Autonomous bottom-up fabrication based on molecular recognition is a powerful approach for engineering structures and devices at the molecular scale. DNA is a versatile construction material that can be programmed to self-assemble into nanoscale structures based on specific complementarity between bases. Here, we aim at developing bio-inspired nanomaterials capable of detecting single nucleotide polymorphism (SNP). We developed a novel SNP biosensor made of DNA-programmed protein nanostructures of which disassembly of the whole structure is triggered by a target DNA oligonucleotide carrying a specific sequence. We designed DNA sequences incorporated in the sensor materials in a way that even a single base mutation in the target DNA (e.g. a single mutation in a 24-mer DNA oligonucleotide) effectively prevents the protein nanostructures from being disassembled. We could detect single nucleotie mutations by monitoring structural changes in the protein nanostructure. The SNP biosensor material is promising for fast identification of SNP in genes of interest.