title: Bis-pyrene-modified unlocked nucleic acids: synthesis, hybridization studies, and fluorescent properties.
abstract: 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.
authors.affiliation: Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M (Denmark); Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic).
authors.forename: Pavla
authors.initials: P
authors.lastname: Perlíková
authors.forename: Maria
authors.initials: M
authors.lastname: Ejlersen
authors.forename: Niels
authors.initials: N
authors.lastname: Langkjaer
authors.forename: Jesper
authors.initials: J
authors.lastname: Wengel
mesh_terms: D020137:Base Pair Mismatch; D005453:Fluorescence; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D009696:Nucleic Acids / Q000187:drug effects*; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000302:isolation & purification; D011721:Pyrenes / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D009696:Nucleic Acids; D009841:Oligonucleotides; D011721:Pyrenes; C030984:pyrene
keywords: fluorescence; nucleic acid hybridization; oligonucleotides; pyrenes; unlocked nucleic acids