New Cyanine–Oligonucleotide Conjugates: Relationships between Chemical Structures and Properties

Abstract

Because the influence of the chemical structure of monomethine cyanine-oligo-2'-deoxyribonucleotide (ODN) conjugates on their binding and fluorescence properties has remained largely undetermined, we synthesized and studied a wide range of conjugates with various structural patterns. Different cyanine dyes such as thiocyanine, quinocyanine, and thiazole orange isomers were obtained. In the case of unsymmetrical cyanines, the linker was attached to either the quinoline or the benzothiazole nucleus. The influence of the ODN counterpart was evaluated by linking the cyanines to the 5'-end or to an internucleotidic phosphate. In the first case, the influence of neighboring nucleic bases was studied, whereas in the second, the stereochemical configuration at the phosphorus atom bearing the cyanine was investigated. We report here on relationships between the structures of the dyes and conjugates and some of their properties, such as the stability and fluorescence changes observed on their hybridization with the target sequence. This study provides useful information towards the design of ODN-cyanine conjugates.

Hybridization‐Sensitive On–Off DNA Probe: Application of the Exciton Coupling Effect to Effective Fluorescence Quenching

“…[9] Much research on linking such a thiazole orange dye to an artificial DNA molecule or DNA analogue and its application to gene analysis has already been reported. [10,11] Indeed, these probes show strong fluorescence, but the quenching efficiency in the single-stranded state is often low. A demonstration of the use of a tethered thiazole orange dye for applications involving peptide nucleic acid (PNA) probe molecules has been reported previously.…”

Exploring Base‐Pair‐Specific Optical Properties of the DNA Stain Thiazole Orange

“…[21][22][23][24][25][26][27][28][29][30][31][32][33] Usually, cyanine dyes or other DNA stains [34,35] have been linked to nucleic acids by means of a flexible tether. Previous work by ourselves and others has shown that the tether plays an important role as far as the responsiveness of fluorescence and the stability of probe-target duplexes are concerned.…”

Fluorescent Color Readout of DNA Hybridization with Thiazole Orange as an Artificial DNA Base

“…[16,17] Thiazole orange (TO) represents a promising alternative as it does not have the potential for photoinduced oxidation of DNA. TO was linked covalently to the phosphodiester [19] or to the 5'-terminus [20] of oligonucleotides. In addition, TO was attached to DNA-binding peptides [21,22] or incorporated as a base surrogate into peptide nucleic acid (PNA) to detect single-base variations.…”