A method for detecting a target
nucleic acid in a sample, the method comprising the following steps: (a)
coupling of an amplification product of the target
nucleic acid, wherein said amplification product is generated if said target
nucleic acid is in the sample, comprising modified nucleotides having a first reactive
moiety to a second reactive
moiety that is linked to a
cysteine protease activator molecule to produce amplification products of the target nucleic acid labelled with a
cysteine protease activator molecule; (b) optionally immobilizing the labelled amplification products on a surface; (c) contacting the optionally immobilized, labelled amplification products with a reversibly inactivated
cysteine protease, wherein the catalytic cysteine residue of the reversibly inactivated
cysteine protease is blocked by a
disulfide bond or a selenylsulfide bond, and reactivating the proteolytic activity of said
cysteine protease by said
cysteine protease activator molecule by
disulfide bond or selenylsulfide bond reduction; (d) contacting the reactivated cysteine protease with a cysteine
protease substrate, wherein said substrate provides a detectable
signal when hydrolysed by said reactivated cysteine protease; and (e) monitoring said detectable
signal, wherein the presence of the detectable
signal is indicative of the presence of said target
nucleotide sequence in said sample.