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  • Title: Base recognition of gap sites in DNA-DNA and DNA-RNA duplexes by short oligonucleotides.
    Author: Yamada K, Ohkubo A, Esaka Y, Kanamori T, Masaki Y, Seio K, Sekine M.
    Journal: Bioorg Med Chem Lett; 2013 Jun 01; 23(11):3448-51. PubMed ID: 23591114.
    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.
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