Comprehensive Study of Thiazole-Orange-Based DNA Dyes

Abstract

The rapid advancement of biotechnology over the recent decades has amplified the importance of DNA detection and quantification assays. Many of these assays, such as gel electrophoresis, microscopy, flow cytometry, and the detection of amplification in quantitative polymerase chain reaction (qPCR), rely on the use of DNA-binding fluorescent dyes. This article presents a comprehensive study of six Thiazole-Orange-based fluorescent DNA-binding dyes: SYBR Safe, SYBR Green, Pico Green, SYTO-16, SYTO-9, and the benzothiazole-based analogue (TOPhBu) of the latter. The selected DNA markers were synthesized at a 10-milligram scale and characterised spectroscopically to quantify their fluorescence enhancement upon binding to double-stranded DNA. The ability of the dyes to detect DNA at low concentrations was evaluated using two new metrics, absolute fluorescence enhancement (AFE) and relative fluorescence enhancement (RFE). Quantum chemical calculations shed new light on the mechanism of their fluorogenicity through modelling the excited state behaviour and DNA binding of the dyes. Their analytical performance was further tested in qPCR experiments. The experimental results of this work highlight some important differences in the sensitivity and qPCR efficiency of the studied DNA-binding dyes which will facilitate the DNA marker selection for analytical purposes and the future development of novel DNA sensors.