title: Base recognition of gap sites in DNA-DNA and DNA-RNA duplexes by short oligonucleotides.
abstract: To increase base recognition capability and sensitivity, we propose the separation of a commonly used single-probe system for oligonucleotide analysis into a set of three probes: a fluorophore-labeled probe, a promoter probe, and a short probe. In this study, we found that the probes of only 4nt in length can selectively bind the corresponding gap site on complexes consisting of the target, fluorophore-labeled probe, and promoter probe, exhibiting a more than 14-fold difference in ligation between the matched and mismatched sequences. Moreover, we demonstrated that the immobilized short probes accurately recognized the sequences of the gap sites.
authors.affiliation: Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Yamada
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ohkubo
authors.forename: Yousuke
authors.initials: Y
authors.lastname: Esaka
authors.forename: Takashi
authors.initials: T
authors.lastname: Kanamori
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Masaki
authors.forename: Kohji
authors.initials: K
authors.lastname: Seio
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000737:chemistry; D015345:Oligonucleotide Probes / Q000737:chemistry / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*
chemical_list: D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D012313:RNA; D004247:DNA