1 Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU2 NAC, Institut for Fysik og Kemi, Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU3 Clinical Physiology and Nuclear Medicine, Department of Clinical Research, Det Sundhedsvidenskabelige Fakultet, SDU4 Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU5 Clinical Physiology and Nuclear Medicine, Department of Clinical Research, Det Sundhedsvidenskabelige Fakultet, SDU
Efficient synthesis of a building block for the incorporation of a bis-pyrene-modified unlocked nucleic acid (UNA) into oligonucleotides (DNA*) was developed. The presence of bis-pyrene-modified UNA within a duplex leads to duplex destabilization that is more profound in DNA*/RNA and less distinct in DNA*/DNA duplexes. Nevertheless, the destabilization effect of bis-pyrene-modified UNA is weaker than that of unmodified UNA. Some oligonucleotides with bis-pyrene-modified UNA incorporations displayed superior mismatch discrimination capabilities. UV/Vis absorption and molecular modeling studies indicate that the pyrene groups of bis-pyrene-modified UNA are located in the major groove of a duplex. Oligonucleotides containing two bis-pyrene-modified UNA monomers showed low pyrene monomer emission in bulge-containing duplexes, high pyrene monomer emission in fully matched duplexes, and 5-(pyrenyl)uracil:pyrene exciplex emission in the single-stranded form. Such fluorescent properties enable the application of bis-pyrene-modified UNA in the development of fluorescence probes for DNA/RNA detection and for detection of deletions at specific positions.