DNA-templated synthesis of cationic styryl dyes

Abstract

Styryl dye is a class of pi-conjugated dye that shows several desirable optical properties, such as high photostability, solvatochromic characteristics, and high fluorescence quantum yields. Due to the responsiveness to the binding with the target biomolecules such as nucleic acids, some of these dyes have been widely employed for biomolecular detection and cellular imaging. These dyes are typically synthesized via an aldol-type reaction between a methyl heterocycle and an aromatic aldehyde in the presence of acid or base as a catalyst. However, the conventional method of synthesizing these dyes is inefficient, time-consuming, and involves the use of excessive chemicals, as each dye must be prepared and isolated before evaluating its optical properties. DNA-templated synthesis has recently emerged as a powerful approach for synthesizing different types of organic molecules. This method allows for the rapid and convenient synthesis of diverse targets at microscopic scales, which is crucial during the discovery phase. The objective of this study is to develop a novel DNA-templated reaction for synthesizing cationic styryl cyanine dyes. The key to the success of the proposed method relies on the electrostatic binding of two cationic coupling partners (the heterocycles and aromatic aldehydes) to the DNA template. This brings the two coupling partners in close proximity and proper orientation for the reaction, resulting in an accelerated formation of the dye. The concept of the DNA-templated synthesis strategy was proven, and it successfully produced the desired styryl dyes from a wide range of substrates in a combinatorial fashion. The success of the dye formation was confirmed by UV-Vis and fluorescence spectroscopy, and in some cases, NMR spectroscopy and mass spectrometry. Importantly, the formation and responsiveness of these dyes to the DNA template, which also acted as the nucleic acid target, could be easily observed in situ. By utilizing different DNA templates and substrates, it was possible to identify new dyes that are responsive to a specific type of DNA template. Lastly, the templated styryl dye synthesis was successfully performed within live HeLa cells. However, nuclease digestion experiments confirm that the cellular RNA acted as the template instead of DNA probably due to the inaccessibility of the latter. Overall, this approach holds potential as a valuable tool for synthesizing and screening dyes that specifically target various types of nucleic acids or organelles within cells.