The invention comprises novel methods and strategies to detect and/or quantify
nucleic acid analytes. The methods involve nucleic acid probes with covalently
conjugated dyes, which are attached either at adjacent nucleotides or at the same
nucleotide of the probe and novel linker molecules to attach the dyes to the probes.
The nucleic acid probes generate a fluorescent signal upon hybridization to complementary
nucleic acids based on the interaction of one of the attached dyes, which is either
an intercalator or a DNA groove binder, with the formed double stranded DNA. The
methods can be applied to a variety of applications including homogeneous assays,
real-time PCR monitoring, transcription assays, expression analysis on nucleic
acid microarrays and other microarray applications such as genotyping (SNP analysis).
The methods further include pH-sensitive nucleic acid probes that provide switchable
fluorescence signals that are triggered by a change in the pH of the medium.
