The present invention provides primers and probes to be used in a method of enhancing hybridization of a probe to a target nucleotide sequence when the target sequence is capable of forming intramolecular secondary structures that interfere with hybridization of the probe to the target sequence. In particular, the invention includes a primer for amplifying a target nucleotide sequence, wherein at least a portion of the target nucleotide sequence can form an intramolecular secondary structure. The primer of the invention includes a primer nucleotide sequence complementary to a portion of the target nucleotide sequence that does not form a secondary structure, and a blocking sequence substantially complementary to at least a portion of the secondary structure-forming region of the amplified target nucleotide sequence, wherein the blocking sequence hybridizes to a portion of the secondary structure-forming region of the amplified target nucleotide sequence and blocks the formation of the secondary structure.