This work was supported by the Academy of Finland (projects 286845, 308578, 303804, 267497), the Jane and Aatos Erkko Foundation, and the Sigrid Jus&#233;lius Foundation. This work was carried out under the Academy of Finland Centers of Excellence Programme (2014&#8211;2019). We acknowledge the provision of facilities and technical support by Aalto University Bioeconomy Facilities and OtaNano &#8211; Nanomicroscopy Center (Aalto-NMC) and Micronova Nanofabrication Center.

The authors have nothing to disclose.

The protocol provides great freedom and accuracy in the shape of produced nanostructures. By changing the design of the DNA origami, the shape of the metal nanostructures can be controlled. The final, exact shape of the metal structures is additionally determined by the mask growth step (Step 9) and to a lesser degree by the mask etching (Step 10) should it not be anisotropic. If the mask growth time is extended enough, the holes in the mask will start to grow shut. This can be used to omit the thinnest features of some structures and control gap sizes, as demonstrated in Shen et al.34 with separated triangles of the bowtie origami (Figures 5B). Conversely, thinner shapes can be better preserved by shortening the oxide growth time. This means that it is possible to tune the optical properties displayed in Figure 6, not just by changing the used origami design, but also by tuning the SiO2 film growth.

If the mask thickness is changed significantly, that change must also be reflected in the SiO2 RIE step. Only a very thin layer of SiO2 should be etched (2-5 nm) to barely pierce through the mask holes. This is the most sensitive and crucial part of the whole process. Since the etching time is extremely short, only 10-20 s, exact settings must be experimentally determined when first attempted with new equipment. This is also true for Step 10.4 as some SiO2 is also etched during the a-Si etching. The extent of etched SiO2 is determined by the selectivity of the used a-Si etch parameters, equipment and even individual equipment calibrations. Care should be taken not to etch away the entire SiO2 layer during these two processes.

Another sensitive step is the SiO2 growth. The growth process is dependent on both the chamber humidity and the current activity of the used TEOS. TEOS degrades as it adsorbs water from the air, causing it to become less effective with age. This can manifest as a significantly slower, less controllable growth rate within months even with proper storage of the chemical.34 If the resulting SiO2 layer is thinner than intended, this can indicate a problem with TEOS rather than chamber humidity. While a lower humidity can also result in lower growth rate and thinner film, the resulting film should also be smoother than normal. Meanwhile a coarse grained and rough layer would conversely indicate a problem with high humidity.

It is also possible to perform this protocol on any other freely chosen substrate with two requirements: It must tolerate both HF etching (Step 12) and the 200-300 &#176;C temperatures of PECVD (Step 6). The temperature can be safely lowered to 100 &#176;C for the PECVD of a-Si if a more sensitive substrate is used, but HF cannot be avoided if the protocol is followed exactly as described. To circumvent HF, the application of an additional sacrificial layer would be required. If the requirement of the HF etching is removed, this protocol would become compatible with a wider selection of substrate materials and metals.

As this protocol consists of commonly used and robust micro- and nanofabrication processes, it could be combined with any number of other microfabrication protocols where small feature sizes and complex metal shapes are desired. In the near future, especially with the coming of low-cost DNA origami mass-production31, there is potential for this method to facilitate both general use and high-throughput nanopatterning for interface-based nanophotonics and plasmonics55.

Structural DNA nanotechnology has rapidly evolved during the recent decade1,2, and the most influential development in the field has arguably been the invention of DNA origami3,4. The DNA origami technique allows fabrication of virtually any nanoshape with accurate structural features3,4. This powerful method can be used in (sub)nanometer-precise spatial arrangement and anchoring of other nano-objects, such as carbon nanotubes5, metal nanoparticles6,7,8,9, enzymes/proteins10,11,12,13 and therapeutic materials14,15,16,17. Importantly, these structures are not merely static, but they can also be programmed to act in a dynamic manner18,19. The countless applications of DNA origami range from drug delivery20,21,22 to molecular electronics/plasmonics5,23,24,25 and from materials science26,27 to novel imaging and calibration techniques28.

Besides the applications mentioned above, the extreme spatial resolution of the DNA origami shapes could be harnessed in nanopatterning and delicate nanoscale lithography29,30. This protocol describes a lithography method for creating discrete and accurate inorganic nanostructures on substrates using DNA origami templates. These templates can be efficiently produced in various shapes and in large quantities31, and deposited effortlessly onto chosen substrates at large scales32. These properties allow a highly parallel fabrication of billions of nanostructures in one step as opposed to commonly used but rather slow electron beam lithography or other scanning-based nanofabrication techniques.

Herein, the fabrication process is demonstrated by creating gold bowtie-shaped structures on silicon nitride and sapphire substrates; in other words, the spatial information of DNA origami is transferred to entirely metallic nanostructures. As discussed here, the technique is not limited to the selected bowtie DNA origami structure since the method enables the use of virtually any DNA origami shape. Moreover, with methodical modifications, the technique can be extended to different metals and substrates paving the way towards fabrication of metasurfaces33.

The surfaces patterned with the DNA origami-mediated fabrication may serve as versatile sensors; for example, they can be used in surface-enhanced Raman spectroscopy (SERS). As a result of the small dimensions of the individual nanoshapes, the created surfaces may find uses in optical and plasmonic applications at the visible wavelength range.

<table border="0" cellpadding="0" cellspacing="0" style="width:1256px;" width="1255">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:351px;">Acetone</td>
			<td style="width:205px;">Honeywell</td>
			<td style="width:165px;">40289H</td>
			<td style="width:535px;">Semiconductor grade ULSI, &#8805; 99.5 %</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Agarose</td>
			<td>Fisher Bioreagents</td>
			<td>1036603</td>
			<td>Low-EEO, multi-purpose and molecular biology grade</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ammonium hydroxide</td>
			<td>Fisher Chemical</td>
			<td>10652251</td>
			<td>25 % ammonia solution, Certified AR for Analysis, d = 0.91</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">BRANSON 5510</td>
			<td>Branson</td>
			<td></td>
			<td>Ultrasonic bath</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dimension Icon</td>
			<td>Bruker</td>
			<td></td>
			<td>Atomic force microscope</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Electron-beam evaporator IM-9912</td>
			<td>Instrumentti Mattila</td>
			<td></td>
			<td>Evaporator for PVD</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ethidium bromide</td>
			<td>Sigma Aldrich</td>
			<td>E8751</td>
			<td>Fluorescent dye for DNA staining</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Eon Microplate spectrophotometer</td>
			<td>BioTek</td>
			<td></td>
			<td>UV/Vis spectrophotometer used for DNA origami concentration measurements</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gel Doc XR+ Documentation System</td>
			<td>BioRad</td>
			<td></td>
			<td>Gel imaging system</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gel Loading Dye, Blue (6&#215;)</td>
			<td>New England Biolabs</td>
			<td>B7021S</td>
			<td>Bromophenol blue-based loading dye for agarose gel electrophoresis</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">G-storm GS1 Thermal cycler</td>
			<td>Gene Technologies</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">HBR 4</td>
			<td>IKA</td>
			<td></td>
			<td>Heating bath</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Hydrofluoric acid</td>
			<td>Honeywell</td>
			<td>40213H</td>
			<td>Semiconductor grade, 49.5-50.5 %</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Isopropanol</td>
			<td>Honeywell</td>
			<td>40301H</td>
			<td>Semiconductor grade VLSI, &#8805; 99.8 %</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Magnesium chloride</td>
			<td>Sigma Aldrich</td>
			<td>M8266</td>
			<td>Anhydrous, &#8805; 98 %</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mini-Sub Cell GT Horizontal Electrophoresis System</td>
			<td>BioRad</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plasmalab 80+ PECVD</td>
			<td>Oxford Instruments</td>
			<td></td>
			<td>PECVD system</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plasmalab 80+ RIE</td>
			<td>Oxford Instruments</td>
			<td></td>
			<td>RIE system</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Poly(ethylene glycol)</td>
			<td>Sigma Aldrich</td>
			<td>89510</td>
			<td>BioUltra, 8,000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PowerPac HC High-Current Power Supply</td>
			<td>BioRad</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sapphire substrate (Al2O3)</td>
			<td>University Wafer</td>
			<td></td>
			<td>Thickness: 430 &#956;m, Polish: DSP, Size: 50.8 mm</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sigma VP</td>
			<td>Zeiss</td>
			<td></td>
			<td>Scanning electron microscope</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Silica gel</td>
			<td>Merck</td>
			<td>1019691000</td>
			<td>With indicator (orange gel), granulate ~1-3 mm</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Single-stranded Scaffold DNA, type p7249</td>
			<td>Tilibit Nanosystems</td>
			<td></td>
			<td>At 100 nM concentration</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Sodium chloride</td>
			<td>Sigma Aldrich</td>
			<td>S9888</td>
			<td>ACS reagent, &#8805; 99.0 %</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Staple strands (oligonucleotides)</td>
			<td>Integrated DNA Technologies</td>
			<td></td>
			<td>Sequences can be ordered e.g. at 100 micromolar in Rnase-free water</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TAE buffer (50&#215;) pH 8.0</td>
			<td>VWR Chemicals</td>
			<td>444125D</td>
			<td>Electran Electrophoresis grade</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Take3 micro-volume plate</td>
			<td>BioTek</td>
			<td></td>
			<td>Used for DNA origami concentration measurements</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tetraethyl orthosilicate</td>
			<td>Sigma Aldrich</td>
			<td>86578</td>
			<td>&#8805; 99.0 % (GC)</td>
		</tr>
	</tbody>
</table>

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 nanofabrication technique is called DNA origami, and it allows high-throughput synthesis of accurate and highly versatile structures with nanometer-level precision. Here, it is shown how the spatial information of DNA origami can be transferred to metallic nanostructures by combining the bottom-up DNA origami with the conventionally used top-down lithography approaches. This allows fabrication of billions of tiny nanostructures in one step onto selected substrates. The method is demonstrated using bowtie DNA origami to create metallic bowtie-shaped antenna structures on silicon nitride or sapphire substrates. The method relies on the selective growth of a silicon oxide layer on top of the origami deposition substrate, thus resulting in a patterning mask for following lithographic steps. These nanostructure-equipped surfaces can be further used as molecular sensors (e.g., surface-enhanced Raman spectroscopy (SERS)) and in various other optical applications at the visible wavelength range owing to the small feature sizes (sub-10 nm). The technique can be extended to other materials through methodological modifications; therefore, the resulting optically active surfaces may find use in development of metamaterials and metasurfaces.

A schematic figure of the bowtie DNA origami design and its structural details are shown in Figure 1. Agarose gel electrophoresis and AFM are used to analyze the DNA origami folding and the quality of PEG purification (Figure 2). The process flow of the nanolithography steps is displayed in Figure 3. Representative AFM images after SiO2 mask growth are shown in Figure 4 (this step is depicted in Figure 3D), while SEM images of the final metal nanostructures can be seen in Figure 5 (this step is depicted in Figure 3H). Figure 6 demonstrates the optical functionality of the metallic nanostructures templated by the bowtie DNA origami.
<table border="1" fo:keep-together.within-page="1">
	<tbody>
		<tr>
			<td colspan="5">Folding buffer (FOB) component concentrations [mM]</td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Tris</td>
			<td>Acetic acid</td>
			<td>EDTA</td>
			<td>Magnesium chloride</td>
			<td>pH</td>
		</tr>
		<tr>
			<td>2.5x FOB</td>
			<td>100</td>
			<td>47.5</td>
			<td>2.5</td>
			<td>31.25</td>
			<td>~8,3</td>
		</tr>
		<tr>
			<td>1x FOB</td>
			<td>40</td>
			<td>19</td>
			<td>1</td>
			<td>12.5</td>
			<td>~8,3</td>
		</tr>
	</tbody>
</table>
Table 1: Composition of the folding buffer (FOB).
<table border="1" fo:keep-together.within-page="1">
	<tbody>
		<tr>
			<td>Temperature range [oC]</td>
			<td>Cooling rate</td>
		</tr>
		<tr>
			<td>90-70</td>
			<td>-0.2 &#176;C / 8 s</td>
		</tr>
		<tr>
			<td>70-60</td>
			<td>-0.1 &#176;C / 8 s</td>
		</tr>
		<tr>
			<td>60-27</td>
			<td>-0.1 &#176;C / 2 s</td>
		</tr>
		<tr>
			<td>12</td>
			<td>Hold until stopped</td>
		</tr>
	</tbody>
</table>
Table 2: Thermal ramp for the bowtie origami folding. After annealing, the origami will be stored at 12 oC until the program is manually stopped.
<table border="1" fo:keep-together.within-page="1">
	<tbody>
		<tr>
			<td>PECVD and RIE parameters</td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Gas</td>
			<td>Gas flow [sccm]</td>
			<td>Chamber pressure [mTorr]</td>
			<td>RF power [W]</td>
			<td>Temperature [oC]</td>
			<td>Duration [s]</td>
		</tr>
		<tr>
			<td>PECVD of a-Si</td>
			<td>5% SiH4 in N2</td>
			<td>500</td>
			<td>1000</td>
			<td>15</td>
			<td>250</td>
			<td>90</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>O2 plasma treatment</td>
			<td>O2</td>
			<td>50</td>
			<td>40</td>
			<td>200</td>
			<td>30</td>
			<td>1200</td>
		</tr>
		<tr>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>RIE of SiO2</td>
			<td>CHF3</td>
			<td>25</td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>Ar</td>
			<td>25</td>
			<td>30</td>
			<td>100</td>
			<td>25</td>
			<td>10-22</td>
		</tr>
		<tr>
			<td>RIE of a-Si</td>
			<td>O2</td>
			<td>8</td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>SF6</td>
			<td>100</td>
			<td>90</td>
			<td>50</td>
			<td>30</td>
			<td>35</td>
		</tr>
		<tr>
			<td>RIE of remaining a-Si</td>
			<td>O2</td>
			<td>8</td>
			<td></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td></td>
			<td>SF6</td>
			<td>100</td>
			<td>90</td>
			<td>50</td>
			<td>30</td>
			<td>35-40</td>
		</tr>
	</tbody>
</table>
Table 3: Process parameters for plasma-enhanced chemical vapor deposition (PECVD) and reactive ion etching (RIE). The process parameters for these devices are specific to individual instruments and they may need to be adapted when used.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/60313/60313fig1.jpg" /> 
Figure 1: Design of the bowtie DNA origami. (A) Schematic representation of the bowtie origami design in which the core structure is shown as double helices and the polyT-overhangs are depicted as wavy lines. (B) Screenshot of a part of the bowtie origami design in the caDNAno software. The red crosses denote the base pair skipping for the twist correction, and the T8-overhangs are added to prevent blunt-end base-stacking. <a href="https://www.jove.com/files/ftp_upload/60313/60313fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/60313/60313fig2.jpg" /> 
Figure 2: Characterization of the bowtie DNA origami structure. (A) Agarose gel electrophoresis of the bowtie structure before and after poly(ethylene glycol) (PEG) purification. The 7249 nucleotides long scaffold is used as reference. (B) Atomic force microscopy (AFM) image of the bowtie structures before the purification. (C) AFM image of the bowtie structures after PEG purification. <a href="https://www.jove.com/files/ftp_upload/60313/60313fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/60313/60313fig3.jpg" /> 
Figure 3: Scheme of fabrication process flow (the dimensions are not in scale). (A) Dice and clean the substrate. (B) Deposit an a-Si layer by plasma-enhanced chemical vapor deposition (PECVD). *It is possible to employ an additional sacrificial layer under the a-Si to enable lift-off with etchant other than HF. (C) Treat the sample surface with O2 plasma and deposit DNA origami onto it. (D) Grow the SiO2 mask in desiccator. (E) Etch a thin layer of SiO2 and through the a-Si underneath it by reactive ion etching (RIE). (F) Deposit metal through the mask by physical vapor deposition (PVD). (G) Lift-off with HF. (H) remove the remaining a-Si by RIE. <a href="https://www.jove.com/files/ftp_upload/60313/60313fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/60313/60313fig4.jpg" />
Figure 4: Representative AFM images of SiO2 film with the DNA origami shaped pattern. (A) 10 &#956;m x 10 &#956;m scanning area demonstrates the high yield of the pattern formation. (B) A closer 3 &#956;m x 3 &#956;m scan shows the accurate individual patterns in the SiO2 film. <a href="https://www.jove.com/files/ftp_upload/60313/60313fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/60313/60313fig5.jpg" /> 
Figure 5: Representative scanning electron microscopy (SEM) images of metallic nanostructures templated with structurally different DNA origami. (A) Cross-shaped DNA origami, i.e., so-called Seeman tile origami54. (B) Bowtie antennas. (C) Chiral double-L (CDL) structures. Insets show individual structures with box sizes of 150 nm x 150 nm. The fabrication yield of exact structures is up to 76% for the bowtie origami and ~ 50% for the other structures displayed here34. This figure has been adapted and modified from Shen et al.34. The figure is reproduced with permission of the authors and published by The American Association for the Advancement of Science, 2018. <a href="https://www.jove.com/files/ftp_upload/60313/60313fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/60313/60313fig6.jpg" /> 
Figure 6: Representative optical/functional properties of resulting nanostructures. (A) Localized surface plasmon resonance (LSPR) measurements of an individual gold bowtie structure with different polarization (color coded as orange and blue). The solid lines are measured spectra and the dashed lines are simulation results. Insets show the SEM image of the measured particle (left) and the model used for simulation (right). (B) Surface enhanced Raman spectroscopy (SERS) of rhodamine 6G and 2,2-bipyridine measured on a surface covered with bowtie nanostructures. The baseline of each sample shows the signal level when the nanostructures were absent. This figure has been adapted and modified from Shen et al.34. The figure is reproduced with permission of the authors and published by The American Association for the Advancement of Science, 2018. <a href="https://www.jove.com/files/ftp_upload/60313/60313fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Supplemental File 1" src="/files/ftp_upload/60313/60313sup1.jpg" /> 
Supplemental File 1: CaDNAno file <a href="https://www.jove.com/files/ftp_upload/60313/bowtie_poly-T.json" target="_blank">Please click here to download this file.</a>
<img alt="Supplemental File 2" src="/files/ftp_upload/60313/60313sup2.jpg" /> 
Supplemental File 2: m13mp18 sequence <a href="https://www.jove.com/files/ftp_upload/60313/m13mp18_sequence.txt" target="_blank">Please click here to download this file.</a>
<img alt="Supplemental File 3" src="/files/ftp_upload/60313/60313sup3.jpg" /> 
Supplemental File 3: Staple strand sequence <a href="https://www.jove.com/files/ftp_upload/60313/bowtie_staple_sequences.xlsx" target="_blank">Please click here to download this file.</a>

Watch this Scientific Journal Video about DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications at JoVE.com

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

Here, we describe a protocol to create discrete and accurate inorganic nanostructures on substrates using DNA origami shapes as guiding templates. The method is demonstrated by creating plasmonic gold bowtie-shaped antennas on a transparent substrate (sapphire).

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

dna-origami-mediated-substrate-nanopatterning-inorganic-structures

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10.5K Views.  Aalto University. Here, we describe a protocol to create discrete and accurate inorganic nanostructures on substrates using DNA origami shapes as guiding templates. The method is demonstrated by creating plasmonic gold bowtie-shaped antennas on a transparent substrate (sapphire).

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

Microfluidic On-chip Capture-cycloaddition Reaction to Reversibly Immobilize Small Molecules or Multi-component Structures for Biosensor Applications

Methods for rapid surface immobilization of bioactive small molecules with control over orientation and immobilization density are highly desirable for biosensor and microarray applications. In this Study, we use a highly efficient covalent bioorthogonal [4+2] cycloaddition reaction between trans-cyclooctene (TCO) and 1,2,4,5-tetrazine (Tz) to enable the microfluidic immobilization of TCO/Tz-derivatized molecules. We monitor the process in real-time under continuous flow conditions using surface plasmon resonance (SPR). To enable reversible immobilization and extend the experimental range of the sensor surface, we combine a non-covalent antigen-antibody capture component with the cycloaddition reaction. By alternately presenting TCO or Tz moieties to the sensor surface, multiple capture-cycloaddition processes are now possible on one sensor surface for on-chip assembly and interaction studies of a variety of multi-component structures. We illustrate this method with two different immobilization experiments on a biosensor chip; a small molecule, AP1497 that binds FK506-binding protein 12 (FKBP12); and the same small molecule as part of an immobilized and in situ-functionalized nanoparticle.

We present a method for rapid, reversible immobilization of small molecules and functionalized nanoparticle assemblies for Surface Plasmon Resonance (SPR) studies, using sequential on-chip bioorthogonal cycloaddition chemistry and antibody-antigen capture.

Methods  for rapid surface immobilization of bioactive small molecules with control over  orientation and immobilization density are highly desirable for ...

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control self-assembly and mimicking this process in vitro will bring about major advances in the areas of materials science and nanotechnology. Among the available biological building blocks, peptides have several advantages as they present substantial diversity, their synthesis in large scale is straightforward, and they can easily be modified with biological and chemical entities1,2. Several classes of designed peptides such as cyclic peptides, amphiphile peptides and peptide-conjugates self-assemble into ordered structures in solution. Homoaromatic dipeptides, are a class of short self-assembled peptides that contain all the molecular information needed to form ordered structures such as nanotubes, spheres and fibrils3-8. A large variety of these peptides is commercially available.
This paper presents a procedure that leads to the formation of ordered structures by the self-assembly of homoaromatic peptides. The protocol requires only commercial reagents and basic laboratory equipment. In addition, the paper describes some of the methods available for the characterization of peptide-based assemblies. These methods include electron and atomic force microscopy and Fourier-Transform Infrared Spectroscopy (FT-IR). Moreover, the manuscript demonstrates the blending of peptides (coassembly) and the formation of a &#34;beads on a string&#34;-like structure by this process.9 The protocols presented here can be adapted to other classes of peptides or biological building blocks and can potentially lead to the discovery of new peptide-based structures and to better control of their assembly.

This paper describes the formation of highly ordered peptide-based structures by the spontaneous process of self-assembly. The method utilizes commercially available peptides and common lab equipment. This technique can be applied to a large variety of peptides and may lead to the discovery of new peptide-based assemblies.

In nature, complex functional structures are formed by the self-assembly of biomolecules under mild conditions. Understanding the forces that control ...

Preparation of Hydrophobic Metal-Organic Frameworks via Plasma Enhanced Chemical Vapor Deposition of Perfluoroalkanes for the Removal of Ammonia

Plasma enhanced chemical vapor deposition (PECVD) of perfluoroalkanes has long been studied for tuning the wetting properties of surfaces. For high surface area microporous materials, such as metal-organic frameworks (MOFs), unique challenges present themselves for PECVD treatments. Herein the protocol for development of a MOF that was previously unstable to humid conditions is presented. The protocol describes the synthesis of Cu-BTC (also known as HKUST-1), the treatment of Cu-BTC with PECVD of perfluoroalkanes, the aging of materials under humid conditions, and the subsequent ammonia microbreakthrough experiments on milligram quantities of microporous materials. Cu-BTC has an extremely high surface area (~1,800 m2/g) when compared to most materials or surfaces that have been previously treated by PECVD methods. Parameters such as chamber pressure and treatment time are extremely important to ensure the perfluoroalkane plasma penetrates to and reacts with the inner MOF surfaces. Furthermore, the protocol for ammonia microbreakthrough experiments set forth here can be utilized for a variety of test gases and microporous materials.

Herein the procedures for plasma enhanced chemical vapor deposition of perfluoroalkanes on microporous materials such as metal-organic frameworks to enhance their stability and hydrophobicity are described. Furthermore, breakthrough testing of milligram quantities of samples is described in detail.

Plasma enhanced chemical vapor deposition (PECVD) of perfluoroalkanes has long been studied for tuning the wetting properties of surfaces. For high ...

Mizoroki-Heck Cross-coupling Reactions Catalyzed by Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium Under Mild Reaction Conditions

Dichloro-bis(aminophosphine) complexes of palladium with the general formula of [(P{(NC5H10)3-n(C6H11)n})2Pd(Cl)2] (where n = 0-2), belong to a new family of easy accessible, very cheap, and air stable, but highly active and universally applicable C-C cross-coupling catalysts with an excellent functional group tolerance. Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium [(P(NC5H10)3)2Pd(Cl)2] (1), the least stable complex within this series towards protons; e.g. in the form of water, allows an eased nanoparticle formation and hence, proved to be the most active Heck catalyst within this series at 100 &#176;C and is a very rare example of an effective and versatile catalyst system that efficiently operates under mild reaction conditions. Rapid and complete catalyst degradation under work-up conditions into phosphonates, piperidinium salts and other, palladium-containing decomposition products assure an easy separation of the coupling products from catalyst and ligands. The facile, cheap, and rapid synthesis of 1,1',1"-(phosphinetriyl)tripiperidine and 1 respectively, the simple and convenient use as well as its excellent catalytic performance in the Heck reaction at 100 &#176;C make 1 to one of the most attractive and greenest Heck catalysts available.
We provide here the visualized protocols for the ligand and catalyst syntheses as well as the reaction protocol for Heck reactions performed at 10 mmol scale at 100 &#176;C and show that this catalyst is suitable for its use in organic syntheses.

Mizoroki-Heck Cross-coupling Reactions Catalyzed by Dichloro{bis[1,1&#039;,1&#039;&#039;-phosphinetriyltripiperidine]}palladium Under Mild Reaction Conditions

Dichloro{bis[1,1',1''-(phosphinetriyl)tripiperidine]}palladium [(P(NC5H10)3)2Pd(Cl)2] (1) is an easy accessible, cheap, and air stable, but highly active Heck catalyst with an excellent functional group tolerance that efficiently operates under mild reaction conditions to give the coupling products in very high yields.

Dichloro-bis(aminophosphine) complexes of palladium with the general formula of [(P{(NC5H10)3-n(C6H11)n})2Pd(Cl)2] (where n = 0-2), belong to a new family ...

Highly Stable, Functional Hairy Nanoparticles and Biopolymers from Wood Fibers: Towards Sustainable Nanotechnology

Nanoparticles, as one of the key materials in nanotechnology and nanomedicine, have gained significant importance during the past decade. While metal-based nanoparticles are associated with synthetic and environmental hassles, cellulose introduces a green, sustainable alternative for nanoparticle synthesis. Here, we present the chemical synthesis and separation procedures to produce new classes of hairy nanoparticles (bearing both amorphous and crystalline regions) and biopolymers based on wood fibers. Through periodate oxidation of soft wood pulp, the glucose ring of cellulose is opened at the C2-C3 bond to form 2,3-dialdehyde groups. Further heating of the partially oxidized fibers (e.g., T = 80 &#176;C) results in three products, namely fibrous oxidized cellulose, sterically stabilized nanocrystalline cellulose (SNCC), and dissolved dialdehyde modified cellulose (DAMC), which are well separated by intermittent centrifugation and co-solvent addition. The partially oxidized fibers (without heating) were used as a highly reactive intermediate to react with chlorite for converting almost all aldehyde to carboxyl groups. Co-solvent precipitation and centrifugation resulted in electrosterically stabilized nanocrystalline cellulose (ENCC) and dicarboxylated cellulose (DCC). The aldehyde content of SNCC and consequently surface charge of ENCC (carboxyl content) were precisely controlled by controlling the periodate oxidation reaction time, resulting in highly stable nanoparticles bearing more than 7 mmol functional groups per gram of nanoparticles (e.g., as compared to conventional NCC bearing &#60;&#60; 1 mmol functional group/g). Atomic force microscopy (AFM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) attested to the rod-like morphology. Conductometric titration, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), dynamic light scattering (DLS), electrokinetic-sonic-amplitude (ESA) and acoustic attenuation spectroscopy shed light on the superior properties of these nanomaterials.

Synthesis schemes to prepare highly stable wood fiber-based hairy nanoparticles and functional cellulose-based biopolymers have been detailed.

Nanoparticles, as one of the key materials in nanotechnology and nanomedicine, have gained significant importance during the past decade. While ...

The Synthesis of [Sn10(Si(SiMe3)3)4]2- Using a Metastable Sn(I) Halide Solution Synthesized via a Co-condensation Technique

The number of well-characterized metalloid tin clusters, synthesized by applying the disproportionation of a metastable Sn(I) halide in the presence of a sterically demanding ligand, has increased in recent years. The metastable Sn(I) halide is synthesized at&#160;&#34;outer space conditions&#34; via the preparative co-condensation technique. Thereby, the subhalide is synthesized in an oven at high temperatures, around 1,300 &#176;C, and at reduced pressure by the reaction of elemental tin with hydrogen halide gas (e.g., HCl). The subhalide (e.g., SnCl) is trapped within a matrix of an inert solvent, like toluene at -196 &#176;C. Heating the solid matrix to -78 &#176;C gives a metastable solution of the subhalide. The metastable subhalide solution is highly reactive but can be stored at -78 &#176;C for several weeks. On heating the solution to room temperature, a disproportionation reaction occurs, leading to elemental tin and the corresponding dihalide. By applying bulky ligands like Si(SiMe3)3, the intermediate metalloid cluster compounds can be trapped before complete disproportionation to elemental tin. Hence, the reaction of a metastable Sn(I)Cl solution with Li-Si(SiMe3)3 gives [Sn10(Si(SiMe3)3)4]2- 1 as black crystals in high yield. 1 is formed via a complex reaction sequence including salt metathesis, disproportionation, and degradation of larger clusters. Further, 1 can be analyzed by various methods like NMR or single crystal X-ray structure analysis.

The Synthesis of [Sn10SiSiMe334]2- Using a Metastable SnI Halide Solution Synthesized via a Co-condensation Technique

The disproportionation reaction of a metastable Sn(I) chloride solution, obtained via the preparative co-condensation technique, is used for the synthesis of a metalloid tin cluster compound.

The number of well-characterized metalloid tin clusters, synthesized by applying the disproportionation of a metastable Sn(I) halide in the presence of a ...

Insights into the Interactions of Amino Acids and Peptides with Inorganic Materials Using Single-Molecule Force Spectroscopy

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals leads to the formation of composite materials with unique properties. In addition, the undesirable process of biofouling is initiated by the adsorption of biomolecules, mainly proteins, on surfaces. This organic layer is an adhesion layer for bacteria and allows them to interact with the surface. Understanding the fundamental forces that govern the interactions at the organic-inorganic interface is therefore important for many areas of research and could lead to the design of new materials for optical, mechanical and biomedical applications. This paper demonstrates a single-molecule force spectroscopy technique that utilizes an AFM to measure the adhesion force between either peptides or amino acids and well-defined inorganic surfaces. This technique involves a protocol for attaching the biomolecule to the AFM tip through a covalent flexible linker and single-molecule force spectroscopy measurements by atomic force microscope. In addition, an analysis of these measurements is included.

Here we present a protocol to measure the force of interactions between a well-defined inorganic surface and either peptides or amino acids by single-molecule force spectroscopy measurements using an atomic force microscope (AFM). The information obtained from the measurement is important to better understand the peptide-inorganic material interphase.

The interactions between proteins or peptides and inorganic materials lead to several interesting processes. For example, combining proteins with minerals ...

Simple Methods for the Preparation of Non-noble Metal Bulk-electrodes for Electrocatalytic Applications

The rock material pentlandite with the composition Fe4.5Ni4.5S8 was synthesized via high temperature synthesis from the elements. The structure and composition of the material was characterized via powder X-ray diffraction (PXRD), M&#246;ssbauer spectroscopy (MB), scanning electron microscopy (SEM), differential scanning calorimetry (DSC) and energy dispersive X-ray spectroscopy (EDX). Two preparation methods of pentlandite bulk electrodes are presented. In the first approach a piece of synthetic pentlandite rock is directly contacted via a wire ferrule. The second approach utilizes pentlandite pellets, pressed from finely ground powder, which is immobilized in a Teflon casing. Both electrodes, whilst being prepared by an additive-free method, reveal high durability during electrocatalytic conversions in comparison to common drop-coating methods. We herein showcase the striking performance of such electrodes to accomplish the hydrogen evolution reaction (HER) and present a standardized method to evaluate the electrocatalytic performance by electrochemical and gas chromatographic methods. Furthermore, we report stability tests via potentiostatic methods at an overpotential of 0.6 V to explore the material limitations of the electrodes during electrolysis under industrial relevant conditions.

A facile preparation method of electrodes using the bulk material Fe4.5Ni4.5S8 is presented. This method provides an alternative technique to conventional electrode fabrication and describes prerequisites for unconventional electrode materials including a straightforward electrocatalytic testing method.

The rock material pentlandite with the composition Fe4.5Ni4.5S8 was synthesized via high temperature synthesis from the elements. The structure and ...

Inkjet Printing All Inorganic Halide Perovskite Inks for Photovoltaic Applications

A method for synthesizing photoactive inorganic&#160;perovskite quantum dot inks and an inkjet printer deposition method, using the synthesized inks, are demonstrated. The ink synthesis is based on a simple wet chemical reaction and the inkjet printing protocol is a facile step by step method. The inkjet printed thin films have been characterized by X-ray diffraction, optical absorption spectroscopy, photoluminescent spectroscopy, and electronic transport measurements. X-ray diffraction of the printed quantum dot films indicates a crystal structure consistent with an orthorhombic room temperature phase with (001) orientation. In conjunction with other characterization methods, the X-ray diffraction&#160;measurements show high quality films can be obtained through the inkjet printing method.

A protocol for synthesizing inorganic-lead-halide hybrid perovskite quantum dot inks for inkjet printing and the protocol for preparing and printing the quantum dot inks in an inkjet printer with post characterization techniques are presented.

A method for synthesizing photoactive inorganic&#160;perovskite quantum dot inks and an inkjet printer deposition method, using the synthesized inks, are ...

In situ FTIR Spectroscopy as a Tool for Investigation of Gas/Solid Interaction: Water-Enhanced CO2 Adsorption in UiO-66 Metal-Organic Framework

In situ infrared spectroscopy is an inexpensive, highly sensitive, and selective valuable tool to investigate the interaction of polycrystalline solids with adsorbates. Vibrational spectra provide information on the chemical nature of adsorbed species and their structure. Thus, they are very useful for obtaining molecular level understanding of surface species. The IR spectrum of the sample itself gives some direct information about the material. General conclusions can be drawn concerning hydroxyl groups, some stable surface species and impurities. However, the spectrum of the sample is &#34;blind&#34; with respect to the presence of coordinatively unsaturated ions and gives rather poor information about the acidity of surface hydroxyls, species decisive for the adsorption and catalytic properties of the materials. Furthermore, no discrimination between bulk and surface species can be made. These problems are solved by the use of probe molecules, substances that interact specifically with the surface; the alteration of some spectral features of these molecules as a result of adsorption provides valuable information about the nature, properties, location, concentration, etc., of the surface sites.
The experimental protocol for in-situ IR studies of gas/sample interaction includes preparation of a sample pellet, activation of the material, initial spectral characterization through the analysis of the background spectra, characterization by probe molecules, and study of the interaction with a particular set of gas mixtures. In this paper we investigate a zirconium terephthalate metal organic framework, Zr6O4(OH)4(BDC)6 (BDC = benzene-1,4-dicarboxylate), namely UiO-66 (UiO refers to University of Oslo). The acid sites of the UiO-66 sample are determined by using CO and CD3CN as molecular probes. Furthermore, we have demonstrated that CO2 is adsorbed on basic sites exposed on dehydroxylated UiO-66. Introduction of water to the system produces hydroxyl groups acting as additional CO2 adsorption sites. As a result, CO2 adsorption capacity of the sample is strongly enhanced.

In situ FTIR Spectroscopy as a Tool for Investigation of Gas/Solid Interaction: Water-Enhanced CO2 Adsorption in UiO-66 Metal-Organic Framework

The use of FTIR spectroscopy for investigation of the surface properties of polycrystalline solids is described. Preparation of sample pellets, activation procedures, characterization with probe molecules and model studies of CO2 adsorption are discussed.

In situ infrared spectroscopy is an inexpensive, highly sensitive, and selective valuable tool to investigate the interaction of polycrystalline solids ...