Nucleic acid hairpin probes and uses thereof

A method for detecting a target nucleotide sequence in a sample, which method comprises the steps of:

• a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions, and wherein at least a portion of said nucleotide sequences located within said double stranded segment and a portion of said nucleotide sequence located within said single stranded loop collectively form a region that is complementary to a target nucleotide sequence to be detected;
• b) contacting the probe provided in step a) with a sample containing or suspected of containing the target nucleotide sequence under conditions that favor intermolecular hybridization between the probe and the target nucleotide sequence over intramolecular hybridization of the probe itself;
• and
• c) assessing the intermolecular hybrid formed in step b).

A method for transcribing and/or amplifying an oligonucleotide probe sequence, which method comprises the steps of:

• a) providing an oligonucleotide probe comprising a nucleotide sequence that forms a hairpin structure having a double stranded segment and a single stranded loop, wherein said loop contains at least 3 nucleotides, said double stranded segment is formed between two complementary nucleotide sequences under suitable conditions and contains a promoter sequence, and wherein at least a portion of said nucleotide sequence located within said single stranded loop is complementary to a DNA sequence and said portion of said nucleotide sequence comprises both ribonucleotide sequence and deoxyribonucleotide sequence;
• b) contacting said probe provided in step a) with said DNA sequence under suitable conditions to form a probe/DNA duplex;
• c) cleaving said ribonucleotide sequence within said portion of said nucleotide sequence complementary to said DNA sequence by RNase H treatment to open said single stranded loop;
• and
• d) synthesizing a RNA sequence using a RNA polymerase that is compatible with said promoter contained within said double stranded segment of said probe,
• whereby at least a portion of said single stranded loop is transcribed.