Name: fabrication of micro-patterned chip with controlled thickness for high-throughput cryogenic electron microscopy
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M.-H.K., S.K., M.L., and J.P. acknowledge the financial support from the Institute for Basic Science (Grant No. IBS-R006-D1). S.K., M.L., and J.P. acknowledge the financial support from Creative-Pioneering Researchers Program through Seoul National University (2021) and the NRF grant funded by the Korean government (MSIT; Grant Nos. NRF-2020R1A2C2101871, and NRF-2021M3A9I4022936). M.L. and J.P. acknowledge the financial support from the POSCO Science Fellowship of POSCO TJ Park Foundation and the NRF grant funded by the Korean government (MSIT; Grant No. NRF-2017R1A5A1015365). J.P. acknowledges the financial support from the NRF grant funded by the Korean government (MSIT; Grant No. NRF-2020R1A6C101A183), and the Interdisciplinary Research Initiatives Programs by College of Engineering and College of Medicine, Seoul National University (2021). M.-H.K. acknowledges the financial support from the NRF grant funded by the Korean government (MSIT; Grant No. NRF-2020R1I1A1A0107416612). The authors thank the staff and crew of the Seoul National University Center for Macromolecular and Cell Imaging (SNU CMCI) for their untiring efforts and perseverance with the cryo-EM experiments. The authors thank S. J. Kim of the National Center for Inter-university Research Facilities for assistance with the FIB-SEM experiments.

1. Fabrication of micro-patterned chip with GO windows (Figure 1)
<ol>
	<li>Deposit the silicon nitride.
	<ol>
		<li>Deposit low-stress silicon nitride (SixNy) on both sides of the Si wafer (4 inch diameter and 100 &#181;m thickness) using low-pressure chemical vapor deposition (LPCVD) at 830 &#176;C and a pressure of 150 mTorr, under a flow of 170 sccm dichlorosilane (SiH2Cl2, DCS) and 38 sccm ammonia (NH3<...

<ol>
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The microfabrication processes for producing micro-patterned chips with GO windows are introduced here. The fabricated micro-patterned chip is designed to regulate the thickness of the vitreous ice layer by controlling the depth of the micro-hole with GO windows depending on the size of the material to be analyzed. A micro-patterned chip with GO windows was fabricated using a series of MEMS techniques and a 2D nanosheet transfer method (Figure 1). The major advantage of using the MEMS fabric...

Cryogenic electron microscopy (cryo-EM) has been developed to resolve the three-dimensional (3D) structure of proteins in their native state1,2,3,4. The technique involves fixing proteins in a thin layer (10-100 nm) of vitreous ice and acquiring projection images of randomly oriented proteins using a transmission electron microscope (TEM), with the sample maintained at liquid nitrogen temperature. Thousands to millions of projection images are acquired and used to reconstruct a 3D structure of the protein by computational algorithms5,6. For successful analysis with cryo-EM, cryo-sample preparation has been automated by plunge-freezing the equipment that controls the blotting conditions, humidity, and temperature. The sample solution is loaded onto a TEM grid with a holey carbon membrane, successively blotted to remove the excess solution, and then plunge-frozen with liquid ethane to produce thin, vitreous ice1,5,6. With the advances in cryo-EM and the automation of sample preparation7, cryo-EM has been increasingly used to solve the structure of proteins, including envelope proteins for viruses and ion channel proteins in the cell membrane8,9,10. The structure of envelope proteins of pathogenic viral particles is important for understanding viral infection pathology, as well as developing the diagnosis system and vaccines e.g., SARS-CoV-211, which caused the COVID-19 pandemic. Moreover, cryo-EM techniques have recently been applied to material sciences, such as for imaging beam-sensitive materials used in battery12,13,14 and catalytic systems14,15 and analyzing the structure of inorganic materials in solution-state16.
Despite noticeable developments in cryo-EM and relevant techniques, limitations exist in cryo-sample preparation, hindering high-throughput 3D structure analysis. Preparing a vitreous ice film with optimal thickness is especially important for obtaining the 3D structure of biological materials with atomic resolution. The ice must be thin enough to minimize background noise from electrons scattered by the ice and to prohibit overlaps of biomolecules along the electron beam path1,17. However, if the ice is too thin, it can cause protein molecules to align in preferred orientations or denature18,19,20. Therefore, the thickness of vitreous ice should be optimized depending on the size of the material of interest. Moreover, extensive effort is typically needed for the sample preparation and manual screening of ice and protein integrity on the prepared TEM grids. This process is extremely time-consuming, which hinders its efficiency for high-throughput 3D structure analysis. Therefore, improvements in the reliability and reproducibility of cryo-EM sample preparation would enhance the utilization of cryo-EM in structural biology and commercial drug discovery, as well as for material science.
Herein, we introduce microfabrication processes for making a micro-patterned chip with graphene oxide (GO) windows designed for high-throughput cryo-EM with controlled ice thickness21. The micro-patterned chip was fabricated using microelectromechanical system (MEMS) techniques, which can manipulate the structure and dimensions of the chip depending on the imaging purposes. The micro-patterned chip with GO windows has a microwell structure that can be filled with the sample solution, and the depth of the microwell can be regulated to control the thickness of the vitreous ice. The strong affinity of GO for biomolecules enhances the concentration of biomolecules for visualization, improving the efficiency of the structure analysis. Furthermore, the micro-patterned chip is composed of an Si frame, which provides high mechanical stability for the grid19, making it ideal for handling the chip during sample preparation procedures and cryo-EM imaging. Therefore, a micro-patterned chip with GO windows fabricated by MEMS techniques provides reliability and reproducibility of cryo-EM sample preparation, which can enable efficient and high-throughput structure analysis based on cryo-EM.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1-methyl-2-pyrrolidinone (NMP)</td>
			<td>Sigma Aldrich, USA</td>
			<td>443778</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetone</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>AFM</td>
			<td>Park Systems, South Korea</td>
			<td>NX-10</td>
			<td></td>
		</tr>
		<tr>
			<td>Aligner</td>
			<td>Midas System, South Korea</td>
			<td>MDA-600S</td>
			<td></td>
		</tr>
		<tr>
			<td>AZ 300 MIF developer</td>
			<td>AZ Electronic Materials USA Corp., USA</td>
			<td>184411</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryo-EM holder</td>
			<td>Gatan, USA</td>
			<td>626 single tilt cryo-EM holder</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryo-plunging machine</td>
			<td>Thermo Fisher SCIENTIFIC, USA</td>
			<td>Vitrobot Mark IV</td>
			<td></td>
		</tr>
		<tr>
			<td>Focused ion beam-scanning electron microscopy (FIB-SEM)</td>
			<td>FEI Company, USA</td>
			<td>Helios NanoLab 650</td>
			<td></td>
		</tr>
		<tr>
			<td>Glow discharger</td>
			<td>Ted Pella Inc., USA</td>
			<td>PELCO easiGlow</td>
			<td></td>
		</tr>
		<tr>
			<td>Graphene oxide (GO) solution</td>
			<td>Sigma Aldrich, USA</td>
			<td>763705</td>
			<td></td>
		</tr>
		<tr>
			<td>Hexamethyldisizazne (HMDS), 98+%</td>
			<td>Alfa Aesar, USA</td>
			<td>10226590</td>
			<td></td>
		</tr>
		<tr>
			<td>Low pressure chemical vapor deposition (LPCVD)</td>
			<td>Centrotherm, Germany</td>
			<td>LPCVD E1200</td>
			<td></td>
		</tr>
		<tr>
			<td>maP1205 positive PR</td>
			<td>Micro resist technology, Germany</td>
			<td>A15139</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium hydroxide (KOH), flake</td>
			<td>DAEJUNG CHEMICALS &#38; METALS Co. LTD., South Korea</td>
			<td>6597-4400</td>
			<td></td>
		</tr>
		<tr>
			<td>Raman Spectrometer</td>
			<td>NOST, South Korea</td>
			<td>Confocal Micro Raman System HEDA</td>
			<td></td>
		</tr>
		<tr>
			<td>Reactive ion etcher (RIE)</td>
			<td>Scientific Engineering, South Korea</td>
			<td>Lab-built</td>
			<td></td>
		</tr>
		<tr>
			<td>SEM</td>
			<td>Carl Zeiss, Germany</td>
			<td>SUPRA 55VP</td>
			<td></td>
		</tr>
		<tr>
			<td>Si wafer</td>
			<td>JP COMMERCE, South Korea</td>
			<td></td>
			<td>4&#34; Silicon wafer, P(B)type, (100), 1-30ohm.c m, DSP, T:100um</td>
		</tr>
		<tr>
			<td>Spin coater</td>
			<td>Dong Ah Trade Corp., South Korea</td>
			<td>ACE-200</td>
			<td></td>
		</tr>
		<tr>
			<td>TEM</td>
			<td>JEOL, Japan</td>
			<td>JEM-2100F</td>
			<td></td>
		</tr>
	</tbody>
</table>

fabrication of micro-patterned chip with controlled thickness for high-throughput cryogenic electron microscopy

A major limitation for the efficient and high-throughput structure analysis of biomolecules using cryogenic electron microscopy (cryo-EM) is the difficulty of preparing cryo-EM samples with controlled ice thickness at the nanoscale. The silicon (Si)-based chip, which has a regular array of micro-holes with graphene oxide (GO) window patterned on a thickness-controlled silicon nitride (SixNy) film, has been developed by applying microelectromechanical system (MEMS) techniques. UV photolithography, chemical vapor deposition, wet and dry etching of the thin film, and drop-casting of 2D nanosheet materials were used for mass-production of the micro-patterned chips with GO windows. The depth of the micro-holes is regulated to control the ice thickness on-demand, depending on the size of the specimen for cryo-EM analysis. The favorable affinity of GO toward biomolecules concentrates the biomolecules of interest within the micro-hole during cryo-EM sample preparation. The micro-patterned chip with GO windows enables high-throughput cryo-EM imaging of various biological molecules, as well as inorganic nanomaterials.

A micro-patterned chip with GO windows was fabricated by MEMS fabrication and 2D GO nanosheet transfer. Chips for micro-patterning were mass-produced, with about 500 chips produced from one 4 in wafer (Figure 1B and Figure 2A,B). The designs of the micro-patterned chips can be manipulated using different designs of the chromium mask (Figure 2) during the photolithography procedure. The fabricated micro-patterned chi...

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Fabrication of Micro-Patterned Chip with Controlled Thickness for High-Throughput Cryogenic Electron Microscopy

A newly developed micro-patterned chip with graphene oxide windows is fabricated by applying microelectromechanical system techniques, enabling efficient and high-throughput cryogenic electron microscopy imaging of various biomolecules and nanomaterials.

A major limitation for the efficient and high-throughput structure analysis of biomolecules using cryogenic electron microscopy (cryo-EM) is the ...

This protocol is important for regulating the thickness of the picture size at the nano scale to successfully observe proteins and nano materials of different sizes using cryo EM.The Mem's fabrication technique allows for the mass production of the microchip. It also enables the selection of depths and designs of the micro pattern wells. Depending on the experimental purposes.The technique can contribute to enhancing the efficiency of high throughput 3D structure analysis of biomolecules which is utilized for commercial drug discovery, and then thin wafers and microchips with risk tending silicon nitro membranes can be tricky. It is important not to bend the wafer or apply forces perpendicular to the silicon nitrate window. Begin to pattern the photo resist, or PR by covering a silicon nitride deposited silicon wafer with hexamethyldisilazane solution and then spin coating the wafer at 3000 RPM for 30 seconds on a spin coder.Bake the coated wafer at 95 degrees Celsius for 30 seconds on a hot plate to render the water surface hydrophobic and ensure a good coating performance with the PR.Next, spin coat the wafer with a positive PR and bake it 100 degrees Celsius for 90 seconds. A spin coated PR has a thickness of 500 nanometers. Expose the PR coated wafer to ultraviolet light for five seconds through a chromium mask using an aligner.Develop the PR for one minute using a developer and rinse twice by immersing the wafer in deionized water. Then dry the PR patterned wafer by blowing nitrogen gas onto the water surface. Following the patterning of the PR.Use a lab built reactive ion etcher at a radio frequency power of 50 watts, and with sulfur hexafluoride gas at three standard cubic centimeters per minute.To etch the exposed silicon nitride at the rate of six angstroms per second. Eliminate the PR by immersing the silicon nitride patterned wafer in acetone at room temperature for 30 minutes. Followed by rinsing the wafer twice in deionized water and drying the wafer with nitrogen gas.To etch the exposed si, immerse the silicon nitride patterned wafer in freshly prepared potassium hydroxide solution. With continuous stirring until the free standing silicon nitride windows can be observed at the opposite side of the patterned wafer. Clean the etched wafer by dipping it several times in a deionized water bath.Then dry the wafer in the air. To eliminate the etching residues, lightly press the boundaries of the chip array with a tweezer and obtain an array of chips to be micro patterned. Then immerse the chip array in freshly prepared potassium hydroxide solution for 30 seconds, followed by rinsing twice, blowing the chips with nitrogen gas and drying them in the air for one hour.For solid support prepare a blank 525 micrometer silicon wafer with the spin coating as demonstrated earlier. Attached to the chipper ray on the silicon wafer before baking the wafer and follow the procedure as described earlier to obtain the micropattern silicon wafer. Eliminate the PR by immersing the pattern chip set in one methyl two pure littanol solution at 60 degrees Celsius overnight.The next day, rinse the chip set twice with deionized water. After drying the pattern chip set with nitrogen, eliminate the PR residues with an oxygen plasma process using 100 standard cubic centimeters per minute of oxygen gas at a radio frequency power of 150 watts for one minute with the reactive ion etcher. Later, immerse the micro patterned chips in potassium hydroxide solution for 30 seconds to fully eliminate the PR residues.Then rinse and completely dry the chip set. Dilute two milligrams per milliliter graphene oxide or solution 10 folds with deionized water and sonicate the diluted solution for 10 minutes to break up aggregates of the sheets. Then centrifuge to the diluted solution at 300 times G for 30 seconds at room temperature.Use a glow discharger at 15 million amperes to glow discharge the silicon etched side of the micro pattern chip for one minute and render the chip's surface with a positive charge. When done, drop three microliters of the solution onto the glow discharge side of the micropattern chip. After one minute, blot the excess solution on the chip with filter paper.Wash the transferred chip with deionized water droplets on a paraffin film and blot the excess with filter paper. Repeat the drop casting procedure twice on the transferred side and once on the opposite side. Dry the transferred chip at room temperature overnight.During the photolithography procedure the designs of the micro pattern chips were manipulated using different designs of the chromium mask. The numbers and the dimensions of the free standing silicon nitride membranes were controlled. It was observed that the fabricated micro patterned chips could have up to 25, 000 suspended holes.The ramen spectrum at the window displayed the representative peaks of the Additionally, the multiply oriented hexagonal defraction patterns indicated that the windows consisted of the multilayer The structure and depth of the micro hole with windows were studied with scanning electron microscopy and atomic force microscopy. A well type structure of the micro hole with the window was observed in the images confirming the possibility of the design of the micro pattern chip with windows. With the help of the micro patterned chip, a few biological specimens and inorganic nanoparticles were imaged with the cryo electron microscope.Optimizing the conditions such as pure coating thickness using intensity and developing time for micro patterning depending on the size and design of the patterns is important. By applying nano pattering techniques such as FIB or even litho graphene smaller some micrometer patterns can be produced which may expand applications of this micro device where it's used with other analytical techniques.

Research

JoVE Journal

Engineering

Fabrication of Gate-tunable Graphene Devices for Scanning Tunneling Microscopy Studies with Coulomb Impurities

Owing to its relativistic low-energy charge carriers, the interaction between graphene and various impurities leads to a wealth of new physics and degrees ...

Preparation of Liquid-exfoliated Transition Metal Dichalcogenide Nanosheets with Controlled Size and Thickness: A State of the Art Protocol

We summarize recent advances in the production of liquid-exfoliated transition metal dichalcogenide (TMD) nanosheets with controlled size and thickness. ...

Studying Dynamic Processes of Nano-sized Objects in Liquid using Scanning Transmission Electron Microscopy

Samples fully embedded in liquid can be studied at a nanoscale spatial resolution with Scanning Transmission Electron Microscopy (STEM) using a ...

A Method for Obtaining Serial Ultrathin Sections of Microorganisms in Transmission Electron Microscopy

Observing cells and cell components in three dimensions at high magnification in transmission electron microscopy requires preparing serial ultrathin ...

Enhanced Electron Injection and Exciton Confinement for Pure Blue Quantum-Dot Light-Emitting Diodes by Introducing Partially Oxidized Aluminum Cathode

Stable and efficient red (R), green (G), and blue (B) light sources based on solution-processed quantum dots (QDs) play important roles in next-generation ...

Single-Digit Nanometer Electron-Beam Lithography with an Aberration-Corrected Scanning Transmission Electron Microscope

We demonstrate extension of electron-beam lithography using conventional resists and pattern transfer processes to single-digit nanometer dimensions by ...

High Throughput Analysis of Liquid Droplet Impacts

Experimental studies of liquid drop impacts on surfaces are often restricted in their scope due to the large range of possible experimental parameters ...

Fabrication and Characterization of Thickness Mode Piezoelectric Devices for Atomization and Acoustofluidics

We present a technique to fabricate simple thickness mode piezoelectric devices using lithium niobate (LN). Such devices have been shown to atomize liquid ...

In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx

In Situ Transmission Electron Microscopy with Biasing and Fabrication of Asymmetric Crossbars Based on Mixed-Phased a-VOx

Resistive switching crossbar architecture is highly desired in the field of digital memories due to low cost and high-density benefits. Different ...

Cryogenic Liquid Jets for High Repetition Rate Discovery Science

This protocol presents a detailed procedure for the operation of continuous, micron-sized cryogenic cylindrical and planar liquid jets. When operated as ...