Modifying the surface features of two-dimensional DNA crystals

DNA double-crossover (DX) molecules are rigid DNA motifs that contain two double helices linked at two different points. It is possible to form hydrogen-bonded two-dimensional crystals from DX molecules and to observe those arrays by atomic force microscopy (AFM) [Winfree, E.; Liu, F.; Wenzler, L.A.; Seeman, N.C. Nature 1998, 394, 539-544]. The sticky ends that hold the arrays together can be varied, so as to include diverse periodic arrangements of molecules in the crystal. The inclusion of extra DNA hairpins designed to protrude from the plane of the crystal provides a topographic label that is detected readily in AFM images: By using these labels, it is possible to produce stripes at predicted spacings on the surface of the crystal. The experiments presented here demonstrate that it is possible to modify these patterns, by both enzymatic and nonenzymatic procedures. We show that a hairpin containing a restriction site can be removed quantitatively from the array. We also demonstrate that a sticky end protruding from the array can be ligated to a hairpin containing its complement. In addition, it is possible to anneal a hairpin to the crystalline array by hydrogen bonding, both in solution and after deposition on a mica surface. The ability to modify these arrays increases the diversity of patterns that can be produced from an initial set of DX components. Thus, a single array can be modified in a large number of ways that can alter its physical or chemical features.