Synthetic molecular machines have been explored to manipulate matter at the molecular level. Here, we designed a multifunctional DNA nano-construct, dubbed a 'DNA minimachine' (DMM), which (i) tightly binds complementary DNA; (ii) recognizes specific fragments with high selectivity and (iii) amplifies output signals. DMM1 detects lower concentrations of both single-stranded DNA and double-stranded DNA compared to a conventional probe. This study sets a direction towards the development of molecular machines for selective, sensitive and cost-efficient DNA analysis.