DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

This protocol combines the bottom-up based DNA origami technique with top-down nanofabrication methods allowing the parallel fabrication of inorganic nanostructures with sub-10 nanometer feature sizes on different substrates. This technique can be used to create billions of accurate nanostructures at one time, virtually in any shape without the need for expensive patterning methods. This method has the potential to be harnessed in sensing applications such as surface enhanced Raman spectroscopy, as well as to create novel optical metasurfaces.

Although this protocol is rather straightforward, more the disciplinary fabrication skills are needed and therefore, visual demonstration will be useful for researchers with a variety of backgrounds. Demonstrating the procedure with Petteri Piskunen will be Sofia Julin, another grad student from our lab. To make the stock of staple strands, mix equal amounts of all of the oligonucleotides needed for the bow tie structure and mix 20 microliters of the M13 MP18 scaffold strand with 40 microliters of the staple stock solution and 40 microliters of 2.5 X folding buffer in a 200 microliter PCR tube.

Then anneal the reaction mixture in a thermocycler from 90 to 27 degrees Celsius as outlined in the table. To prepare the substrate, immerse approximately seven by seven millimeters chips cut from a sapphire wafer in a glass container of 52 degrees Celsius acetone for at least 15 minutes before transferring the chips into a glass container of isopropanol for two minutes of sonication. At the end of sonication, use tweezers to remove the chips from the isopropanol and immediately dry the chips with nitrogen at the highest flow possible with the chip surfaces parallel to the direction of the flow.

For plasma-enhanced chemical vapor deposition of the amorphous silicon layer, place the dried chips into the plasma-enhanced chemical vapor deposition instrument and set the deposition parameters according to the instrument model and calibration to grow approximately 50 nanometers of amorphous silicon. For oxygen plasma treatment of the amorphous silicon layer, place the chips into the reactive ion etching instrument and set the etching parameters to generate oxygen plasma according to the instrument model and calibration. Then run the oxygen plasma treatment program.

Within 30 minutes of the oxygen plasma treatment, mix five microliters of folded and purified DNA origami solution with four microliters of folding buffer and one microliter of one molar magnesium chloride. Deposit 10 microliters of the DNA origami mixture onto each oxygen plasma-treated chip and cover the chips for a five minute incubation at room temperature. At the end of the incubation, wash the chip surfaces with 100 microliters of distilled water, rinsing the water back and forth a few times with the pipette while avoiding touching the centers of the chips.

After ashing two to three more times as just demonstrated, immediately dry the chips with nitrogen flow. To grow a silicon dioxide mask, mix 100 grams of silica gel with 30 milliliters of distilled water. Place the silica gel mixture into a desiccator and separate the gel with a perforated plate.

After 24 hour, place the chips with adsorbed DNA origami onto the perforated platform in the desiccator and place a vial containing 10 milliliters of tetraethyl orthosilicate on one side of the chips and a vial containing 10 milliliters of 25%ammonium hydroxide on the other side of the chips. Then seal the chamber for a 20 hour incubation at room temperature. At the end of the incubation, a silicon dioxide film will have formed on the areas without the DNA origami structures, creating a 10 to 20 nanometer patterned mask with DNA origami shaped holes.

For reactive ion etching of the silicon dioxide, place the chips into the reactive ion etching instrument and set the etching parameters to etch only two to five manometers of the silicon dioxide to reveal the amorphous silicon layer beneath the holes in the silicon dioxide mask. All of the etching parameters should be optimized for the chosen instruments, as the correct parameters depend on the type of equipment and specific set up. Some iterations might be needed.

After running the anisotropic silicon dioxide plasma etching program, set the etching parameters to pierce through the 50 nanometer amorphous silicon layer. Then run the isotropic silicon plasm etching program. For physical vapor deposition, load the chips into the evaporation chamber of the physical vapor deposition instrument and select an adhesive target metal.

Set the thickness control program for the target material and thickness and start the electron beam, aligning the beam to the target and increasing the beam current until a deposition rate of 0.05 nanometers per second is reached. Then evaporate until a final thickness of two nanometers is reached. At the end of the evaporation, select the second target metal without venting the chamber or interrupting the process and set the thickness.

Align the electron beam to the target until a 0.05 nanometers per second deposition rate is achieved before evaporating until a 20 nanometer thickness is reached. The DNA origami shaped metal structure will be created through the silicon dioxide mask holes with the total height of 22 nanometers. After venting the chamber, remove samples.

For hydrofluoric acid liftoff, immerse the samples in hydrofluoric acid-based etchant and use plastic tweezers to stir the samples gently. Wait for the silicon dioxide layer to etch completely and the metal layer to detach before rinsing the samples with double distilled water and isopropanol. Then dry the samples with a nitrogen flow as demonstrated.

For reactive ion etching of the remaining amorphous silicon, place the chips into the reactive ion etching instrument and set the etching parameters for through removal of all 50 nanometers of the amorphous silicon. Run the isotropic amorphous silicon plasma etching program to remove the remaining amorphous silicon. Then remove the samples from the reactive ion etching equipment and store them in a covered container.

Agarose gel electrophoresis and atomic force microscopy can be used to analyze the DNA origami folding and the quality of the polyethylene glycol purification. Here, representative atomic force microscopy images after silicon dioxide mask growth are shown. While in these images, scanning electron microscopy of the final metal nanostructures can be observed.

In these graphs, the optical functionality of the metallic nanostructures, templated by the bow tie DNA origami, was analyzed. Silicon dioxide mask growth is crucial to the process and is rather sensitive to the humidity and reactivity of TEOS. Therefore, these parameters should be carefully controlled for reproducibility.

If the DNA origami technique is further combined with highly ordered DNA patterns, it could pave the way for the fabrication of metamaterials and surfaces at the visible wavelength range.