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.
Publication types
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Comparative Study
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Research Support, Non-U.S. Gov't
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Research Support, U.S. Gov't, Non-P.H.S.
MeSH terms
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Base Pairing
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Base Sequence
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Benzothiazoles
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Carbocyanines / chemistry
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Carbocyanines / metabolism*
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Cations / chemistry
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Cations / metabolism
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Circular Dichroism
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Coloring Agents / chemistry
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Coloring Agents / metabolism*
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Dimerization
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Intercalating Agents / chemistry
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Intercalating Agents / metabolism*
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Molecular Structure
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Nucleic Acid Conformation*
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Poly A / chemistry
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Poly A / metabolism
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Poly T / chemistry
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Poly T / metabolism
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Poly dA-dT / chemistry
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Poly dA-dT / metabolism*
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Polydeoxyribonucleotides / chemistry
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Polydeoxyribonucleotides / metabolism*
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Spectrometry, Fluorescence
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Temperature
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Viscosity
Substances
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Benzothiazoles
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Carbocyanines
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Cations
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Coloring Agents
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Intercalating Agents
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Polydeoxyribonucleotides
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Poly A
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Poly T
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poly(dA)
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poly d(I-C)
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Poly dA-dT
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3,3'-dipropyl-2,2'-thiadicarbocyanine
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polydeoxyadenylic acid-polythymidylic acid