We would like to acknowledge the entire Maurer group at Washington University whose collective knowledge has made this protocol possible. Funding for this work is provided by the National Institute of Mental Health (1R01MH085495).

1. Preparation of the Patterned Master (Figure 1)
<ol>
<li>Center the silicon wafer on the spin-coater and rinse the wafer with acetone during the initial step of the two-cycle spin program in Table 1. The acetone will evaporate during the second step of the spin program leaving a clean, dry wafer.</li>
<li>Apply approximately 1 mL AZ9245 photoresist/in (in diameter) to the wafer and spin-coat using the conditions described in Table 1.</li>
<li>Soft-bake the photoresist-coated wafer at 110&deg;C for 2 m using a high-u...

<ol>
	<li>Wilbur, J., Kumar, A., Biebuyck, H., Kim, E., Whitesides, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microcontact+printing+of+self-assembled+monolayers:+Applications+in+microfabrication.">Microcontact printing of self-assembled monolayers: Applications in microfabrication.</a> Nanotechnology. 7, 452-457 (1996).</li><li>Chang, J., Brewer, G., Wheeler, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+modified+microstamping+technique+enhances+polylysine+transfer+and+neuronal+cell+patterning.">A modified microstamping technique enhances polylysine transfer and neuronal cell patterning.</a> Biomaterials. 24, 2863-2870 (2003).</li><li>Lange, S., Benes, V., Kern, D., Horber, J., Bernard, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microcontact+printing+of+DNA+molecules.">Microcontact printing of DNA molecules.</a> Analytical Chemistry. , 1641-1647 (2004).</li><li>Xia, Y., Mrksich, M., Kim, E., Whitesides, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microcontact+printing+of+octadecylsiloxane+on+the+surface+of+silicon+dioxide+and+its+application+in+microfabrication.">Microcontact printing of octadecylsiloxane on the surface of silicon dioxide and its application in microfabrication.</a> J. Am. Chem. Soc. , 9576-9577 (1995).</li><li>Mrksich, M., Dike, L., Tien, J., Ingber, D., Whitesides, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Using+microcontact+printing+to+pattern+the+attachment+of+mammalian+cells+to+self-assembled+monolayers+of+alkanethiolates+on+transparent+films+of+gold+and+silver.">Using microcontact printing to pattern the attachment of mammalian cells to self-assembled monolayers of alkanethiolates on transparent films of gold and silver.</a> Experimental Cell Research. , 305-313 (1997).</li><li>Prime, K. L., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adsorption+of+proteins+onto+surfaces+containing+end-attached+oligo(ethylene+oxide)+-+a+model+system+using+self-assembled+monolayers.">Adsorption of proteins onto surfaces containing end-attached oligo(ethylene oxide) - a model system using self-assembled monolayers.</a> J. Am. Chem. Soc. 115, 10714-10721 (1993).</li><li>Raghavan, S., Desai, R., Kwon, Y., Mrksich, M., Chen, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micropatterned+Dynamically+Adhesive+Substrates+for+Cell+Migration.">Micropatterned Dynamically Adhesive Substrates for Cell Migration.</a> Langmuir. , 17733-17738 (2010).</li><li>Rogers, J., Bao, Z., Baldwin, K., Dodabalapur, A., Crone, B., Raju, V. R., Kuck, V., Katz, H., Amundson, K., Ewing, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paper-like+electronic+displays:+Large-area+rubber-stamped+plastic+sheets+of+electronics+and+microencapsulated+electrophoretic+inks.">Paper-like electronic displays: Large-area rubber-stamped plastic sheets of electronics and microencapsulated electrophoretic inks.</a> Proc Natl Acad Sci U S A. 98, 4835-4840 (2001).</li><li>Yanker, D., Maurer, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+printing+of+trichlorosilanes+on+glass+for+selective+protein+adsorption+and+cell+growth.">Direct printing of trichlorosilanes on glass for selective protein adsorption and cell growth.</a> Molecular Biosystems. 4, 502-504 (2008).</li><li>Johnson, D., Maurer, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recycling+and+reusing+patterned+self-assembled+monolayers+for+cell+culture.">Recycling and reusing patterned self-assembled monolayers for cell culture.</a> Chemical Communications. , 520-522 (2011).</li><li>Herne, T., Tarlov, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+DNA+probes+immobilized+on+gold+surfaces.">Characterization of DNA probes immobilized on gold surfaces.</a> J. Am. Chem. Soc. , 8916-8920 (1997).</li><li>Hanson, E., Schwartz, J., Nickel, B., Koch, N., Danisman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bonding+self-assembled,+compact+organophosphonate+monolayers+to+the+native+oxide+surface+of+silicon.">Bonding self-assembled, compact organophosphonate monolayers to the native oxide surface of silicon.</a> J. Am. Chem. Soc. , 16074-16080 (2003).</li><li>Johannes, M., Cole, D., Clark, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atomic+force+microscope+based+nanofabrication+of+master+pattern+molds+for+use+in+soft+lithography.">Atomic force microscope based nanofabrication of master pattern molds for use in soft lithography.</a> Applied Physics Letters. , (2007).</li><li>Bessueille, F., Pla-Roca, M., Mills, C. A., Martinez, E., Samitier, J., Errachid, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Submerged+microcontact+printing+(S&#x03BC;CP):+An+unconventional+printing+technique+of+thiols+using+high+aspect+ratio,+elastomeric+stamps.">Submerged microcontact printing (S&#x03BC;CP): An unconventional printing technique of thiols using high aspect ratio, elastomeric stamps.</a> Langmuir. , 12060-12063 (2005).</li><li>Xia, Y., Whitesides, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extending+microcontact+printing+as+a+microlithographic+technique.">Extending microcontact printing as a microlithographic technique.</a> Langmuir. , 2059-2067 (1997).</li><li>Biasco, A., Pisignano, D., Krebs, B., Pompa, P. P., Persano, L., Cingolani, R., Rinaldi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformation+of+microcontact-printed+proteins+by+atomic+force+miroscopy+molecular+sizing.">Conformation of microcontact-printed proteins by atomic force miroscopy molecular sizing.</a> Langmuir. , 5154-5158 (2005).</li><li>Shen, K., Qi, J., Kam, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microcontact+printing+of+proteins+for+cell+biology.">Microcontact printing of proteins for cell biology.</a> J Vis Exp. (22), e1065-e1065 (2008).</li><li>Piner, R., Zhu, J., Xu, F., Hong, S., Mirkin, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term="Dip-pen"+nanolithography.">"Dip-pen" nanolithography.</a> Science. 283, 661-663 (1999).</li><li>Ryan, D., Parviz, B. A., Linder, V., Semetey, V., Sia, S. K., Su, J., Mrksich, M., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patterning+multiple+aligned+self-assembled+monolayers+using+light.">Patterning multiple aligned self-assembled monolayers using light.</a> Langmuir. , 9080-9088 (2004).</li></ol>

A number of issues can arise in the lithographic production of the master used for PDMS stamp creation. Underexposure of the resist-coated wafer results in hazy and indistinct patterns and overexposure of the resist-coated wafer results in enlarged or missing features. In general, masters with large feature sizes (&gt;10 &mu;m) are relatively easy to pattern and develop, while masters with smaller features can require extensive optimization of photopatterning and development parameters (beyond the parameters recommended ...

<table border="1">
	<tbody>
		<tr>
			<th>Name of the reagent</th>
			<th>Company</th>
			<th>Catalogue number</th>
			<th>Comments (optional)</th>
		</tr>
		<tr>
			<td>Silicon wafer</td>
			<td>Wafer Reclaim Services</td>
			<td>&nbsp;</td>
			<td>2 inch</td>
		</tr>
		<tr>
			<td>Spin coater/hot plate		</td>
			<td>Brewer Science</td>
			<td>Cee 200CB Spin-Bake System</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>AZ9245 Photoresist		</td>
			<td>Mays Chemical Company</td>
			<td>105880034-1160</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Direct-write photolithography system		</td>
			<td>Microtech s.r.l.</td>
			<td>LW325 LaserWriter System</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Mask Aligner		</td>
			<td>HTG</td>
			<td>3HR</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>AZ 400K Developer		</td>
			<td>Mays Chemical Company</td>
			<td>105880018-1160</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Sylgard 182 Silicone Elastomer Kit	</td>
			<td>Dow Corning</td>
			<td>&nbsp;</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>25 mm no. 1 round glass coverslips</td>
			<td>VWR</td>
			<td>16004-310</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Plasma Oxidizer		</td>
			<td>Diener</td>
			<td>Femto</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Titanium pieces	Kamis 		</td>
			<td>Incorporated</td>
			<td>&nbsp;</td>
			<td> 99.95% pure</td>
		</tr>
		<tr>
			<td>Gold pellets			 </td>
			<td>Kamis Incorporated</td>
			<td>&nbsp;</td>
			<td>99.999% pure</td>
		</tr>
		<tr>
			<td>Electron-beam evaporator</td>
			<td>Kurt J. Lesker	</td>
			<td>PVD 75 Thin Film Deposition System</td>
			<td>with electron-beam accessory</td>
		</tr>
		<tr>
			<td>Hexadecanethiol		</td>
			<td>Alfa Aesar</td>
			<td>A11362</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>1-mercaptoundec-11-yl)tetra(ethyleneglycol)		</td>
			<td>Sigma Aldrich</td>
			<td>674508</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Ethanol			 </td>
			<td>Pharmco-aaper</td>
			<td>111000200</td>
			<td>200 proof, absolute</td>
		</tr>
		<tr>
			<td>Parafilm	</td>
			<td>VWR	</td>
			<td>52858-000</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>DPBS			 </td>
			<td>VWR</td>
			<td>4500-434</td>
			<td>Without calcium and magnesium</td>
		</tr>
		<tr>
			<td>Mouse Laminin I	</td>
			<td>VWR	</td>
			<td>95036-762</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Human Plasma Fibronectin		</td>
			<td>Invitrogen</td>
			<td>33016-015</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>AlexaFluor&reg; 647 carboxylic acid, succinimidyl ester		</td>
			<td>Invitrogen</td>
			<td>A-20006</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>MitoTracker Red 580		</td>
			<td>Invitrogen</td>
			<td>M22425</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>AlexaFluor&reg; 350 carboxylic acid, succinimidyl ester	</td>
			<td>Invitrogen</td>
			<td>	A-10168</td>
			<td>&nbsp;</td>
		</tr>
		<tr>
			<td>Anti-laminin antibody</td>
			<td>Fisher Scientific</td>
			<td>AB2034MI</td>
			<td>&nbsp;</td>
		</tr>
	</tbody>
</table>

creating two-dimensional patterned substrates for protein and cell confinement

Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.1 While microcontact printing can be employed to directly print a large number of molecules, including proteins,2 DNA,3 and silanes,4 the formation of self-assembled monolayers (SAMs) from long chain alkane thiols on gold provides a simple way to confine proteins and cells to specific patterns containing adhesive and resistant regions. This confinement can be used to control cell morphology and is useful for examining a variety of questions in protein and cell biology. Here, we describe a general method for the creation of well-defined protein patterns for cellular studies.5 This process involves three steps: the production of a patterned master using photolithography, the creation of a PDMS stamp, and microcontact printing of a gold-coated substrate. Once patterned, these cell culture substrates are capable of confining proteins and/or cells (primary cells or cell lines) to the pattern.
The use of self-assembled monolayer chemistry allows for precise control over the patterned protein/cell adhesive regions and non-adhesive regions; this cannot be achieved using direct protein stamping. Hexadecanethiol, the long chain alkane thiol used in the microcontact printing step, produces a hydrophobic surface that readily adsorbs protein from solution. The glycol-terminated thiol, used for backfilling the non-printed regions of the substrate, creates a monolayer that is resistant to protein adsorption and therefore cell growth.6 These thiol monomers produce highly structured monolayers that precisely define regions of the substrate that can support protein adsorption and cell growth. As a result, these substrates are useful for a wide variety of applications from the study of intercellular behavior7 to the creation of microelectronics.8
While other types of monolayer chemistry have been used for cell culture studies, including work from our group using trichlorosilanes to create patterns directly on glass substrates,9 patterned monolayers formed from alkane thiols on gold are straight-forward to prepare. Moreover, the monomers used for monolayer preparation are commercially available, stable, and do not require storage or handling under inert atmosphere. Patterned substrates prepared from alkane thiols can also be recycled and reused several times, maintaining cell confinement.10

Watch this Scientific Journal Video about Creating Two-Dimensional Patterned Substrates for Protein and Cell Confinement at JoVE.com

Creating Two-Dimensional Patterned Substrates for Protein and Cell Confinement

Self-assembled monolayers (SAMs) formed from long chain alkane thiols on gold provide well-defined substrates for the formation of protein patterns and cell confinement. Microcontact printing of hexadecanethiol using a polydimethylsiloxane (PDMS) stamp followed by backfilling with a glycol-terminated alkane thiol monomer produces a pattern where protein and cells adsorb only to the stamped hexadecanethiol region.

Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.1  While microcontact printing ...

creating-two-dimensional-patterned-substrates-for-protein-cell

Research

JoVE Journal

Bioengineering

12.5K Views.  Washington University in St. Louis. Self-assembled monolayers (SAMs) formed from long chain alkane thiols on gold provide well-defined substrates for the formation of protein patterns and cell confinement. Microcontact printing of hexadecanethiol using a polydimethylsiloxane (PDMS) stamp followed by backfilling with a glycol-terminated alkane thiol monomer produces a pattern where protein and cells adsorb only to the stamped hexadecanethiol region.

Video: Creating Two-Dimensional Patterned Substrates for Protein and Cell Confinement

Self-assembled monolayers (SAMs) formed from long chain alkane thiols on gold provide well-defined substrates for the formation of protein patterns and cell confinement.  Microcontact printing of hexadecanethiol using a polydimethylsiloxane (PDMS) stamp followed by backfilling with a glycol-terminated alkane thiol monomer produces a pattern where protein and cells adsorb only to the stamped hexadecanethiol...

cell co-culture patterning using aqueous two-phase systems

Cell Co-culture Patterning Using Aqueous Two-phase Systems

Aqueous two-phase systems were used to simultaneously pattern multiple populations of cells. This fast and easy method for cell patterning takes advantage of the phase separation of aqueous solutions of dextran and polyethylene glycol and the interfacial tension that exists between the two polymer...

photopatterning proteins and cells in aqueous environment using tio2 photocatalysis

Photopatterning Proteins and Cells in Aqueous Environment Using TiO2 Photocatalysis

We describe a protocol for modifying cell affinity of a scaffold surface in aqueous environment. The method takes advantage of titanium dioxide photocatalysis to decompose organic film in the photo-irradiated region. We show that it can be used to create microdomains of scaffolding proteins, both ex situ and in...

Photopatterning Proteins and Cells in Aqueous Environment Using TiO2 Photocatalysis

evaluation of keratinocyte proliferation on two- and three-dimensional type i collagen substrates

Evaluation of Keratinocyte Proliferation on Two- and Three-dimensional Type I Collagen Substrates

Here, we present a protocol for the preparation of two different forms of culture substrates utilizing type I collagen. Depending on how collagen is handled, collagen molecules either maintain two-dimensional, non-fibrous form or reassemble into three-dimensional, fibril form. Cell proliferation on type I collagen is drastically affected by fibril...

printing thermoresponsive reverse molds for the creation of patterned two-component hydrogels for 3d cell culture

Printing Thermoresponsive Reverse Molds for the Creation of Patterned Two-component Hydrogels for 3D Cell Culture

A bioprinter was used to create patterned hydrogels based on a sacrificial mold.  The poloxamer mold was backfilled with a second hydrogel and then eluted, leaving voids which were filled with a third hydrogel. This method uses fast elution and good printability of poloxamer to generate complex architectures from...

generation of multicue cellular microenvironments by uv-photopatterning of three-dimensional cell culture substrates

Generation of Multicue Cellular Microenvironments by UV-Photopatterning of Three-Dimensional Cell Culture Substrates

Traditionally, cell culture is performed on planar substrates that poorly mimic the natural environment of cells in vivo. Here we describe a method to produce cell culture substrates with physiologically relevant curved geometries and micropatterned extracellular proteins, allowing systematic investigations into cellular sensing of these extracellular...

external excitation of one-dimensional patterned neuronal cultures

Then, plug the single electrode pair to the operational amplifier that amplifies the signal from the generator. Apply a single pulse of bipolar square wave with a 50% duty cycle and amplitude of 22 volts. Use a bipolar wave with no DC component to avoid electrolysis that may occur at the electrodes. Apply the pulse lasting from 10 microseconds to four milliseconds to ensure effective stimulation, but prevent cell...

External Excitation of One-Dimensional Patterned Neuronal Cultures

This video demonstrates a technique for stimulating line-patterned neuronal cultures with a uniform, unidirectional electric...

two- and three-dimensional live cell imaging of dna damage response proteins

Two- and Three-Dimensional Live Cell Imaging of DNA Damage Response Proteins

This protocol describes a method for visualizing a DNA double-strand break signaling protein activated in response to DNA damage as well as its localization during...

in-vivo detection of protein-protein interactions on micro-patterned surfaces

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

This video shows experiments with subsequent analysis of protein-protein interactions by the use of micro-patterned surfaces. The approach offers the possibility to detect protein interactions in living cells and combines high throughput capabilities with the possibility to extract quantitative information.

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

cell patterning on photolithographically defined 
parylene-c: sio2 substrates

Cell Patterning on Photolithographically Defined 
Parylene-C: SiO2 Substrates

This protocol describes a microfabrication-compatible method for cell patterning on SiO2. A predefined parylene-C design is photolithographically printed on SiO2 wafers. Following incubation with serum (or other activation solution) cells adhere specifically to (and grow according to the conformity of) underlying parylene-C, whilst being repulsed by SiO2...

Cell Patterning on Photolithographically Defined 
Parylene-C: SiO2 Substrates

protocol for analysis and consolidation of trackmate outputs for measuring two-dimensional cell motility using nuclear tracking

Protocol for Analysis and Consolidation of TrackMate Outputs for Measuring Two-Dimensional Cell Motility using Nuclear Tracking

This protocol for high-throughput measurement of cell motility in HaCaT keratinocytes describes methods for collecting and processing images of cell nuclei and performing particle tracking using the ImageJ plugin TrackMate.

creating adhesive and soluble gradients for imaging cell migration with fluorescence microscopy

Creating Adhesive and Soluble Gradients for Imaging Cell Migration with Fluorescence Microscopy

A method for the assembly of adhesive and soluble gradients in a microscopy chamber for live cell migration studies is described. The engineered environment combines antifouling surfaces and adhesive tracks with solution gradients and therefore allows one to determine the relative importance of guidance...

origami inspired self-assembly of patterned and reconfigurable particles

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

We describe experimental details of the synthesis of patterned and reconfigurable particles from two dimensional (2D) precursors. This methodology can be used to create particles in a variety of shapes including polyhedra and grasping devices at length scales ranging from the micro to centimeter...

a standard and reliable method to fabricate two-dimensional nanoelectronics

A Standard and Reliable Method to Fabricate Two-Dimensional Nanoelectronics

The article aims to introduce a standard and reliable fabrication procedure for the development of future low dimensional nanoelectronics.

exfoliation and analysis of large-area, air-sensitive two-dimensional materials

Exfoliation and Analysis of Large-area, Air-Sensitive Two-Dimensional Materials

A method for exfoliating large thin flakes of air sensitive two-dimensional materials and safely transporting them for analysis outside of a glovebox is presented.

creating venn diagrams and protein-protein interaction networks for disease-associated genes and drug targets

Creating Venn Diagrams and Protein-Protein Interaction Networks for Disease-Associated Genes and Drug Targets

expanding nanopatterned substrates using stitch technique for nanotopographical modulation of cell behavior

Expanding Nanopatterned Substrates Using Stitch Technique for Nanotopographical Modulation of Cell Behavior

A protocol for producing a large area of nanopatterned substrate from small nanopatterned molds for study of nanotopographical modulation of cell behavior is...

two-dimensional polyacrylamide gel electrophoresis: a separation technique for analysis of proteins in complex protein mixture based on charge and molecular weight

In this video, we demonstrate a two-dimensional gel electrophoresis method that separates individual proteins from a complex protein mixture obtained from tumor tissues of human nonfunctional pituitary adenoma (NFPA). The proteins are separated based on their electric charge in the first dimension and further separated based on molecular weights in the second...

Two-Dimensional Polyacrylamide Gel Electrophoresis: A Separation Technique for Analysis of Proteins in Complex Protein Mixture Based on Charge and Molecular Weight

deacetylation assays to unravel the interplay between sirtuins (sirt2) and specific protein-substrates

Deacetylation Assays to Unravel the Interplay between Sirtuins SIRT2 and Specific Protein-substrates

This protocol describes the required steps to execute in vitro and in vivo deacetylation assays in order to establish the role of proteins as specific deacetylation substrates for sirtuins and further study the role of reversible - lysine acetylation as a post-translational...

Deacetylation Assays to Unravel the Interplay between Sirtuins (SIRT2) and Specific Protein-substrates

Creating Transient Cell Membrane Pores Using a Standard Inkjet Printer

Bioprinting has a wide range of applications and significance, including tissue engineering, direct cell application therapies, and biosensor microfabrication.1-10 Recently, thermal inkjet printing has also been used for gene transfection.8,9 The thermal inkjet printing process was shown to temporarily disrupt the cell membranes without affecting cell viability. The transient pores in the membrane can be used to introduce molecules, which would otherwise be too large to pass through the membrane, into the cell cytoplasm.8,9,11
The application being demonstrated here is the use of thermal inkjet printing for the incorporation of fluorescently labeled g-actin monomers into cells. The advantage of using thermal ink-jet printing to inject molecules into cells is that the technique is relatively benign to cells.8, 12 Cell viability after printing has been shown to be similar to standard cell plating methods1,8. In addition, inkjet printing can process thousands of cells in minutes, which is much faster than manual microinjection. The pores created by printing have been shown to close within about two hours. However, there is a limit to the size of the pore created (~10 nm) with this printing technique, which limits the technique to injecting cells with small proteins and/or particles. 8,9,11
A standard HP DeskJet 500 printer was modified to allow for cell printing.3, 5, 8 The cover of the printer was removed and the paper feed mechanism was bypassed using a mechanical lever. A stage was created to allow for placement of microscope slides and coverslips directly under the print head. Ink cartridges were opened, the ink was removed and they were cleaned prior to use with cells. The printing pattern was created using standard drawing software, which then controlled the printer through a simple print command. 3T3 fibroblasts were grown to confluence, trypsinized, and then resuspended into phosphate buffered saline with soluble fluorescently labeled g-actin monomers. The cell suspension was pipetted into the ink cartridge and lines of cells were printed onto glass microscope cover slips. The live cells were imaged using fluorescence microscopy and actin was found throughout the cytoplasm. Incorporation of fluorescent actin into the cell allows for imaging of short-time cytoskeletal dynamics and is useful for a wide range of applications.13-15

A description of the methods used to convert an HP DeskJet 500 printer into a bioprinter. The printer is capable of processing living cells, which causes transient pores in the membrane. These pores can be utilized to incorporate small molecules, including fluorescent G-actin, into the printed cells.

Bioprinting has a wide range of applications and significance, including tissue engineering, direct cell application therapies, and biosensor ...

Cells can sense and migrate towards higher concentrations of adhesive cues such as the glycoproteins of the extracellular matrix and soluble cues such as growth factors. Here, we outline a method to create opposing gradients of adhesive and soluble cues in a microfluidic chamber, which is compatible with live cell imaging. A copolymer of poly-L-lysine and polyethylene glycol (PLL-PEG) is employed to passivate glass coverslips and prevent non-specific adsorption of biomolecules and cells. Next, microcontact printing or dip pen lithography are used to create tracks of streptavidin on the passivated surfaces to serve as anchoring points for the biotinylated peptide arginine-glycine-aspartic acid (RGD) as the adhesive cue. A microfluidic device is placed onto the modified surface and used to create the gradient of adhesive cues (100% RGD to 0% RGD) on the streptavidin tracks. Finally, the same microfluidic device is used to create a gradient of a chemoattractant such as fetal bovine serum (FBS), as the soluble cue in the opposite direction of the gradient of adhesive cues.

A method for the assembly of adhesive and soluble gradients in a microscopy chamber for live cell migration studies is described. The engineered environment combines antifouling surfaces and adhesive tracks with solution gradients and therefore allows one to determine the relative importance of guidance cues.

Cells can sense and migrate towards higher concentrations of adhesive cues such as the glycoproteins of the extracellular matrix and soluble cues such as ...

Cell patterning platforms support broad research goals, such as construction of predefined in vitro neuronal networks and the exploration of certain central aspects of cellular physiology. To easily combine cell patterning with Multi-Electrode Arrays (MEAs) and silicon-based &#8216;lab on a chip&#8217; technologies, a microfabrication-compatible protocol is required. We describe a method that utilizes deposition of the polymer parylene-C on SiO2&#160;wafers. Photolithography enables accurate and reliable patterning of parylene-C at micron-level resolution. Subsequent activation by immersion in fetal bovine serum (or another specific activation solution) results in a substrate in which cultured cells adhere to, or are repulsed by, parylene or SiO2 regions respectively. This technique has allowed patterning of a broad range of cell types (including primary murine hippocampal cells, HEK 293 cell line, human neuron-like teratocarcinoma cell line, primary murine cerebellar granule cells, and primary human glioma-derived stem-like cells). Interestingly, however, the platform is not universal; reflecting the importance of cell-specific adhesion molecules. This cell patterning process is cost effective, reliable, and importantly can be incorporated into standard microfabrication (chip manufacturing) protocols, paving the way for integration of microelectronic technology.

This protocol describes a microfabrication-compatible method for cell patterning on SiO2. A predefined parylene-C design is photolithographically printed on SiO2 wafers. Following incubation with serum (or other activation solution) cells adhere specifically to (and grow according to the conformity of) underlying parylene-C, whilst being repulsed by SiO2 regions.

Cell patterning platforms support broad research goals, such as construction of predefined in vitro neuronal networks and the exploration of certain ...

Ordering Single Cells and Single Embryos in 3D Confinement: A New Device for High Content Screening

Biological cells are usually observed on flat (2D) surfaces. This condition is not physiological, and phenotypes and shapes are highly variable. Screening based on cells in such environments have therefore serious limitations: cell organelles show extreme phenotypes, cell morphologies and sizes are heterogeneous and/or specific cell organelles cannot be properly visualized. In addition, cells in vivo are located in a 3D environment; in this situation, cells show different phenotypes mainly because of their interaction with the surrounding extracellular matrix of the tissue. In order to standardize and generate order of single cells in a physiologically-relevant 3D environment for cell-based assays, we report here the microfabrication and applications of a device for in vitro 3D cell culture. This device consists of a 2D array of microcavities (typically 105 cavities/cm2), each filled with single cells or embryos. Cell position, shape, polarity and internal cell organization become then normalized showing a 3D architecture. We used replica molding to pattern an array of microcavities, &#8216;eggcups&#8217;, onto a thin polydimethylsiloxane (PDMS) layer adhered on a coverslip. Cavities were covered with fibronectin to facilitate adhesion. Cells were inserted by centrifugation. Filling percentage was optimized for each system allowing up to 80%. Cells and embryos viability was confirmed. We applied this methodology for the visualization of cellular organelles, such as nucleus and Golgi apparatus, and to study active processes, such as the closure of the cytokinetic ring during cell mitosis. This device allowed the identification of new features, such as periodic accumulations and inhomogeneities of myosin and actin during the cytokinetic ring closure and compacted phenotypes for Golgi and nucleus alignment. We characterized the method for mammalian cells, fission yeast, budding yeast, C. elegans with specific adaptation in each case. Finally, the characteristics of this device make it particularly interesting for drug screening assays and personalized medicine.

We report a device and a new method to study cells and embryos. Single cells are precisely ordered in microcavity arrays. Their 3D confinement is a step towards 3D environments encountered in physiological conditions and allows organelle orientation. By controlling cell shape, this setup minimizes variability reported in standard assays.

Biological cells are usually observed on flat (2D) surfaces. This condition is not physiological, and phenotypes and shapes are highly variable. Screening ...

Fluorescence Recovery after Merging a Droplet to Measure the Two-dimensional Diffusion of a Phospholipid Monolayer

We introduce a new method to measure the lateral diffusivity of a surfactant monolayer at the fluid-fluid interface, called fluorescence recovery after merging (FRAM). FRAM adopts the same principles as the fluorescence recovery after photobleaching (FRAP) technique, especially for measuring fluorescence recovery after bleaching a specific area, but FRAM uses a drop coalescence instead of photobleaching dye molecules to induce a chemical potential gradient of dye molecules. Our technique has several advantages over FRAP: it only requires a fluorescence microscope rather than a confocal microscope equipped with high power lasers; it is essentially free from the selection of fluorescence dyes; and it has far more freedom to define the measured diffusion area. Furthermore, FRAM potentially provides a route for studying the mixing or inter-diffusion of two different surfactants, when the monolayers at a surface of droplet and at a flat air/water interface are prepared with different species, independently.

We present a new technique to measure the lateral diffusion of a surface active species at the fluid-fluid interface by merging a droplet monolayer onto a flat monolayer.

We introduce a new method to measure the lateral diffusivity of a surfactant monolayer at the fluid-fluid interface, called fluorescence recovery after ...

Substrate nanotopography has been shown to be a potent modulator of cell phenotype and function. To dissect nanotopography modulation of cell behavior, a large area of nanopatterned substrate is desirable so that enough cells can be cultured on the nanotopography for subsequent biochemical and molecular biology analyses. However, current nanofabrication techniques have limitations to generate highly defined nanopatterns over a large area. Herein, we present a method to expand nanopatterned substrates from a small, highly defined nanopattern to a large area using stitch technique. The method combines multiple techniques, involving soft lithography to replicate poly(dimethylsiloxane) (PDMS) molds from a well-defined mold, stitch technique to assemble multiple PDMS molds to a single large mold, and nanoimprinting to generate a master mold on polystyrene (PS) substrates. With the PS master mold, we produce PDMS working substrates and demonstrate nanotopographical modulation of cell spreading. This method provides a simple, affordable yet versatile avenue to generate well-defined nanopatterns over large areas, and is potentially extended to create micro-/nanoscale devices with hybrid components.

A protocol for producing a large area of nanopatterned substrate from small nanopatterned molds for study of nanotopographical modulation of cell behavior is presented.

Substrate nanotopography has been shown to be a potent modulator of cell phenotype and function. To dissect nanotopography modulation of cell behavior, a ...

Type I collagen, useful as a substrate for cell culture, exists in two forms: the two-dimensional, non-fibrous form and three-dimensional, fibril form. Both forms can be prepared with the same type I collagen. In general, the non-fibrous form promotes cell adhesion and proliferation. The fibril form (gels) provides more physiological conditions in many types of cells; therefore, gel culture is useful for examining physiological behaviors of cells, such as drug efficacy.
Researchers can select the appropriate form according to the purpose of its use. For example, in the case of keratinocytes, on-gel culture has been used as a wound healing model. FEPE1L-8, a keratinocyte cell line cultured on the non-fibrous form of type I collagen, promote cell adhesion. Notably, keratinocyte proliferation is slower on the fibril form than the non-fibrous form. Protocols for the preparation of type I collagen for cell culture are simple and have wide applications depending on the experimental needs.

Here, we present a protocol for the preparation of two different forms of culture substrates utilizing type I collagen. Depending on how collagen is handled, collagen molecules either maintain two-dimensional, non-fibrous form or reassemble into three-dimensional, fibril form. Cell proliferation on type I collagen is drastically affected by fibril formation.

Type I collagen, useful as a substrate for cell culture, exists in two forms: the two-dimensional, non-fibrous form and three-dimensional, fibril form. ...

Patterning the Geometry of Human Embryonic Stem Cell Colonies on Compliant Substrates to Control Tissue-Level Mechanics

Human embryonic stem cells demonstrate a unique ability to respond to morphogens in vitro by self-organizing patterns of cell fate specification that correspond to primary germ layer formation during embryogenesis. Thus, these cells represent a powerful tool with which to examine the mechanisms that drive early human development. We have developed a method to culture human embryonic stem cells in confined colonies on compliant substrates that provides control over both the geometry of the colonies and their mechanical environment in order to recapitulate the physical parameters that underlie embryogenesis. The key feature of this method is the ability to generate polyacrylamide hydrogels with defined patterns of extracellular matrix ligand at the surface to promote cell attachment. This is achieved by fabricating stencils with the desired geometric patterns, using these stencils to create patterns of extracellular matrix ligand on glass coverslips, and transferring these patterns to polyacrylamide hydrogels during polymerization. This method is also compatible with traction force microscopy, allowing the user to measure and map the distribution of cell-generated forces within the confined colonies. In combination with standard biochemical assays, these measurements can be used to examine the role mechanical cues play in fate specification and morphogenesis during early human development.

Extracellular matrix ligands can be patterned onto polyacrylamide hydrogels to enable the culture of human embryonic stem cells in confined colonies on compliant substrates. This method can be combined with traction force microscopy and biochemical assays to examine the interplay between tissue geometry, cell-generated forces, and fate specification.

Human embryonic stem cells demonstrate a unique ability to respond to morphogens in vitro by self-organizing patterns of cell fate specification that ...

Automated Two-dimensional Spatiotemporal Analysis of Mobile Single-molecule FRET Probes

Single-molecule F&#246;rster resonance energy transfer (smFRET) is a versatile technique reporting on distances in the sub-nanometer to nanometer range. It has been used in a wide range of biophysical and molecular biological experiments, including the measurement of molecular forces, characterization of conformational dynamics of biomolecules, observation of intracellular colocalization of proteins, and determination of receptor-ligand interaction times. In a widefield microscopy configuration, experiments are typically performed using surface-immobilized probes. Here, a method combining single-molecule tracking with alternating excitation (ALEX) smFRET experiments is presented, permitting the acquisition of smFRET time traces of surface-bound, yet mobile probes in plasma membranes or glass-supported lipid bilayers. For the analysis of recorded data, an automated, open-source software collection was developed supporting (i) the localization of fluorescent signals, (ii) single-particle tracking, (iii) determination of FRET-related quantities including correction factors, (iv) stringent verification of smFRET traces, and (v) intuitive presentation of the results. The generated data can conveniently be used as input for further exploration via specialized software, e.g., for the assessment of the diffusional behavior of probes or the investigation of FRET transitions.

This article presents a method for spatiotemporal analysis of mobile, single-molecule F&#246;rster resonance energy transfer (smFRET)-based probes using widefield fluorescence microscopy. The newly developed software toolkit allows the determination of smFRET time traces of moving probes, including the correct FRET efficiency and the molecular positions, as functions of time.

Single-molecule F&#246;rster resonance energy transfer (smFRET) is a versatile technique reporting on distances in the sub-nanometer to nanometer range. ...

The extracellular matrix is an important regulator of cell function. Environmental cues existing in the cellular microenvironment, such as ligand distribution and tissue geometry, have been increasingly shown to play critical roles in governing cell phenotype and behavior. However, these environmental cues and their effects on cells are often studied separately using in vitro platforms that isolate individual cues, a strategy that heavily oversimplifies the complex in vivo situation of multiple cues. Engineering approaches can be particularly useful to bridge this gap, by developing experimental setups that capture the complexity of the in vivo microenvironment, yet retain the degree of precision and manipulability of in vitro systems.
This study highlights an approach combining ultraviolet (UV)-based protein patterning and lithography-based substrate microfabrication, which together enable high-throughput investigation into cell behaviors in multicue environments. By means of maskless UV-photopatterning, it is possible to create complex, adhesive protein distributions on three-dimensional (3D) cell culture substrates on chips that contain a variety of well-defined geometrical cues. The proposed technique can be employed for culture substrates made from different polymeric materials and combined with adhesive patterned areas of a broad range of proteins. With this approach, single cells, as well as monolayers, can be subjected to combinations of geometrical cues and contact guidance cues presented by the patterned substrates. Systematic research using combinations of chip materials, protein patterns, and cell types can thus provide fundamental insights into cellular responses to multicue environments.

Traditionally, cell culture is performed on planar substrates that poorly mimic the natural environment of cells in vivo. Here we describe a method to produce cell culture substrates with physiologically relevant curved geometries and micropatterned extracellular proteins, allowing systematic investigations into cellular sensing of these extracellular cues.