Groove-binding unsymmetrical cyanine dyes for staining of DNA: syntheses and characterization of the DNA-binding

Abstract

Two new crescent-shaped unsymmetrical cyanine dyes have been synthesised and their interactions with DNA have been investigated by different spectroscopic methods. These dyes are analogues to a minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known intercalating cyanine dye BO was extended with a benzothiazole substituent. To investigate how the identity of the extending heterocycle affects the binding to DNA, the new dyes BETO and BOXTO have a benzothiazole group and a benzoxazole moiety, respectively. Whereas BEBO showed a heterogeneous binding to calf thymus DNA, linear and circular dichroism studies of BOXTO indicate a high preference for minor groove binding. BETO also binds in the minor groove to mixed sequence DNA but has a contribution of non-ordered and non-emissive species present. A non-intercalative binding mode of the new dyes, as well as for BEBO, is further supported by electrophoresis unwinding assays. These dyes, having comparable spectral properties as the intercalating cyanine dyes, but bind in the minor groove instead, might be useful complements for staining of DNA. In particular, the benzoxazole substituted dye BOXTO has attractive fluorescence properties with a quantum yield of 0.52 when bound to mixed sequence DNA and a 300-fold increase in fluorescence intensity upon binding.

Time-resolved electrophoretic analysis of mobility shifts for dissociating DNA ligands

“…The unwinding can be detected with high specificity, because when enough intercalating ligand has been added the introduction of positive supercoiling reverses the unwinding effect, so that the mobility shift passes through a characteristic minimum. This effect has been used to support intercalation of for instance the classical intercalator ethidium bromide [11][12][13] and to demonstrate unwinding by YO-PRO [14] in agreement with its proposed intercalative binding [15]. Conversely, the absence of this structural perturbation of the DNA is often used to support groove-binding, a mode of DNA interaction which has gained interest in recent years due to its stronger sequence recognition than intercalation [16,17].…”

Positive Charged Polymer as a Probe for DNA Determination by Resonance Light Scattering

“…17 All of these stocks should be stored at 4˚C. A PBS buffer solution (pH 7.0) was used to control the acidity of the system.…”

“…The concentration of DNA could be determined according to the absorbance values at 260.0 nm. 17 The positive-charged polymer, which has a molecular weight of 34 kD, included about 125 repeat units per molecule. Every polymer molecule could bind with ~105 DNA molecules, while the binding ratio between the repeat unit of the polymer and DNA was about 1.19:1.…”

Microwave synthesis and fluorescence properties of homo- and heterodimeric monomethine cyanine dyes TOTO and their precursors

“…Bis-intercalating TOTO-1 dyes have a weak fluorescence in the free state, but they sharply (more than 1000 times) increase fluorescence due to binding with DNA (4) and, therefore, they are widely used in biological, medical and drug development areas as fluorescent labels and probes (8)(9)(10)(11)(12)(13)(14)(15). They found also applications in genetic studies and modern diagnostic methods (1)(2)(3), for examples, in the case of the polymerase chain reaction for cancer diagnostics at early stages of the disease; for diagnostics of infection diseases (1)(2)(3)(4), including AIDS; for the identification of DNA samples in criminal law (16,17); flow cytometry (18), DNA sequencing (19,20) and quantification of nucleic acids in capillary and gel electrophoresis (21)(22)(23). Besides, they are commonly applied to lasers (24), electronics (25), nonlinear optics (26) and solar cells (27).…”