Patent ID: 7262007

Claim:
A dye-labeled oligonucleotide for labeling a nucleic acid molecule having a target sequence section, the oligonucleotide comprising: a) a loop section having a loop sequence substantially complementary to the target sequence; b) a first stem section having at least three nucleosides and arranged at one end of the loop section; c) a second stem section having at least three nucleosides and arranged at another end of the loop section, with the first and second stem sections substantially complementary for hybridizing with one another; and d) a fluorophore, which is bound to a position of the first stem section; wherein the second stem section has at least one quencher nucleoside selected from the group consisting of guanosine, 7-deazaguanosine and 7-deazaadenosine; wherein the quencher nucleoside is not more than four bases away from a coupling site of the fluorphore with the fluorophore linked to the first stem section by a suitable spacer; and wherein the sequence of the first and second stem section and the sequence of the loop section, as well as the position and type of fluorophore are suitably selected relative to one other, such that in a hybridized state of the two stem sections, the fluorophore and the quencher nucleoside can interact for fluorescence quenching, and that no fluorescence quenching of the fluorophore can take place during hybridization of the loop section with the target sequence section and break-up of the hybridized stem sections.