A novel surface-enhanced Raman scattering (SERS) sensing system which operates by the self-assembly of Ag nanoparticles (AgNPs) onto the nanocomposite of AgNPs and graphene oxide (AgNP-GO) in the presence of two complementary DNAs has been developed. In this system, AgNP-GO serves as a SERS-active substrate. The AgNPs with the modification of non-fluorescent 4-mercaptobenzoic acid (4-MBA) act as highly efficient Raman probes for DNA hybridization. When probe DNAs on AgNP-GO are complementary to target DNAs on AgNPs functionalized with 4-MBA, the DNA hybridization occurring directs the self-assembly of AgNPs onto AgNP-GO, leading to the creation of SERS hot spots. Due to the fact that partial 4-MBA molecules are located in the region of the hot spots, their SERS signals are greatly enhanced, indicating successful DNA hybridization. It is noteworthy that the size of AgNPs contributes significantly to the enhancement of SERS activity. The detection limit of the target DNAs at the pM level can be achieved through the self-assembly of large sized AgNPs onto AgNP-GO. More importantly, the AgNP-AgNP-GO system shows reproducible SERS signals in proportion to the logarithm of the target DNA concentrations spanning from 10(-6) to 10(-12) M and the excellent capability for multiplex DNA detection.