Single-molecule accommodation of streptavidin in nanometer-scale wells formed in DNA nanostructures.

Tape-like DNA nanostructures of 26 nm width with regularly arranged nanometer-scale wells have been prepared by bundling nine DNA helices. Just one streptavidin tetramer (d = 5 nm) is size-selectively captured in each 6.8 x 10 x 2.0 nm well when two biotins are attached to two opposite edges of the well. Accordingly, precise streptavidin nanoarray of 28 nm periods is constructed. The tetramers captured in the wells showed remarkable stability under repetitive AFM scanning. On the other hand, double-sized wells accommodated two tetramers inside, presumably because the distance between the two biotins is too large to cooperatively "anchor" a tetramer.