The transport of nucleic acids through membrane pores is a fundamental biological process that occurs in all-living organisms. The aim of our research is to control the transport of nucleic acids through a biological nanopore. Along these lines, we are engineering Cytolysin A (ClyA) nanopores to translocate double-stranded DNA at favorable conditions of ionic strength and transmembrane potential. We also describe an artificial DNA transporter based on a ClyA nanopore that is able to recognize and chaperone a specific DNA molecule across a biological membrane under a fixed transmembrane potential. We incorporated a DNA unit on the top of the biological nanopore to form a membrane-bound molecular machine that transports selected DNA molecules through the nanopore. The transported DNA strand is then released by a simple mechanism based on DNA strand displacement on the other side of the lipid membrane. Notably, this molecular machine does not allow the translocation of either not specific ssDNA or non-tethered dsDNA. It works without external intervention and is modulated by two single-stranded DNA molecules: one attached to the nanopore that promotes the capture of a specific DNA cargo and a second molecule, at the other side of the membrane, that behaves as ‘fuel’ and promotes the release of each transported DNA cargo. Similarly to biological transporters, our device is capable of carrying and shuttle a specific substrate and it might be used to transport genetic information across biological membranes for future biomedical applications.