Influence of cyanine dye structure on self-aggregation and interaction with nucleic acids: A kinetic approach to TO and BO binding

Biver, Tarita; Boggioni, Alessia; Secco, Fernando; Turriani, Elisa; Venturini, Marcella; Yarmoluk, S. M.

doi:10.1016/j.abb.2007.04.034

Cited by 68 publications

(88 citation statements)

References 55 publications

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“…Subsequent investigations have shown that not only acridines [24][25][26][27] but cyanines as well [28,29] interact with DNA according to the sequential mechanism, although the details of the kinetic behaviour have revealed that the step leading to DS I formation is preceded by an ever faster step where a precursor complex is formed. Differently from other systems where the nature of the precursor complex was believed to be essentially electrostatic, in the DNA/cyanine systems electrostatic interactions play only a partial role in the stabilization of the precursor complex [30].…”

Section: Basic Reaction Mechanismsmentioning

confidence: 99%

Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

Biver

Secco

Venturini

2008

Coordination Chemistry Reviews

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Section: Basic Reaction Mechanismsmentioning

confidence: 99%

Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

Biver

Secco

Venturini

2008

Coordination Chemistry Reviews

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“…For example, they can be used as a laser or textile dyes, photosensitizers for silver halide emulsion, for optical recording materials, etc. [21][22][23]. In recent years, interest for synthesis and application of styrylcyanine dyes has grown due to their use as a fluorescent probes in bioanalytical methods for DNA or RNA analyses [24,25].…”

Section: Introductionmentioning

confidence: 99%

Crystal structure and synthesis of benzimidazole substituted acrylonitriles and benzimidazo[1, 2-a]quinolines

2009

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The benzimidazole compounds and benzoannulated cyclic benzimidazole analogues, such as benzimidazo[1,2-a]quinolines, are a part of our wider investigation on biologically active compounds, potential antitumor drugs. Here, we present the synthesis of two compounds,[2-(1H-benzimidazol-2-yl)-3-(4-bromophenyl)-acrylonitrile, 5] and [2-bromo-benzimidazo[1,2-a]quinoline-6-carbonitrile, 7] and their crystal structures revealed by X-ray single crystal diffractometry. We also report the molecular and crystal structures of two additional compounds [2-(1H-benzimidazol-2-yl)-3-(4-cyanophenyl)-acrylonitrile, 4] and [benzimidazo[1,2-a]quinoline-2,6-dicarbonitrile, 6], whose synthesis and spectroscopic characterization have been published earlier by us too (Hranjec and Karminski-Zamola, Molecules 12:1817, 2007). The compounds 4 and 5 crystallize as monohydrates. The dihedral angles calculated between phenyl and benzimidazole ring reflect not significant deviation from molecular planarity in the crystalline state for 4 and 5, while benzoannulated cyclic benzimidazole derivatives 6 and 7 are essentially planar. The crystal structures of 4 and 5 are characterized by O-HÁÁÁN and N-HÁÁÁO hydrogen bonds between water molecule of crystallization and imidazole NH group as well as CN group, while in 6 and 7 only weak C-HÁÁÁN intermolecular hydrogen bonds exist. Although, crystal packings are analogous in 4 and 5, the molecular conformations differ slightly. In 6 there is one C-HÁÁÁN hydrogen bond that do not exist in 7.

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“…A stock solution of TO at 200 μM in 150 mM PBS was also prepared. Following addition of the TO, the samples could be measured immediately since equilibrium between TO and DNA duplexes occurs extremely rapidly even at room temperature [12, 13]. All fluorescent measurements were at room temperature.…”

Section: Methodsmentioning

confidence: 99%

A Convenient Thiazole Orange Fluorescence Assay for the Evaluation of DNA Duplex Hybridization Stability

et al. 2009

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Objective-A simple and rapid method for measuring the hybridization stability of duplexes of DNAs and other oligomers in different environments is described. When added to an oligomer duplex, the thiazole orange (TO) dye intercalates and in this state is fluorescent. Therefore, when duplex dissociation occurs, the release of TO results in a detectable change in fluorescence intensity. This assay was developed primarily to screen antisense oligomer duplexes that are stable in serum and in the cytoplasm but unstable in the presence of their target messenger RNA (mRNA).Methods-The two antisense oligomers of this investigation were both 25 mer phosphorothioate (PS) DNAs, one directed against the RIα mRNA and the other directed against the mdr1 mRNA. The former duplex was first used in the solution studies, in most cases duplexed with a 16 mer phosphodiester (PO) complementary DNA (i.e., PS-DNA25/PO-cDNA16). Both duplexes were then tested in a series of cell studies using SK-BR-3 (RIα+), KB-G2 (mdr1++), and KB-31 (mdr1+/−) cells.Results-Preliminary measurements in solution showed that maximum fluorescence was achieved when more than ten TO molecules were bound to each duplex. When a 25 mer PO-DNA or PO-RNA with the base sequence of the RIα mRNA was added, the dramatic change in fluorescence intensity that followed signified dissociation of the antisense DNA from the study duplex and reassociation with the target DNA. Kinetic measurements showed that this process was completed in about 3 min. Fluorescent measurements of SK-BR-3 (RIα+) cells incubated at 37°C with the anti-RIα study duplex over time showed a maximum at the point where the loss of fluorescence due to dissociation of the study duplex, probably by an antisense mechanism, began to dominate over the increasing fluorescence due to continuing cellular accumulation. A similar result was observed in the KB-G2 (mdr1+) cells incubated with the anti-mdr1 study duplex.Conclusions-When study duplexes shown to be stable in serum were incubated with their target cells, the assay successfully detected evidence of dissociation, most likely by an antisense mechanism. Thus, a TO fluorescence assay has been developed that is capable of detecting the dissociation of DNA duplexes.

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Influence of cyanine dye structure on self-aggregation and interaction with nucleic acids: A kinetic approach to TO and BO binding

Cited by 68 publications

References 55 publications

Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

Crystal structure and synthesis of benzimidazole substituted acrylonitriles and benzimidazo[1, 2-a]quinolines

A Convenient Thiazole Orange Fluorescence Assay for the Evaluation of DNA Duplex Hybridization Stability

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