly dA-dT; C012944:3,3'-dipropyl-2,2'-thiadicarbocyanine; C084838:polydeoxyadenylic acid-polythymidylic acid