G-quadruplex (G4) is a unique nucleic acid structure that forms within guanine (G)-rich sequences. This unique structure is formed when a four-stranded structure is produced within a single-stranded G-rich sequence; four G molecules form a square planar arrangement, the G-quartet, and the G-quartets are stacked on top of each other to form the G4 structure in DNA (G4DNA) and RNA (G4RNA). G4s have been implicated in many biological roles, such as DNA replication, transcription initiation, epigenetic modifications, and RNA metabolism. Importantly, G4s are known to be involved in neurological diseases. However, the neuro-physiological functions of G4 remains unclear. Here we show the biological function of a novel G4 binding protein DNAPTP6 in LC-MS/MS analysis on immunoprecipitates of mouse brain tissues using G4 recognition antibody. DNAPTP6 has two Intrinsically Disordered Regions (IDRs) and a coiled coil domain (CCD), and it expresses as a component of stress granules in cells. Purified DNAPTP6 protein binds to G4RNA via CCD in vitro, and the CCD-deficient DNAPTP6 mutant protein don’t form cytoplasmic granules in cells. In FRET analysis, DNAPTP6 protein unfolds G4RNA structure in Mark2 RNA. In addition, overexpression of DNAPTP6 significantly reduces protein translation of Mark2 mRNA in cells. MARK2 protein is highly expressed in axons and dendrites in neurons, and its expression affects the extension of neurites. Taken together, DNAPTP6 binds to G4RNA, thereby unfolding the structure, which may affect the dendritic morphology.