Colorimetric and fluorescent detection of nucleic acid by styryl dyes

Abstract

Nucleic acid staining dyes are essential tools for the analysis and visualizing of DNA/RNA in vitro and in cellular applications. Although there are several commercially available dyes developed during the past few decades, the selection is still relatively limited, and they are often very costly and associated with undesirable characteristics such as toxicity. Consequently, the discovery of nontoxic, readily available dyes, with desirable and controllable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many desirable properties including a straightforward synthesis procedure, excellent photostability, tunable optical properties, and high responsiveness towards nucleic acid targets with low background fluorescence signals. In addition, because of their strong absorption in the visible region together with solvatochromic behaviors, styryl dyes are also potentially useful as colorimetric stains for rapid and inexpensive detection of nucleic acids. In this study, novel dicationic styryl dyes with positively charged quaternary ammonium modifiers are designed to improve the binding affinity and optical responsiveness with DNA through the favorable electrostatic interaction with the negatively charged phosphate backbones. To explore new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets, optical characteristics of the newly synthesized styryl dyes have been examined in the presence and absence of DNA in various sequence contexts. The obtained results both experimental and theoretical supported that the dicationic styryl dyes outperformed the analogous monocationic styryl dyes in terms of their binding interaction and optical response towards DNA. Moreover, it was found that not only the optical properties but also the selectivity against different DNA sequences can be affected by the nature of the electron-donating substituent on the dyes’ molecule thus providing opportunities for fine-tuning of the dyes properties to meet the demand for specific applications. Applications of the developed dyes for cellular imaging of nucleic acids and aptamer-based mercury(II) detection platforms have also been successfully demonstrated.