MagiProbe: a novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator (II)

MagiProbe is a fluorescence quenching-based oligonucleotide probe and applicable to homogeneous nucleic acid assays. Further advantage of this probe is its inherent ability to discriminate between matched and mismatched duplex without reliance on the difference of thermal stability. To improve discriminating ability, the relationships between a position of mismatch in MagiProbe and a power of discrimination were studied. This resulted that intercalation of pyrene was destabilized by a mismatch but still stabilized by neighboring matched base pairs. To afford multiplexing capacity of nucleic acid detection assays to MagiProbe, a variety of differently colored fluorophores were tested in this system. Although each fluorophore showed a different response to hybridization, a couple of promising fluorophores were founded.