Chemistry is ideally placed to replicate biomolecular structures with tuneable building materials.O fp articular interest are molecular nanopores,which transport cargo across membranes,a si nDNAs equencing.A dvanced nanopores control transport in response to triggers,b ut this cannot be easily replicated with biogenic proteins.H ere we use DNA nanotechnology to build asynthetic molecular gate that opens in response to aspecific protein. The gate self-assembles from six DNAs trands to form ab ilayer-spanning pore,a nd al id strand comprising ap rotein-binding DNAa ptamer to block the channel entrance.Addition of the trigger protein, thrombin, selectively opens the gate and enables a3 30-fold increase inw the transport rate of small-molecule cargo.The molecular gate incorporates in delivery vesicles to controllably release enclosed cytotoxic drugs and kill eukaryotic cells.The generically designed gate may be applied in biomedicine,biosensing or for building synthetic cells.

Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA–membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA–bilayer interactions will guide the rational design of membrane-targeting nanostructures.