The binding of ligands to receptors within a nanoscale
small space
is relevant in biology, biosensing, and affinity filtration. Binding
in confinement can be studied with biological systems but under the
limitation that essential parameters cannot be easily controlled including
receptor type and position within the confinement and its dimensions.
Here we study molecular recognition with a synthetic confined nanopore
with controllable pore dimension and molecular DNA receptors at different
depth positions within the channel. Binding of a complementary DNA
strand is studied at the single-molecule level with atomic force microscopy.
Following the analysis, kinetic association rates are lower for receptors
positioned deeper inside the pore lumen while dissociation is faster
and requires less force. The phenomena are explained by the steric
constraints on molecular interactions in confinement. Our study is
the first to explore recognition in DNA nanostructures with atomic
force microscopy and lays out new tools to further quantify the effect
of nanoconfinement on molecular interactions.