Fluorescent triplex-forming DNA oligonucleotides labeled with a thiazole orange dimer unit

Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above

“…through the quinoline moiety) and this provided a large increase (+14.2 °C) in triplex stability in high Mg 2+ buffer compared to the unlabelled triplex. However, as found previously for other TO modifications, 29 a second TO Q6 unit did not confer any additional triplex stabilisation (Fig. S2 † ).…”

“…In this context, a TO dimer has been incorporated into modified TFOs that are known as ‘ECHO probes’ (exciton controlled hybridization sensitive fluorescent oligonucleotide). 29 However, no triplex formation was seen at pH 8 (essential for important in vitro enzymatic reactions such as PCR), and the stabilising effect was not additive; two TO dimers did not enhance triplex stability over that obtained from a single addition. Other studies have been carried out on parallel triplexes using terminal (3′ and 5′) or single internal TO units, but in neither case was stable parallel triplexes reported at pH 7.…”

Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions

“…ECHO probes have been proposed for use as reporter primers for genotyping of SNP regions [ 84 ], and have been shown to be useful for RNA detection and imaging in live cells, bacteria, and complex tissue samples [ 85 , 86 , 87 , 88 ]. A shortcoming of ECHO probes is their non-specific binding to dsDNA, as well as to each other, due to the intrinsic affinity of the TO dimers to DNA [ 80 , 88 , 89 ]. Attempts to address such problems, however, involved the incorporation of unnatural bases that prevent cross-probe reaction [ 88 ], or the conjugation of the ECHO probes to bulky protein or nanoparticles to avoid diffusion of probes into specific cell organelles [ 90 ].…”

Thiazole orange-conjugated peptide nucleic acid for fluorescent detection of specific DNA sequences and site-selective photodamage

“…1,2 Therefore, various TO-based probes have been already synthesized to detect DNA or RNA. [3][4][5][6][7][8][9][10][11][12][13][14] In most cases, dsDNA was rst denatured at elevated temperatures and the resultant ssDNA was subjected to the probes. Accordingly, the pioneering work by Dervan's group was attractive in that no denaturation process was required for the detection.…”

“…14 Recently, triplex-forming oligonucleotides were labeled with two TO units and used for exciton-controlled hybridization-sensitive uorescent detection. 10 In addition to these uorescent properties, TO acts as a photo-induced generator of singlet oxygen ( 1 O 2 ) by transferring the energy from its triplet state to ground state oxygen. [15][16][17] The 1 O 2 formed in turn induces damage in dsDNA through oxidation of nucleobases.…”