title: Unlocked nucleic acids with a pyrene-modified uracil: synthesis, hybridization studies, fluorescent properties and i-motif stability.
abstract: The synthesis of two new phosphoramidite building blocks for the incorporation of 5-(pyren-1-yl)uracilyl unlocked nucleic acid (UNA) monomers into oligonucleotides has been developed. Monomers containing a pyrene-modified nucleobase component were found to destabilize an i-motif structure at pH 5.2, both under molecular crowding and noncrowding conditions. The presence of the pyrene-modified UNA monomers in DNA strands led to decreases in the thermal stabilities of DNA*/DNA and DNA*/RNA duplexes, but these duplexes' thermal stabilities were better than those of duplexes containing unmodified UNA monomers. Pyrene-modified UNA monomers incorporated in bulges were able to stabilize DNA*/DNA duplexes due to intercalation of the pyrene moiety into the duplexes. Steady-state fluorescence emission studies of oligonucleotides containing pyrene-modified UNA monomers revealed decreases in fluorescence intensities upon hybridization to DNA or RNA. Efficient quenching of fluorescence of pyrene-modified UNA monomers was observed after formation of i-motif structures at pH 5.2. The stabilizing/destabilizing effect of pyrene-modified nucleic acids might be useful for designing antisense oligonucleotides and hybridization probes.
authors: Pavla
authors: P
authors: Perlíková
authors: Kasper K
authors: KK
authors: Karlsen
authors: Erik B
authors: EB
authors: Pedersen
authors: Jesper
authors: J
authors: Wengel
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D009696:Nucleic Acids / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism*; D011721:Pyrenes / Q000737:chemistry*; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D013050:Spectrometry, Fluorescence; D044366:Transition Temperature; D014498:Uracil / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009696:Nucleic Acids; D009841:Oligonucleotides; D011721:Pyrenes; D014498:Uracil; D012313:RNA; D004247:DNA; C030984:pyrene