Abstract Diagnosing gastric cancer with a high accuracy helps in identifying at early stage and for a better treatment. A transcription factor, SRY-box containing gene-17 (SOX-17) shows a crucial role in the gastric cancer progression is desired as biomarker on a high-performance sensing platform, dimicroelectrodes Junction (DMEJ), constructed by the hybrid of single-walled carbon nanotube (SWCN) and gold urchin (GU) surface to detect the specific SOX-17 target oligonucleotide. SWCN was modified on DMEJ and GU conjugated capture DNA was immobilized on SWCN through the electrostatic interaction of GU by (3-Aminopropyl)triethoxysilane. Morphological analyses by FESEM and FETEM revealed the attachment of GU on SWCN with a uniform fashion. SWCN-GU modified DMEJ has enhanced an ideal electric flow and reflecting the capture DNA attachment. Reached the limit of detection at 1 aM, calculated on a linear curve (atto- to femto-molar) with the regression coefficient of R2 = 0.9909[y = 1.1226x + 1.3727]. Further, specificity of SOX-17 was confirmed by interacting complementary, single- and five-mismatched sequences of the target. In addition, the target DNA solution mixed human serum and control sequences did not interfere with the specific duplex formation, indicating the non-biofouling on DMEJ surface. This SWCN-GU constructed DMEJ surface helps to identify lower expression of SOX-17 and diagnosing gastric cancer progression.