Methods, kits and compositions pertaining to linear beacons

A method for determining a PCR amplified nucleic acid, said method comprising:

• a) contacting a sample comprising nucleic acid to be PCR amplified with at least one polymer comprising at least one linked energy donor moiety and at least one linked energy acceptor moiety wherein said donor and acceptor moieties are separated by at least a portion of a probing nucleobase sequence and wherein said polymer does not form a stem and loop hairpin and is further characterized in that the efficiency of transfer of energy between said donor and acceptor moieties, when the polymer is solvated in aqueous solution, is substantially independent of at least two variables selected from the group consisting of:
• i) nucleobase sequence length separating the at least one energy donor moiety from the at least one energy acceptor moiety;
• ii) spectral overlap of the at least one linked energy donor moiety and the at least one linked energy acceptor moiety;
• iii) presence or absence of magnesium in the aqueous solution;
• and the
• iv) ionic strength of the aqueous solution;
• b) contacting the sample with primers and other reagents for PCR amplification;
• c) PCR amplifying the nucleic acid;
• d) determining hybridization of the polymer to a target sequence within the amplified nucleic acid wherein the target sequence present in the sample is correlated with a change in detectable signal associated with at least one donor or acceptor moiety of the polymer;
• and
• e) determining the presence, absence or amount of PCR amplified nucleic acid in the sample.