DNA-Origami-Driven Lithography for Patterning on Gold Surfaces with Sub-10 nm Resolution

The unique properties of DNA programmability and self-assembly enable its wide utilization in many scientific fields. For example, these properties have been used as a means to provide precise organization of matter at the nanoscale level. For the past decade, researchers have used a method named “DNA origami” by which a long, circular single stranded DNA scaffold (the genome of the M13 virus) is folded to a specific shape using hundreds of short oligonucleotides (staple strands) that have been rationally designed. DNA origami methodology has allowed the folding of DNA into two and three-dimensional structures, and the organization of biomolecules, nanophotonics and electronic components with a resolution of 6 nm/ pixel. However, in most applications, DNA nanostructures are only utilized to hold the chemical species in place while the DNA nanostructure remains assembled. Presented here is an innovative method to chemically immobilize nucleic acid patterns on a surface with sub-10 nm resolution.

Researchers led by Professor Ramon Eritja from the Institute for Advanced Chemistry of Catalonia in Spain proposed a study on the use of a two-dimensional DNA-origami as a template to transfer, and covalently attach DNA with a pre-programmed pattern on a surface. “We aimed at introducing a method that exploits the inherent programmability of DNA origami combined with our expertise in bulk-like surface chemistry techniques to immobilize predefined DNA nanopatterns on surfaces with high spatial resolution and addressability” said Dr. Isaac Gállego, a lead author in the study. Their technique incorporated the utilization of modified staple strands in programmed positions of the DNA -origami stamp, acting as DNA ink. Their work is now published in Advanced Materials.

In order to preprogram the pattern, twelve staple strands were replaced by the 5′-thiol-modifed oligonucleotides (DNA ink) in specific positions within the DNA origami stamp. “We used the term “DNA ink” for the modified staples and stamp for the DNA origami frame due to the similarities with and ink printing process.” said Dr. Brendan Manning. The research team used a disulfide group to protect the thiol groups of the DNA ink staples from reacting with neighboring staples. The 12 DNA ink staples were mixed and thermally annealed according to Rothemund’s technique. Fully assembled origami structures were then ready to be utilized as a DNA stamp to transfer the information stored in its structure onto a surface.

The stamping method developed allowed the research team to address matter on surfaces within the nanoscale range without the need to have the DNA structural template present. The fact that each staple within the origami structure has a unique sequence enables hundreds of strands to be modified as DNA ink, and subsequently be specifically hybridized with any DNA linked molecule or nanomaterial of interest therefore yielding an intrinsic addressable nanostructure. The research team also observed that in addition to the thiol groups, it was possible to immobilize the oligonucleotides with other chemistries and on other surfaces.

“This approach can be utilized in the formation of addressable DNA patterns with sub-10 nanometer resolution to atomically flat gold surfaces, something that no one has achieved before” said Isaac Gállego. This technique can be easily extended to other surfaces that use varying covalent strategies. Moreover, it can be combined with photolithography and DNA origami lattice formation methods and scaled up to generate micrometer scale patterns. The DNA -origami stamp method presented here brings the opportunity for a more versatile and robust functionalization and patterning of surfaces for the creation of metamaterials with applications in nanoelectronics and photonics. Furthermore, it can be seen that the immobilization process can be visualized by SPR opening novel avenues for the development of highly organized sensing surfaces.