Systematic study of SYBR green chromophore reveals major improvement with one heteroatom difference

Abstract

Five nucleic acid binding cyanine dyes were synthesized and their photophysical properties were evaluated. Changing a single heteroatom in the chromophore causes major differences both in brightness and photostability between...

Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization

“…Similar enhancement of Stoke's shift was also found by Zhang et al [23] and Peng et al [24] when replacing chloride by amine group. The same was also observed in our previous studies [15]. Together with the Stoke's shifts, quantum yield is an important way to evaluate fluorescent probes since it tells how much of the absorbed photons are emitted and therefore it can illuminate which dyes could be potentially strongly fluorescent.…”

“…In this study, we have synthesized five new nucleic acid-binding cyanine dyes to study how different functional groups affect to the nature of the quality of the dyes in photophysical measurements. In our previous paper, we concluded that a single heteroatom could change the qualities of the dyes drastically and oxazolium moiety seemed to produce better dyes [15]. With that in mind, we were interested to see the effect of the thiazolium moiety.…”

“…Trusting the results will open new ideas for developing dyes in the future. The five new synthesized cyanine dyes and selection of the commercial cyanine dyes were compared to our previously published cyanine dyes [15] to get deeper information on how these modifications affect the fluorescence behavior.…”

“…All used reagents and materials were commercially available and used as received unless otherwise mentioned. All dyes were synthesized with a modified and developed synthesis method previously published by our group [15] based on protocols found in literature [16,17].…”

“…for related plots. Data for dyes 6-9 was taken from our previous article [15] to be compared with the dyes (1-5) here presented. Reported excitation maxima were used to record emission spectra and vice versa for each dye.…”