Functionalization and self-assembly of DNA bidimensional arrays

Abstract

Oligonucleotides carrying amino, thiol groups, as well as fluorescein, c-myc peptide sequence and nanogold at internal positions were prepared and used for the assembly of bidimensional DNA arrays.

Keywords: DNA bidimensional arrays; DNA tile; gold nanoparticles; self-assembly.

Figure 1

The A-B* DNA tile system [6]. (a) Each tile is formed by 5 oligonucleotides that are represented in different colors. (b) Topological AFM image of the A-B* DNA lattice assembled on mica. Brighter (taller) diagonal ridges correspond to rows of the topological marker (hairpins present on tile B*) and fainter bands to DNA tile A. (c) Detailed AFM image of a small area of the DNA array. (d) 3-D image of the AFM image shown in Figure 1(c) showing the lines of protruding hairpins used as topological markers. The apexes of these protruding hairpins have been selected to introduce selected chemical groups.

Figure 1

The A-B* DNA tile system [6]. (a) Each tile is formed by 5 oligonucleotides that are represented in different colors. (b) Topological AFM image of the A-B* DNA lattice assembled on mica. Brighter (taller) diagonal ridges correspond to rows of the topological marker (hairpins present on tile B*) and fainter bands to DNA tile A. (c) Detailed AFM image of a small area of the DNA array. (d) 3-D image of the AFM image shown in Figure 1(c) showing the lines of protruding hairpins used as topological markers. The apexes of these protruding hairpins have been selected to introduce selected chemical groups.

Figure 2

(a) Topological AFM image of the A-B* DNA lattice carrying amino groups assembled on mica. Brighter (taller) diagonal ridges correspond to rows of the topological marker (hairpins present on tile B*) and fainter bands to DNA tile A. (b) Topological AFM image of the A-B* DNA lattice carrying fluorescein groups assembled on mica.

Figure 3

(a) Topological AFM image of the A-B* DNA lattice carrying nanogold assembled on mica. Brighter (taller) diagonal ridges correspond to rows of the topological marker (hairpins present on tile B*) and fainter bands to DNA tile A. (b) 3-D image of the AFM image shown in 5 (a) showing the position of the topological markers.

Scheme 1

Steps used in the formation of the amino-modified A-B* DNA array. A phosphoramidite of the thymidine carrying an amino group is used to introduce the amino group at one specific site at the apex of one of the topological loops of tile B* described by Winfree et al. [6]. Annealing of the appropriate oligonucleotides yielded the desired DNA lattice that was then deposited on mica substrates.

Scheme 2

Synthesis of oligonucleotides carrying fluorescein, c-myc peptide and nanogold at the apex of one of the topological loops of tile B* described by Winfree et al. [6].