Label-free SERS-based detection of DNA is considered as one of the most prospective analytical methods for portable and express bioanalysis. In this work, the SERS platform based on the functional surface plasmon polariton supported ordered structure is proposed as an extremely convenient and effective tool for the detection of specific DNA sequences. The designed SERS structure makes possible DNA analyses in near-real time using the portable Raman spectrometer, with high reproducibility and accuracy of the results and the detection limits of the order of 10(-14) M. In order to overcome challenges, connected to meticulous affiliation and evaluation of Raman signals, principal component analysis (PCA) of raw SERS data was used for data evaluation. SERS results reproducibility was achieved through the creation of a periodical structure with homogenous distribution of plasmon energy, when the analysis functionality was implemented through the grafting of the oligonucleotide to gold surface and its further interaction with complementary, mispaired and noncomplementary oligonucleotides. It was demonstrated experimentally that with the SERS platform it is possible not only to detect and recognize pure DNA but also the simultaneous presence of complementary and mispaired DNA with estimation of their relative concentrations. Moreover, the developed SERS sensor demonstrated the perfect stability over 3 months storage period without loss of functionality.