Nucleic acid aequence identification (SERRS beacons)

The invention provides modified molecular beacons detectable by surface enhanced Raman spectroscopy (SERS) and related materials, processes, and methods of use. Examples methods provide for the determination of the presence or absence of a target nucleotide sequence in a sample nucleic acid by (a) providing a detection agent, which agent comprises: (i) a probe comprising a target complement sequence (TCS) being complementary to the target sequence and flanking the TCS, first and second oligonucleotide arms, said first and second oligonucleotide arms forming a stem duplex, and said first arm incorporating a first label moiety being detectable by SERS (e.g. a fluoroscein dye) and said second arm terminating in a second label moiety being detectable by SERS, which second arm further includes a surface seeking group (SSG - e.g. an azo-benzotriazole) capable of promoting association of the second label onto an enhancing surface ii) associated with said probe via said SSG, an enhancing surface, such that said first and second label moieties are in close proximity to each other and to the enhancing surface (b) exposing the sample to the detection agent, (c) detecting hybridisation of the TCS to any target sequence present in the sample by a change in the SERS spectra of said agent