Comparing mono- and divalent DNA groove binding cyanine dyes—Binding geometries, dissociation rates, and fluorescence properties

Eriksson, Maja; Westerlund, Fredrik; Mehmedovic, Merima; Lincoln, Per; Westman, Gunnar; Larsson, Anette; Åkerman, Björn

doi:10.1016/j.bpc.2006.03.009

Cited by 7 publications

(6 citation statements)

References 35 publications

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“…The set of asymmetric cyanine dyes in Figure allowed the size, charge, DNA affinity, and binding mode to be varied in a systematic fashion. Furthermore, these dyes are strongly fluorescent in the bound state, while the fluorescence is essentially negligible when the dyes are free in aqueous solution. , For a given type of chromophore the fluorescence intensity will therefore be taken to be proportional to the bound amount of the corresponding dye molecules.…”

Section: Discussionmentioning

confidence: 99%

“…One possibility is that the tails are negatively charged as with T7 and bridged by the divalent cationic dyes, which are in excess. Nonelectrostatic interactions may also be involved, however, because the tendency of phage aggregation seems to be stronger with BOXTO-PRO which is also divalent but expected to be less hydrophilic . It should be remembered, however, that the two samples were exposed to dyes for different times.…”

Section: Discussionmentioning

confidence: 99%

“…The above interpretations of K rel rely on the assumption that the binding modes of YO-PRO 17 and BOXTO-PRO, which were determined with DNA free in solution, also apply when the DNA is inside the T5 capsid. The spectral similarity in both emission (Figure ) and excitation spectra (Supporting Information) strongly supports that YO-PRO binds in the same manner to DNA inside phages as to DNA free in solution (i.e., by intercalation).…”

Section: Discussionmentioning

confidence: 99%

“…Finally, we investigate the effect of DNA extension on the effective phage-binding constant by comparing YO-PRO and BOXTO-PRO. These dyes have the same charge and similar size but differ in the mode of DNA-binding: YO-PRO intercalates and subsequently extends and unwinds the DNA, − whereas BOXTO-PRO is groove-bound and does not perturb the helix to same extent 1 Structure of the dyes used in this study: (a) YO; (b) YO-PRO; (c) YOYO; (d) BOXTO-PRO. …”

Section: Introductionmentioning

confidence: 99%

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Binding of Intercalating and Groove-Binding Cyanine Dyes to Bacteriophage T5

et al. 2007

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The interaction between four related cyanine dyes and bacteriophage T5 is investigated with fluorescence and absorption spectroscopy. The dyes, which differ in size, charge, and mode of DNA-binding, penetrate the capsid and bind the DNA inside. The rate of association decreases progressively with increasing dye size, from a few minutes for YO to more than 50 h for YOYO (at 37 degrees C). The relative affinity for the phage DNA is a factor of about 0.2 lower than for the same T5-DNA when free in solution. Comparison of groove-bound BOXTO-PRO and intercalating YO-PRO shows that the reduced affinity is not due to DNA extension but perhaps influenced by competition with other cationic DNA-binding agents inside the capsid. Although, the extent of dye binding to the phages decreases with increasing external ionic strength, the affinity relative to free DNA increases, which indicates a comparatively weak screening of electrostatic interactions inside the phage. The rate of binding increases with increasing ionic strength, reflecting an increase in effective pore size of the capsid as electrostatic interactions are screened and/or a faster diffusion of the dye through the DNA matrix inside the capsid as the DNA affinity is reduced. A combination of electron microscopy, light scattering, and linear dichroism show that the phages are intact after YO-PRO binding, whereas a small degree of capsid rupture cannot be excluded with BOXTO-PRO.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Binding of Intercalating and Groove-Binding Cyanine Dyes to Bacteriophage T5

et al. 2007

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“…Among several methods to study the dissociation of the drug from DNA, the sequestration of the drug using surfactant has been studied quite extensively. The drug sequestration by surfactant was first introduced by Muller and Crothers and subsequently investigated by several research groups. − The sequestration of the drug molecules is important to not only understand the drug–DNA binding process but also help us to remove the excess drugs (in the case of drug overdose) or removal of mutagens from the cellular body. − …”

Section: Introductionmentioning

confidence: 99%

Controlled Sequestration of DNA Intercalated Drug by Polymer–Surfactant Supramolecular Assemblies

2016

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Triblock copolymer and surfactant based supramolecular assemblies have been used for the controlled sequestration of the DNA intercalator. The triblock copolymer micelles do not affect the molecules that are intercalated in the DNA. However, on addition of charged surfactant to the triblock copolymer micellar solution, sequestration of the intercalated molecules from DNA to the polymer-surfactant supramolecular assemblies takes place. Such sequestration of the intercalated molecules in the polymer-surfactant supramolecular assemblies has been explained on the basis of the charged surface formed in the polymer micelles due to the addition of surfactants. Sequestration of the intercalated molecules from the DNA to the polymer-surfactant supramolecular assemblies has been monitored through the ground state absorption, steady state, and time-resolved emission measurements. It is shown that the extent of sequestration of the intercalated molecules can be finely tuned by tuning the concentration of the surfactant in the triblock copolymer solution. Quantitative sequestration of the intercalated molecules by the supramolecular assemblies has been achieved. Such controlled sequestration of the DNA intercalated molecules by polymer-surfactant supramolecular assemblies can be used to study the binding of drug with DNA and may be useful in applications like detoxification in the case of drug overdose.

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Acridone–Pterocarpan Conjugate: A Hybrid Molecular Probe for Recognition of Nucleic Acids

et al. 2013

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Chemical fusion of a naturally occurring pharmacophore (pterocarpan) with a fluorophore (acridone) by thermally induced cascade sigmatropic rearrangement leads to the formation of a structurally different class of DNA binding ligands. Competitive binding assay in the presence of a classical minor groove binder shows the possibility of DNA minor groove binding by the ligand 4a. High cell viability of the prepared molecular probes was of utility for nuclear staining as well as cell cycle analysis through fluorescence‐activated cell sorting (FACS).

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Comparing mono- and divalent DNA groove binding cyanine dyes—Binding geometries, dissociation rates, and fluorescence properties

Cited by 7 publications

References 35 publications

Binding of Intercalating and Groove-Binding Cyanine Dyes to Bacteriophage T5

Binding of Intercalating and Groove-Binding Cyanine Dyes to Bacteriophage T5

Controlled Sequestration of DNA Intercalated Drug by Polymer–Surfactant Supramolecular Assemblies

Acridone–Pterocarpan Conjugate: A Hybrid Molecular Probe for Recognition of Nucleic Acids

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