Fluorescent Oligonucleotides with Bis(prop-2-yn-1-yloxy)butane-1,3-diol Scaffold Rapidly Detect Disease-Associated Nucleic Acids

Biomedical research and clinical work demand rapid and reliable detection of disease-associated nucleic acids. Fluorescent oligonucleotides that bind precisely, and sense target DNA or RNA, are useful tools for simple hybridization-based assays. Although a plethora of oligonucleotide modifications are reported in the literature, they often result in poor coupling yields and are very expensive. We describe the synthesis of a new bisalkyne butane-1,3-diol scaffold and its efficient coupling into oligonucleotide sequences. We hypothesized that covalent attachment of multiple (2/4) fluorescent groups to the scaffold within oncogene-specific oligonucleotides could lead to beneficial detection of target DNA. To test this, we post-synthetically conjugated the oligonucleotides with azide-derivative dyes (2/4 per sequence): perylene, 5JOE, and (phenylethynyl)­pyrene. We investigated the biophysical and photophysical properties of the oligonucleotide–dye conjugates and confirmed a “light up” fluorescent sensing mechanism of the probes upon target binding. However, fluorescence of the probes was not sensitive to mismatches. Nevertheless, “clicked” probes showed a high specificity of binding to complementary target, with the difference in T_m over 10 °C for matched vs mismatched duplex. When applied together, the mismatch-induced difference in temperature melting and fluorescence-based discrimination of the target-bound vs single-stranded probe state allowed us to apply the perylene conjugates to detect mutations in human oncogenes. Due to the beneficial target binding properties of the perylene labeled probes, along with the high fluorescence intensity of probe:target duplexes, human oncogenes could be detected in a convenient and fast (2.5 h) bead-based assay.