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

Significance Statement

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.

About the author

Isaac Gállego received his B.S. in Biochemistry and his Ph.D. in Biotechnology (2010) at the Autonomous University of Barcelona in the laboratory of Prof. Daban. He then joined, for a short period of time the Eritja laboratory at the IRB in Barcelona followed by a postdoctoral position in the laboratory of Prof. Hud at Georgia Tech (2012-2016). Currently is a career development fellow in Phil Holliger’s laboratory at the MRC-LMB.

His interest revolves around the self-assembly and biophysics of nucleic acids, with particular interest in technological applications and the origins of life. In the last years, his work has been focused on the use of the DNA origami methodology for the development of nanosensors and surface patterning, and the self-replication of nucleic acids in prebiotic conditions.

About the author

Brendan Manning received his PhD in Chemistry from University College Dublin, Ireland in 2010. He was a post-doctoral researcher at IQAC-CSIC Barcelona before joining Biokit-Werfen. He is a Manager of Molecular Diagnostics at T2 Biosystems Inc.

About the author

Dr. Mònica Mir received her PhD in Chemistry in the area of Biosensors in 2006 (University Rovira i Virgili, Spain). That year she moved to Max Planck Institute for Polymer Research in Prof Knoll laboratory in Mainz (Germany), and in 2008 she started in the Nanobioengineering group at Institute for Bioengineering of Catalonia (IBEC) in Spain, where one year later she got a stable senior CIBER researcher position.

Her research interest is in the field of biosensor technologies based on DNA, enzymes, antibodies and aptamers bioreceptors, using electrochemistry and optical for sensing transduction. She has participated in several European projects and she is the co-author of more than 40 publications.

About the author

Prof. Josep Samitier Director of the Institute for Bioengineering of Catalonia (IBEC), Group leader of the Nanobioengineering group at IBEC and Full Professor of Electronics and Biomedical Engineering in the Physics Faculty (Electronic Department) University of Barcelona. He received the Barcelona City Prize of Technology in 2003.

About the author

Ramon Eritja is Research Professor of the Department of Chemical and Biomolecular Nanotechnology at the Institute for Advanced Chemistry of Catalonia (IQAC, CSIC). Currently he is group leader of the Nucleic Acid Chemistry Group at IQAC, CSIC. He graduated and did his Ph. D. at the University of Barcelona. He was postdoctoral researcher in Dr. Itakura’s (Beckman Research Institute at Hope, CA, USA) and Dr. Caruthers’s (University of Colorado at Boulder, USA) laboratories. He was Group Leader and responsible of DNA synthesis facility at EMBL, Heidelberg, Germany for 5 years (1994-1999). He was member of the Institute for Biomedical Research of Barcelona, (IRB Barcelona, 2007-2012) as well as member of the Networking Center on Bioengineering, Biomaterials and Nanomedicine of Spain (CIBER-BBN, 2007-present). He was Director of the IQAC during 2012-2016. Research interest in the following areas: Development of novel RNA derivatives; non-canonical DNA structures; DNA bidimensional arrays and DNA origami and oligonucleotide-peptide conjugates.

About the author

Dr. J. Daniel Prades is Tenured Associate Professor at the Department of Electronics and Biomedical Engineering in the Faculty of Physics of the University of Barcelona. He is interested in micro-nano technologies for low power devices, with special focus on sensors. He was awarded in 2013 by the European Research Council with a Starting Grant.

Reference

Isaac Gállego1, Brendan Manning1, Joan Daniel Prades2, Mònica Mir3, Josep Samitier3 and Ramon Eritja1. DNA -Origami-Driven Lithography for Patterning on Gold Surfaces with Sub-10 nm Resolution. Advanced Materials volume 29 (2017) pages 1-7.

Show Affiliations
  1. Institute for Advanced Chemistry of Catalonia (IQAC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spanish National Research Council (CSIC), Barcelona, 08034, Spain.
  2. MIND-IN2UB, Department of Engineering: Electronics, University of Barcelona, Barcelona, 08028, Spain
  3. Institute for Bioengineering of Catalonia (IBEC), Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, 08028, Spain

 

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