Name: preparation of mica and silicon substrates for dna origami analysis and experimentation
Uploaded: 2015-07-23T14:00:00
Description: Watch this Scientific Journal Video about Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation at JoVE.com

The authors thank Dr. Gary Bernstein for use of the AFM.

1. Experiment Planning and Material Preparation
<ol>
	<li>Determine the design, concentration, and functionality of the DNA origami that will be used in the experiments.14-16 Here, we use a DNA origami rectangle design prepared in 1x TAE/Mg2+ solution (40 mM Tris-base, 20 mM acetic acid, 2 mM EDTA and 12 mM magnesium acetate, pH 8.0).17</li>
	<li>Autoclave all tips, tubes, and containers to be used. These materials must all be autoclave compatible.</li>
	<li>Prepare a supply of sterile ...

<ol>
	<li>Rothemund, P. W. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Folding+DNA+to+create+nanoscale+shapes+and+patterns.">Folding DNA to create nanoscale shapes and patterns.</a> Nature. 440, 297-302 (2006).</li><li>Anderson, E. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+a+nanoscale+DNA+box+with+a+controllable+lid.">Self-assembly of a nanoscale DNA box with a controllable lid.</a> Nature. 459, 73-77 (2009).</li><li>Wang, Z., Ding, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+DNA+Self-Assemblies+as+Templates+for+Functional+Nanostructures.">Engineering DNA Self-Assemblies as Templates for Functional Nanostructures.</a> Acc. Chem. Res. 47, 1654-1662 (2014).</li><li>Xu, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Graphene+Visualizes+the+First+Water+Adlayers+on+Mica+at+Ambient+Conditions.">Graphene Visualizes the First Water Adlayers on Mica at Ambient Conditions.</a> Science. 329, 1188-1191 (2010).</li><li>Bustamante, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Circular+DNA-molecules+imaged+in+air+by+scanning+force+microscopy.">Circular DNA-molecules imaged in air by scanning force microscopy.</a> Biochemistry. 31, 22-26 (1992).</li><li>Hsueh, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Localized+Nanoscopic+Surface+Measurements+of+Nickel-Modified+Mica+for+Single-Molecule+DNA+Sequence+Sampling.">Localized Nanoscopic Surface Measurements of Nickel-Modified Mica for Single-Molecule DNA Sequence Sampling.</a> ACS Appl Mater. Interfaces. 2, 3249-3256 (2010).</li><li>Pastre, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Anionic+polyelectrolyte+adsorption+on+mica+mediated+by+multivalent+cations:+A+solution+to+DNA+imaging+by+atomic+force+microscopy+under+high+ionic+strengths.">Anionic polyelectrolyte adsorption on mica mediated by multivalent cations: A solution to DNA imaging by atomic force microscopy under high ionic strengths.</a> Langmuir. 22, 6651-6660 (2006).</li><li>Woo, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Self-assembly+of+two-dimensional+DNA+origami+lattices+using+cation-controlled+surface+diffusion.">Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion.</a> Nature Communications. 5, 4889 (2014).</li><li>Vesenka, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Substrate+preparation+for+reliable+imaging+of+DNA+molecules+with+the+scanning+force+microscope.">Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope.</a> Ultramicroscopy. 42-44, 1243-1249 (1992).</li><li>Albrechts, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adsorption+studies+of+DNA+origami+on+silicon+dioxide.">Adsorption studies of DNA origami on silicon dioxide.</a> , (2010).</li><li>Sarveswaran, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adhesion+of+DNA+Nanostructures+and+DNA+Origami+to+lithographically+patterned+self-assembled+monolayers+in+Si[100].">Adhesion of DNA Nanostructures and DNA Origami to lithographically patterned self-assembled monolayers in Si[100].</a> Proc. of SPIE-Soc. Opt. Eng. 7637, 76370M-1 (2010).</li><li>Kern, W., Puotien, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cleaning+solutions+based+on+hydrogen+peroxide+for+use+in+silicon+semiconductor+technology.">Cleaning solutions based on hydrogen peroxide for use in silicon semiconductor technology.</a> RCA Rev. 31, 187-206 (1970).</li><li>Pillers, M., Goss, V., Lieberman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron-Beam+Lithography+and+Molecular+Liftoff+for+Directed+Attachment+of+DNA+Nanostructures+on+Silicon:+Top-down+Meets+Bottom-up.">Electron-Beam Lithography and Molecular Liftoff for Directed Attachment of DNA Nanostructures on Silicon: Top-down Meets Bottom-up.</a> Acc. Chem. Res. 47, 1759-1767 (2014).</li><li>Sacc&#225;, B., Niemery, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+Origami:+The+Art+of+Folding+DNA.">DNA Origami: The Art of Folding DNA.</a> Angew. Chem. Int. Ed. 51, 58-66 (2012).</li><li>Douglas, S. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+prototyping+of+3D+DNA-origami+shapes+with+caDNAno.">Rapid prototyping of 3D DNA-origami shapes with caDNAno.</a> Nucleic Acids Res. 37, 5001-5006 (2009).</li><li>Ben-Ishay, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Designing+a+Bio-responsive+Robot+from+DNA.">Designing a Bio-responsive Robot from DNA.</a> Origami. J. Vis. Exp. (77), e50268 (2013).</li><li>Woo, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Programmable+molecular+recognition+based+on+the+geometry+of+DNA+nanostructures.">Programmable molecular recognition based on the geometry of DNA nanostructures.</a> Nature Chemistry. 3, 620-627 (2011).</li><li>Schlegel, M. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cation+sorption+on+the+muscovite+(001)+surface+in+chloride+solutions+using+high-resolution+X-ray+reflectivity.">Cation sorption on the muscovite (001) surface in chloride solutions using high-resolution X-ray reflectivity.</a> Geochim. Cosmochim. Acta. 70, 3549-3565 (2006).</li><li>Rasband, W. S., Howarter, J. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=National+Institutes+of+Health.">National Institutes of Health.</a> Langmuir. 22, 11142-11147 (2006).</li><li>Kershner, R. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Placement+and+orientation+of+individual+DNA+shapes+on+lithographically+patterned+surfaces.">Placement and orientation of individual DNA shapes on lithographically patterned surfaces.</a> Nature Nanotechnology. 4, 557-561 (2009).</li><li>Hung, A. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-area+spatially+ordered+arrays+of+gold+nanoparticles+directed+by+lithographically+confined+DNA+origami.">Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami.</a> Nature Nanotechnology. 5, 121-126 (2010).</li><li>Sarveswaran, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=et+al.Adhesion+of+DNA+nanostructure+and+DNA+origami+to+lithographically+patterned+self-assembled+monolayers+on+Si[100.">et al.Adhesion of DNA nanostructure and DNA origami to lithographically patterned self-assembled monolayers on Si[100.</a> Proc. SPIE-Int. Soc. Opt. Eng. 7637, 76370M (2010).</li><li>Pillers, M. A., Lieberman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermal+stability+of+DNA+origami+on+mica.">Thermal stability of DNA origami on mica.</a> J. Vac. Sci. Technol. B. 32, 040602 (2014).</li><li>Song, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Direct+Visualization+of+Transient+Thermal+Response+of+a+DNA.">Direct Visualization of Transient Thermal Response of a DNA.</a> Origami. J. Am. Chem. Soc. 134, 9844 (2012).</li><li>Wei, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+the+thermal+behavior+of+DNA+origami+nanostructures.">Mapping the thermal behavior of DNA origami nanostructures.</a> J. Am. Chem. Soc. 135 (16), 6165-6176 (2013).</li><li>Hyojeong Kim, ., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stability+of+DNA+Origami+Nanostructures+under+Diverse+Chemical+Environments.">Stability of DNA Origami Nanostructures under Diverse Chemical Environments.</a> Chem. Mater. 26, 5265-5273 (2014).</li></ol>

There are several steps that need to be emphasized to attain consistent and ideal results. For mica samples, following a strict and thorough rinsing and drying regime, as in steps 3.3 and 3.4, will ensure that high quality images of individual DNA origami can be attained using AFM without the various problems outlined in the Representative Results section. Of primary importance for silicon samples is the cleanliness of the substrate. Following the cleaning procedures outlined in step 5.2 thoroughly and meticulously will ...

First introduced in 2006, DNA origami utilizes the self-assembling nature of DNA oligonucleotides to produce designable and highly ordered nanostructures.1 A myriad of structures have been reported, ranging from smiley faces to latched 3-dimensional boxes.2 DNA origami can be functionalized with various biomolecules and nanostructures, giving rise to research applications in nanoelectronics, medicine, and quantum computing.3 However, the analysis and many future applications are not only dependent on structural design, but also on the adhesion of the DNA origami nanostructures to surfaces. The methods described in this manuscript pertain to the preparation of DNA origami samples on two types of substrates: mica and functionalized silicon oxide.
Mica is the substrate of choice for DNA origami studies because it is atomically flat, with a layer height of 0.37 nm &#177; 0.02 nm.4 It is also easily cleaned, making sample preparation and atomic force microscopy (AFM) studies straightforward. Muscovite mica contains a high density of potassium in each cleavage plane, but these ions diffuse away from the mica surface when in water. To mediate the binding of DNA origami to the mica substrate, Mg2+ is used to reverse the negative charge of the mica and electrostatically bind the DNA phosphate backbone to the substrate (Figure 1A).5 Mixtures of annealed DNA in the presence of large excesses of staple strands give high coverage and good images on mica because the adhesion of DNA origami to the Mg2+-terminated surface is much stronger than the adhesion of single-stranded oligonucleotides (staple strands). Other positively charged ions, including Ni2+ and Co2+ can be used to control the adhesion of DNA on mica.6,7 Changing the concentration of monovalent and divalent cations in solution can mediate adhesion and surface diffusion rates of DNA origami.8 However, the protocol for preparing mica substrates and depositing and rinsing the origami is often not explicitly described in published manuscripts.9 Without a clear protocol, reproducible results can be difficult to obtain.
Mica is an insulator, so it is not suitable as a substrate for some applications in nanoelectronics. Silicon passivated with a thin native oxide has desirable electronic properties, including compatibility with prior complimentary metal-oxide semiconductor (CMOS) processing to create input/output structures and topographic features. Silicon wafers stored in air are passivated with either a thick thermal oxide or thin native oxide film that is relatively dirty, with a high particulate count. Silicon oxide has a much lower surface charge density than mica, and the charge density is highly dependent on oxide preparation and history. At magnesium ion concentrations above 150 mM, good coverages (up to 4/&#181;m2) of rectangular DNA origami can be achieved on oxygen plasma treated silicon substrates; however, this concentration and coverage may change depending on the size and design of the nanostructures being used.10 An alternative protocol for tuning the surface charge is to attach a cationic self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) (Figure 1B) to the oxide. The primary amine on APTES can be protonated at pH values below 9, modifying the charge and hydrophobicity of the substrate.11 For a complete monolayer of APTES to be successfully deposited, the silicon must be appropriately cleaned using Radio Corporation of America (RCA) protocols. These protocols include treatments in ammonium hydroxide and hydrogen peroxide solutions (RCA1) to remove organic residues and particle contaminants. A short etch in aqueous hydrofluoric acid solution removes the native oxide layer along with any ionic contaminants that adhere to the oxide. Finally, samples are exposed to a hydrochloric acid and hydrogen peroxide solution (RCA2) to remove metal and ionic contaminants and form a thin, uniform oxide layer.12 Most cleanrooms have designated hoods for CMOS cleaning protocols, with strict rules about what can be used in these areas. A common problem comes in the form of ions such as sodium, which can disrupt the electronic properties of CMOS structures by creating midbandgap traps.13 Ions commonly used in DNA origami preparation and deposition buffers could contaminate the CMOS baths and cause problems for other researchers using the clean room. For this reason, our group uses a &#39;dirty&#39; CMOS cleaning bench arranged specifically for the small samples used for DNA origami research. This process is a good alternative to the traditional cleanroom set-up and may be suitable for laboratories that do not have access to a cleanroom CMOS bench.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Eppendorf epT.I.P.S. Reloads, capacity 2-200 &#956;L&#160;</td>
			<td>VWR International, LLC</td>
			<td>22491733</td>
			<td>10 reload tray of 96 tips</td>
		</tr>
		<tr>
			<td>Microcentrifuge Tubes, Polypropylene</td>
			<td>VWR International, LLC</td>
			<td>87003-290</td>
			<td>0.65 mL, natural</td>
		</tr>
		<tr>
			<td>Research Plus Pippete - Single Channel - 20-200 &#956;L</td>
			<td>A. Daigger &#38; Company, Inc.</td>
			<td>EF8960F-3120000054 EACH</td>
			<td>Adjustable Volume</td>
		</tr>
		<tr>
			<td>Research Plus Pippete - Single Channel - 2-20 &#956;L</td>
			<td>A. Daigger &#38; Company, Inc.</td>
			<td>EF8960D-3120000038 EACH</td>
			<td>Adjustable Volume</td>
		</tr>
		<tr>
			<td>Scotch 237 Permanent Double-Sided Tape</td>
			<td>Office Depot, Inc.</td>
			<td>602710</td>
			<td>3/4&#34; x 300&#34;, Pack of 2</td>
		</tr>
		<tr>
			<td>Vortex Mixer</td>
			<td>Thermo Scientific</td>
			<td>M37610-33Q</td>
			<td></td>
		</tr>
		<tr>
			<td>Wafer container single, 2&#34; (50 mm), 60 mm x 11 mm</td>
			<td>Electron Microscopy Sciences</td>
			<td>64917-2</td>
			<td>6 per pack</td>
		</tr>
		<tr>
			<td>6&#34; Wafer, P-type, &#60;100&#62; orientation, w/ primary flat</td>
			<td>Nova Electronic Materials, Ltd.</td>
			<td>GC49266</td>
			<td></td>
		</tr>
		<tr>
			<td>Powder-Free Nitrile Examination Gloves</td>
			<td>VWR International, LLC</td>
			<td>82062-428</td>
			<td>Catalog number is for size large</td>
		</tr>
		<tr>
			<td>High Accuracy Noncontact probes with Au reflective coating</td>
			<td>K-Tek Nanotechnology, Inc.</td>
			<td>HA_NC/15</td>
			<td></td>
		</tr>
		<tr>
			<td>Autoclave Pan</td>
			<td>A. Daigger &#38; Company, Inc.</td>
			<td>NAL692-5000 EF25341C</td>
			<td></td>
		</tr>
		<tr>
			<td>Sol-Vex II Aggressive Gloves, Size: 9-9.5; 15 mil, 13 inch - 1 dz</td>
			<td>Spectrum Chemical Mfg. Corp.</td>
			<td>106-15055</td>
			<td>Before use, rinse with water and scrub together until no bubbles form on the gloves.</td>
		</tr>
		<tr>
			<td>Tweezers PTFE 200 mm Square</td>
			<td>Dynalon Corp.</td>
			<td>316504-0002</td>
			<td></td>
		</tr>
		<tr>
			<td>Muscovite Mica Sheets V-5 Quality</td>
			<td>Electron Microscopy Sciences</td>
			<td>71850-01</td>
			<td>10 per pack</td>
		</tr>
		<tr>
			<td>Mica Disc, 10 mm</td>
			<td>Ted Pella, Inc</td>
			<td>50</td>
			<td>Mica discs are optional</td>
		</tr>
		<tr>
			<td>Scriber Diamon Pen for Glassware</td>
			<td>VWR International, LLC</td>
			<td>52865-005</td>
			<td></td>
		</tr>
		<tr>
			<td>Scintillation Vials, Borosilicate Glass, with Screw Cap - 20 mL</td>
			<td>VWR International, LLC</td>
			<td>66022-060</td>
			<td>Case of 500, with attached polypropylene cap and pulp foil liner</td>
		</tr>
		<tr>
			<td>4 x 5 Inch Top PC-200 Hot Plate, 120 V/60 Hz</td>
			<td>Dot Scientific, Inc.</td>
			<td>6759-200</td>
			<td></td>
		</tr>
		<tr>
			<td>Straight-Sided Glass Jars, Wide Mouth</td>
			<td>VWR International, LLC</td>
			<td>89043-554</td>
			<td>Case of 254, caps with pulp/vinyl liner attached</td>
		</tr>
		<tr>
			<td>Standar-Grade Glass Beaker, 250 mL Capacity</td>
			<td>VWR International, LLC</td>
			<td>173506</td>
			<td></td>
		</tr>
		<tr>
			<td>Beakers, PTFE</td>
			<td>VWR International, LLC</td>
			<td>89026-022</td>
			<td>For use with HF</td>
		</tr>
		<tr>
			<td>Shallow form watch glass, 3&#34;</td>
			<td>VWR International, LLC</td>
			<td>66112-107</td>
			<td>Case of 12</td>
		</tr>
		<tr>
			<td>Plastic Storage Container</td>
			<td>VWR International, LLC</td>
			<td>470195-354</td>
			<td>For secondary container</td>
		</tr>
		<tr>
			<td>General-Purpose Liquid-In-Glass Thermometers</td>
			<td>VWR International, LLC</td>
			<td>89095-564</td>
			<td></td>
		</tr>
		<tr>
			<td>High precision and ultra fine tweezers</td>
			<td>Electron Microscopy Sciences</td>
			<td>78310-0</td>
			<td></td>
		</tr>
		<tr>
			<td>Polycarbonate Faceshield</td>
			<td>Fisher Scientific, Inc.</td>
			<td>18-999-4542</td>
			<td></td>
		</tr>
		<tr>
			<td>Neoprene Apron</td>
			<td>Fisher Scientific, Inc.</td>
			<td>19-810-609</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium Gluconate, Calgonate</td>
			<td>W.W Grainger, Inc.</td>
			<td>13W861</td>
			<td>Tube, 25 g</td>
		</tr>
		<tr>
			<td>Hydrogen Peroxide 30 % CR ACS 500 mL</td>
			<td>Fisher Scientific, Inc.</td>
			<td>H325 500</td>
			<td>HARMFUL, TOXIC</td>
		</tr>
		<tr>
			<td>3-Aminopropyltriethoxysilane</td>
			<td>Gelest Inc.</td>
			<td>SIA0610.0-25GM</td>
			<td>Let warm to room temperature before use.</td>
		</tr>
		<tr>
			<td>Ammonium hydroxide, 2.5 L</td>
			<td>Fisher Scientific, Inc.</td>
			<td>A669-212</td>
			<td>HARMFUL, TOXIC</td>
		</tr>
		<tr>
			<td>Hydrochloric acid</td>
			<td>Fisher Scientific, Inc.</td>
			<td>A144-212</td>
			<td>HARMFUL, TOXIC</td>
		</tr>
		<tr>
			<td>Hydrofluoric acid</td>
			<td>Fisher Scientific, Inc.</td>
			<td>A147-1LB</td>
			<td>HARMFUL, TOXIC</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MultiMode Nanoscope IIIa</td>
			<td>Veeco Instruments, Inc.</td>
			<td>n/a</td>
			<td>Any AFM capable of tapping mode is suitable for analysis</td>
		</tr>
		<tr>
			<td>Dunk basket</td>
			<td>Made in lab</td>
			<td>Made in lab</td>
			<td>The dunk basket was made using the bottom of a PTFE bottle with holes drilled in, PTFE handle, and all PTFE screws.</td>
		</tr>
	</tbody>
</table>

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.

Two variables dictate the coverage of DNA origami on the substrate: solution concentration and exposure time. The adsorption characteristics of DNA origami on mica and APTES functionalized silicon oxide have been previously reported.13 The relationship between the concentration of DNA origami in the deposition solution and the final coverages on mica are summarized in Table 1 and Figure 2, showing increasing concentration results in increased coverage. The time-dependence of b...

Watch this Scientific Journal Video about Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation at JoVE.com

Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation

Reproducible cleaning processes for substrates used in DNA origami research are described, including bench-top RCA cleaning and derivatization of silicon oxide. Protocols for surface preparation, DNA origami deposition, drying parameters, and simple experimental set-ups are illustrated.

The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of ...

Research

JoVE Journal

Chemistry

Origami Inspired Self-assembly of Patterned and Reconfigurable Particles

There are numerous techniques such as photolithography, electron-beam lithography and soft-lithography that can be used to precisely pattern two ...

Isolation and Preparation of Bacterial Cell Walls for Compositional Analysis by Ultra Performance Liquid Chromatography

The bacterial cell wall is critical for the determination of cell shape during growth and division, and maintains the mechanical integrity of cells in the ...

Folding and Characterization of a Bio-responsive Robot from DNA Origami

The DNA nanorobot is a hollow hexagonal nanometric device, designed to open in response to specific stimuli and present cargo sequestered inside. Both ...

Preparation of Macroporous Epitaxial Quartz Films on Silicon by Chemical Solution Deposition

This work describes the detailed protocol for preparing piezoelectric macroporous epitaxial quartz films on silicon(100) substrates. This is a three-step ...

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

DNA origami nanostructures hold an immense potential to be used for biological and medical applications. However, low-salt conditions and nucleases in ...

Assembly of Gold Nanorods into Chiral Plasmonic Metamolecules Using DNA Origami Templates

The inherent addressability of DNA origami structures makes them ideal templates for the arrangement of metal nanoparticles into complex plasmonic ...

Growth of Gold Dendritic Nanoforests on Titanium Nitride-coated Silicon Substrates

In this study, a high-power impulse magnetron sputtering system is used to coat a flat and firm titanium nitride (TiN) film on silicon (Si) wafers, and a ...

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

Structural DNA nanotechnology provides a viable route for building from the bottom-up using DNA as construction material. The most common DNA ...

Preparation of Nanoparticles for ToF-SIMS and XPS Analysis

Nanoparticles have gained increasing attention in recent years due to their potential and application in different fields including medicine, cosmetics, ...

Single-Molecule SERS Measurements Enabled by Plasmonic DNA Origami Nanoantennas

Single-Molecule Surface-Enhanced Raman Scattering Measurements Enabled by Plasmonic DNA Origami Nanoantennas

Single-Molecule Surface-Enhanced Raman Scattering Measurements Enabled by Plasmonic DNA Origami Nanoantennas (Video) | JoVE 

Surface-enhanced Raman scattering (SERS) has the capability to detect single molecules for which high field enhancement is required. Single-molecule (SM) ...