Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation.
The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of these applications require interaction with and adhesion of DNA nanostructures to a substrate. Due to its atomically flat and easily cleaned nature, mica has been the substrate of choice for DNA origami experiments. However, the practical applications of mica are relatively limited compared to those of semiconductor substrates. For this reason, a straightforward, stable, and repeatable process for DNA origami adhesion on derivatized silicon oxide is presented here. To promote the adhesion of DNA nanostructures to silicon oxide surface, a self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) is deposited from an aqueous solution that is compatible with many photoresists. The substrate must be cleaned of all organic and metal contaminants using Radio Corporation of America (RCA) cleaning processes and the native oxide layer must be etched to ensure a flat, functionalizable surface. Cleanrooms are equipped with facilities for silicon cleaning, however many components of DNA origami buffers and solutions are often not allowed in them due to contamination concerns. This manuscript describes the set-up and protocol for in-lab, small-scale silicon cleaning for researchers who do not have access to a cleanroom or would like to incorporate processes that could cause contamination of a cleanroom CMOS clean bench. Additionally, variables for regulating coverage are discussed and how to recognize and avoid common sample preparation problems is described.
Department of Chemistry and Biochemistry, University of Notre Dame; mpillers@nd.edu.
Michelle A
MA
Pillers
Department of Chemistry and Biochemistry, University of Notre Dame.
Rebecca
R
Shute
Department of Chemical and Biomolecular Engineering, University of Notre Dame.
Adam
A
Farchone
Department of Chemistry, Physics, and Engineering Studies, Chicago State University.
Keenan P
KP
Linder
Department of Chemical and Biomolecular Engineering, University of Notre Dame.
Rose
R
Doerfler
Department of Technology, Ivy Tech Community College, South Bend, Indiana.
Corey
C
Gavin
Department of Chemistry, Physics, and Engineering Studies, Chicago State University.
Valerie
V
Goss
Department of Chemistry and Biochemistry, University of Notre Dame.
Marya
M
Lieberman
D000538:Aluminum Silicates / Q000737:chemistry*; D064753:Ammonium Hydroxide / Q000737:chemistry; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D006861:Hydrogen Peroxide / Q000737:chemistry; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D009690:Nucleic Acid Conformation; D012825:Silicon / Q000737:chemistry*; D012822:Silicon Dioxide / Q000737:chemistry
D000538:Aluminum Silicates; D064753:Ammonium Hydroxide; D012822:Silicon Dioxide; D004247:DNA; D006861:Hydrogen Peroxide; C011934:mica; D012825:Silicon