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

Abstract

The programmability [1] and self-assembly properties of DNA provides means of precise organization of matter at the nanoscale. [2] DNA origami allows the folding of DNA into twodimensional [3] and three-dimensional [4] structures, and has been used to organize biomolecules, [2b, e, 5] nanophotonic [2a, c, f, 6] and electronic [7] components with a resolution of 6 nm / pixel. [8] Two-dimensional DNA origami has been also used as a platform to organize other chemical [9] species that can then be placed on technologically relevant substrates. [2c, 10] Nevertheless, these approaches have only used the DNA nanostructure to hold the chemical species on the surface and, to the best of our knowledge, have never been utilized to immobilize nucleic acids patterns on surfaces with sub-10 nm resolution providing an enable 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 Submitted to 2 platform for potential applications such as multiplexed biochemical assays. [11] to the creation of metasurfaces [12] with potentially reconfigurable features. Revised ManuscriptHerein we report on the use of a two-dimensional DNA origami as a template to covalently attach DNA with a pre-programmed pattern on a surface (see Scheme 1). The method utilizes the incorporation of modified staple strands in programmed positions of the DNA origami (DNA origami stamp), acting as DNA ink. Once the DNA origami is immobilized on the surface, the modified staples can react with the surface creating a defined DNA pattern (Stamping step). The pattern can then be exposed upon denaturation of the DNA origami stamp (Unmasking step), allowing the non-bound staples to be rinsed off of the surface. As a proof-of-principle of this methodology, we have created a linear pattern of thiolmodified DNA ink on gold surfaces. The formation of the linear pattern was revealed by the successful formation of bead-on-a-string-like structures (here named "chains" for simplicity) composed of gold nanoparticles conjugated with thiol-oligonucleotides (OGNP) that are hybridized to the DNA ink pattern (Development step). The linear pattern provided a direct evidence of the stamping process and was chosen as a simple geometry that can be statistically analysed in our experimental setup. Montecarlo Simulations have been used for better understanding of our statistical results and to determine key elements governing the process that can be used for future optimization of pattern information transfer with DNA origami stamp methodology. Furthermore, we have studied the development of more complex patterns using Montecarlo Simulations.We demonstrate that our approach can be employed to form DNA patterns with sub-10 nm resolution to flat gold surfaces, an unsolved goal to date. This methodology can thus be extended to other surfaces utilizing different covalent strategies. [10b, 13] M...

Nanoscale patterning of self-assembled monolayer (SAM)-functionalised substrates with single molecule contact printing

“…36 We would like to point out that this ability deterministically limit steric hindrance through printed deposition would be particularly beneficial for precise arrangements of larger objects of a non-biological nature. Previous reported results [22][23][24] and our own studies have shown a similar technique applied to large gold nanoparticles, supporting the broadness of this asset. As described in more detail in ESI section 2, † we used a similar strategy as with previous studies to directly deposit thiol-functionalised DNA strands onto bare gold substrates.…”

“…However, direct covalent attachment of proteins to the SAM could be implemented through a secondary conjugation between the protein and an orthogonal reactive group on a two-component SAM. 38 Most importantly, in contrast to a printing onto bare gold surfaces [22][23][24] this generalised approach of printing onto a predeposited SAM enables the overall principle to be universally applied to nearly any type of substrate material where a stable (see ESI note 2.3 †), functional monolayer can be covalently or even non-covalently deposited. This opens the door for fabricating functional, nanometer-precise, single-molecule arrays on two-dimensional materials such as graphene and dichalcogenides, silanised silicates, ceramics, other metals such as titanium, semi-conducting substrates like ITO or even cheap plastics.…”

“…As an alternative strategy, several studies have employed a transfer process for placing patterns of DNA strands on either streptavidin coated gold films, 21 gold nanoparticles 22,23 or bare gold substrates. 24 In these cases, specific functional groups such as biotin or thiol on the deposited DNA strands were chosen according to the substrate. Although these do preserve both the global morphology as well as internal resolution of individual molecules within DNA nanostructures, in each case they remain limited to specific substrates (e.g.…”

DNA-Origami-Aided Lithography for Sub-10 Nanometer Pattern Printing

“…Statistical analysis of the distribution of nanoparticle alignment showed a decay of the frequency upon increment of number of OGNP in a chain and that the apparent, statistically significant maximum number of particles in a chain was significantly below to the 12 DNA ink programmed on the printed pattern [5]. The statistical analysis and Monte Carlo simulations were used to create a computational model.…”

“…However, to the best of our knowledge, DNA origami methodology has not been utilized to transfer and covalently bind the patterns on surfaces with sub-10 nm resolution. Herein we report on the use of a two-dimensional DNA origami as a template that bears pre-programmed patterns that can be lithographically transferred to a surface [5] (Figure 1). …”