Topography-controlled alignment of DNA origami nanotubes on nanopatterned surfaces

Abstract

The controlled positioning of DNA nanostructures on technologically relevant surfaces represents a major goal along the route toward the full-scale integration of DNA-based materials into nanoelectronic and sensor devices. Previous attempts to arrange DNA nanostructures into defined arrays mostly relied on top-down lithographic patterning techniques combined with chemical surface functionalization. Here we combine two bottom-up techniques for nanostructure fabrication, i.e., self-organized nanopattern formation and DNA origami self-assembly, in order to demonstrate the electrostatic self-alignment of DNA nanotubes on topographically patterned silicon surfaces. Self-organized nanoscale ripple patterns with periodicities ranging from 20 nm to 50 nm are fabricated by low-energy ion irradiation and serve as substrates for DNA origami adsorption. Electrostatic interactions with the charged surface oxide during adsorption direct the DNA origami nanotubes to the ripple valleys and align them parallel to the ripples. By optimizing the pattern dimensions and the Debye length of the adsorption buffer, we obtain an alignment yield of ∼70%. Since this novel and versatile approach does not rely on any chemical functionalization of the surface or the DNA nanotubes, it can be applied to virtually any substrate material and any top-down or bottom-up nanopatterning technique. This technique thus may enable the wafer-scale fabrication of ordered arrays of functional DNA-based nanowires.

Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays

“…A powerful strategy to enhance nanoarrays is to co‐immobilize protein and DNA in order to exploit the unique properties of the two biopolymers. Of particular interest is the deposition of highly structured bottom‐up DNA origami nanomaterials that complement the atomically ill‐defined top‐down nanoislands . The rationally designed DNA nanostructures offer excellent control over molecular dimensions and can bind in defined stoichiometry or molecular orientation on the nanoislands .…”

“…top-down nanoislands. [11][12][13][14][15] The rationally designed DNA nanostructures offer excellent control over molecular dimensions [16][17][18][19][20][21] and can bind in defi ned stoichiometry or molecular orientation on the nanoislands. [11][12][13]22 ] DNA origami have also been used as nanoscale immobilization platforms for smaller molecular cargo including proteins, [23][24][25][26][27][28][29][30] but in this case the platforms were only randomly bound to the substrate surface.…”

Recent Developments in Bio-Nanoelectronics Devices: A Review

“…DNA was connected between oligonucleotides, the oligonucleotides connected to the gold electrodes having disulphide ends. [84][85][86][87][88] The formed DNA oligonucleotides were reacted with the solution of Ag 2+ ions. As the result, the ions get attached to the negatively charged phosphate of the DNA molecules.…”

Multiscale structured germanium nanoripples as templates for bioactive surfaces

“…1 As a single-step method to fabricate regular patterns over large surface areas, it can potentially overcome the limits of conventional lithographic methods, when nanometric features and high-throughput production capability are required; 2 hence, ion beam induced nanopattern formation has been investigated for different applications, such as electronic 3 -and bio-devices. 4 To date, a comprehensive theoretical description of all the mechanisms governing the ripple and dot formation is still under debate. According to the Bradley and Harper theory 5 and its non-linear generalization for the long time limit, 6 the self-organized pattern formation is the product of a competition between a curvature-dependent roughening instability by surface sputtering, and a surface smoothening process by thermal diffusion or other relaxation mechanisms.…”