A benzindole substituted carbazole cyanine dye: a novel targeting fluorescent probe for parallel c-myc G-quadruplexes

Abstract

Many organic ligands were synthesized to recognize G-quadruplexes. However, different kinds of G-quadruplexes (G4s) possess different structures and functions. Therefore, selective recognition of certain types of G4s is important for the study of G4s. In this paper, a novel cyanine dye, 3-(2-(4-vinylpyridine))-6-(2-((1-(4-sulfobutyl))-3,3-dimethyl-2-vinylbenz[e]indole)-9-ethyl-carbazole (9E PBIC), composed of benzindole and carbazole was designed and synthesised. The studies on UV-vis and fluorescence properties of the dye with different DNA forms showed that the dye exhibits almost no fluorescence under aqueous buffer conditions, but it increased over 100 fold in the presence of c-myc G4 and 10-30 fold in the presence of other G4s, while little in the presence of single/double-stranded DNA, indicating that it has excellent selectivity to c-myc 2345 G4. For the binding studies the dye is interacted with the c-myc 2345 G-quadruplex by using the end-stack binding model. It can be said that the dye is an excellent targeting fluorescent probe for c-myc G-quadruplexes.

Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands

“…The same effect was observed for the carbazole ligand with triazole substituent [13]. It seems that the low fluorescence intensity of the ligand is associated with the loss of its flat structure by the rotation of benzothiazolium arm coupled by double bond C=C with a carbazole skeleton [32] or self-quenching due to dimer formation.…”

Selective, pH‐Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4‐Dimethylamino(phenyl)‐Substituted Berberine Derivatives

“…In this context, quadruplex DNA has been identified as a very important analyte, because of its activity in many biological processes, such as transcription regulation [6,7] or telomerase inhibition [7,8] . As a result, fluorescent probes have been developed and employed widely for the selective detection of G4‐DNA structures [9–19] . Such probes usually consist of a G4‐DNA‐binding molecule whose emission properties change upon association to the target G4‐DNA.…”

“…For an efficient detection, however, either the emission intensity of the otherwise non‐fluorescent ligand has to increase strongly or the emission energy has to shift distinctly. Thus, several organic fluorophores have been introduced that serve this purpose, for example benzimidazole, [9] benzindole, [10] triazine, [11] coumarin, [12] cyanine, [13] pyridinium, [14,15] quinolinium, [15,16] quinolizinium, [15,17] triangulenium [18] and benzothiazole [19] based dyes. Among the promising compound classes for this application are also DNA‐binding natural products with suitable fluorescence properties, because these compounds usually provide sufficient affinity, and often selectivity, towards DNA, along with the required biocompatibility.…”

A novel fluorescent long-chain fatty acid-substituted dye: labeling and biodegrading ofMicrothrix parvicella

“…Carbazole derivatives in particular are excellent electron-donating chromophores for creating uorescent probes with large Stokes shis, excellent stability, and high quantum yields. [16][17][18] Here, we created and characterized a carbazole uorescent probe (FP1, Fig. 1) modied by LCFAs (hexadecanoic acid).…”