title: 'Cyclicons' as hybridization-based fluorescent primer-probes: synthesis, properties and application in real-time PCR.
abstract: We have studied the use of 'pseudocyclic oligonucleotides' (PCOs) (Jiang et al. Bioorg. Med. Chem. 1999, 7, 2727) as hybridization-based fluorescent probes. The resulting fluorescent tag-attached PCOs are called 'cyclicons'. Cyclicons consist of two oligonucleotides linked to each other through 3'-3' or 5'-5' ends. One of the oligos is the probe or primer-probe sequence that is complementary to a target nucleic acid (mRNA/DNA), and the other is a modifier oligo that is complementary to one of the ends of the probe oligo. A fluorescence molecule and a quencher molecule are attached at an appropriate position in the cyclicons. In the absence of the target nucleic acid, the fluorophore and the quencher are brought in close proximity to each other because of the formation of an intramolecular cyclic structure, resulting in fluorescence quenching. When the cyclicon hybridizes to the complementary target nucleic acid strand, the intramolecular cyclic structure of the cyclicon is destabilized and opened up, separating the fluorophore and quencher groups, resulting in spontaneous fluorescence emission. Fluorescent studies in the presence and absence of a target nucleic acid suggest that cyclicons exist in intramolecular cyclic structure form in the absence of the target and form the duplex with the target sequence when present. Both the cyclicons are useful for nucleic acid detection. The studies with DNA polymerase on 5'-5'-attached cyclicons suggest that the presence of quencher moiety in the probe sequence does not inhibit chain elongation by polymerase. The experiments with a 5'-5'-attached cyclicon suggest the new design serves as an efficient unimolecular primer-probe in real-time PCR experiments.
authors.affiliation: Hybridon, Inc., Milford, MA 01757, USA.
authors.forename: E R
authors.initials: ER
authors.lastname: Kandimalla
authors.forename: S
authors.initials: S
authors.lastname: Agrawal
mesh_terms: D001345:Autoradiography; D002352:Carrier Proteins; D004247:DNA / Q000378:metabolism; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012313:RNA / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019914:Taq Polymerase / Q000378:metabolism; D014407:Tumor Cells, Cultured; D004124:p-Dimethylaminoazobenzene / Q000031:analogs & derivatives* / Q000378:metabolism
chemical_list: D002352:Carrier Proteins; D005456:Fluorescent Dyes; C415788:Mtbp protein, mouse; D015345:Oligonucleotide Probes; C063127:4-(4-dimethylaminophenylazo)benzoic acid; D012313:RNA; D004247:DNA; D004124:p-Dimethylaminoazobenzene; D019914:Taq Polymerase