The invention provides a method for reducing background in hybridization
reactions of nucleic acids involving at least two homologous probes,
wherein at least one of the probes is non-linear, or two homologous target
sequences and a non-linear probe. Background is reduced by introducing an
intended mismatch with a target sequence in at least one of the probes.
The presence of the mismatch reduces the specificity of probes not
entirely complementary to a target sequence to such an extent that the
background signal is reduced. A set of mixed homologous probes, wherein at
least one of the probes is non-linear, comprising such specific mismatch
is also provided. The set can be used for the detection of variants of a
family of nucleic acids, for instance a number of HIV variants. The
invention also provides kits for carrying out the methods according to the
invention.
