double stranded state i e hybridized state of the oligonucleotide probe e g bagwell et al nucleic acids research 22 12 2424 2425 1994 bagwell ep 0 601 889 a2 the fluorescence signals can differ by as much as a factor of 20 between the single stranded and double stranded states when the fluorescer and quencher are separated by 20 bases this effect is most probably due to the fact that in the single stranded state the oligonucleotide exists as a flexible random coil structure which allows the ends of the oligonucleotide to be in close proximity while in the double stranded state the oligonucleotide exists as a rigid extended structure which separates the fluorescer and quencher thus using this arrangement one sees relatively efficient quenching of the fluorescer when the oligonucleotide probe is in the single stranded or unhybridized state and relatively inefficient quenching of the fluorescer when the oligonucleotide probe is in the double stranded or hybridized state preferably fluorescer molecules are fluorescent organic dyes derivatized for attachment to the terminal 3 u2032 carbon or terminal 5 u2032 carbon of the probe via a linking moiety preferably quencher molecules are also organic dyes which may or may not be fluorescent depending on the embodiment of the invention for example in a preferred embodiment of the invention the quencher molecule is fluorescent generally whether the quencher molecule is fluorescent or simply releases the transferred energy from the.