20.109(F13): Mod 3 Day 2 Phage nanowires

Fabricating nanocomposites with M13 phage

Today's Goal

In an effort to increase efficiency in our solar cells, we need to test two nano-composites of titanium dioxide nanowires containing either aligned gold nanoparticles, or aligned SWNTs in their core. By using a combinatorial approach of panning and bio-templating these structures can be achieved via M13 phage.

Panning

Phage display has been used for decades as a tool for discovery. This technique exploits natural selection and identifies functional peptide sequences that can be fused to the phage coat. Most often it’s the p3 protein at the phage tip that’s used for phage display because, despite the limited number of displayed peptides per phage (on the order of 5), there is enough flexibility to accommodate peptides of 20 to 30 amino acids. The other protein used for phage display, p8, is presented at much higher copy number per phage (on the order of 2700) but it has limited flexibilty. The semi-crystalline packing of p8 on the phage coat restricts fusions to only 4 to 6 neutral or negatively charged amino acids. For scientists who can tolerate a mix of p8 proteins on the phage coat for their work, there are phage-display variations that mix and match fusion and wild-type proteins on a phage coat, but for those who want phage of a particular form, the options are limited.

Nonetheless, peptides with remarkably diverse functions have been isolated with phage display. Once the fusion site is chosen, a library of sequences encoding random peptides can be synthesized and cloned. In this way a pool of phage, each with different fusions, can be made. Finally, the phage pool can be screened for interesting behaviors or properties. Peptide-fusion proteins to p8 or p3 that include stop codons or intolerable sequences are largely lost from the population after the first round of “panning.” Other phage that can bind to a substance of interest or show enzyme activity or glow green…, these remain and can be directly isolated from the pool or further enriched by a second, third, fourth round of panning. Ultimately anywhere from 10 to 1000 candidate sequences may remain from a starting pool of 1 billion [3].

Despite phage display techniques being available for more than a generation, this tool has been applied only recently to the search for novel materials. Largely it’s been Angela Belcher and her lab who highlighted and then demonstrated the usefulness of this search tool for finding peptides that interact with materials to meet human needs. That M13 could interact with inorganic materials could not have been predicted from the original genetic studies on the phage, but there was also no one who had tried it. Phage that can bind to cobalt oxide, gold, iridium and indium tin oxide are all in-hand thanks to their work (e.g see reference [4]). Today you will harvest a phage that can bind to single-walled carbon nanotubes (SWNTs) and TiO2 since these can be used to build nanocomposites that will be assembled into a photovoltaic device before this module is over.

Biotemplating

Biotemplating utilizes biological materials to fabricate and or organize unique nanomaterial structures. A variety of benefits are associated with biotemplated synthesis methods over traditional synthesis methods. From the fabrication standpoint, biotemplating can reduce the environmental impact of materials synthesis. Biotemplating has been shown to enable synthesis of materials at lower temperatures and pressures as well as milder reagents than traditional synthesis methods. From the stand point of organization, biotemplating has been utilized to achieve unique structures over broad length scales. These structures are either unattainable or significantly more difficult to create without biotemplating. Figure 1 reports biological templates and the respective length scales each enable fabrication over (Sotiropoulou, et al).

For this module, biotemplating of titania on the M13 phage will be explored. For this process, the M13 phage will serve as a nucleation site for the precursor molecule, titanium isopropoxide to form titania via the following reaction:

Ti{OCH(CH3)2}4 + 2 H2O → TiO2 + 4 (CH3)2CHOH

As this reaction occurs very rapidly and is water sensitive by nature. As a result we will perform this reaction at -40C to slow down the reaction kinetics and perform it in 95% ethanol to give moer control to the hydrolysis reaction.

Protocols

Part 1: React SWNTs:phage with Ti(I-pro)4

Today's lab has some safety hazards and you must work extremely carefully. Lab coats, gloves and goggles are a must when you're at the chemical hood. The reaction of the complexed phage with the titanium will take place in the hood at supercooled temperatures (a bath at ~ -40°C). Once the titanium has been deposited on the surface of the phage, the solution is less hazardous, though you should still treat the materials with care since no reactions run to completion

For SWNT phage only:

1. Retrieve your dialyzed samples.
2. Carefully transfer the contents of the dialysis bag to a 15 ml falcon tube. This is best done by carefully holding the dialysis bag vertically while you remove one of the alligator clips, cover the open end of the tubing with the falcon tube, then invert the tubing and the falcon tube so the complexed phage solution can be collected.
3. If there are any nanowires remaining in the dialysis tube after you have emptied the contents, rinse the nanowires out using 1 ml of the NaCl dialysis buffer and add the volume to the 15 ml falcon tube.
4. Use the markings on the tube to estimate the volume of the nanowires.
5. Vortex the nanowires if they look clumpy.

Bath set-up

For all groups:

1. Chill your complexed phage on ice on your bench until you are ready to react it with the titanium.
2. Calculate the amount of material necessary for making TiO2 Nano composites. The reaction should take place in a 95% ethanol solution. You have two choices:
   • a. If your phage volume is less than 250 uL total. You may simply use 5 ml of 95% ethanol.
   • b. If your phage volume is > 250 uL total, calculate how much 100% ethanol you would need to add to achieve a 95% solution. Assume that your phage solution is 100% water.
3. Add ethanol volume from a. or b. without phage to a 250 mL erlenmyer flask with a stir bar and set aside.
4. Prepare a super-cooled bath:
   • Mix ethylene glycol and ethanol in a 1:1 volume ratio (make up a total of 100 mL).
   • Place the 250ml Erlenmeyer flask with your ethanol solution + stir bar inside an evaporation dish in the fume hood on a stir plate.
   • Fill the evaporation dish with the ethylene glycol and ethanol mixture match the liquid level inside the Erlenmeyer flask.
   • Add ~10 dry ice chunks to the evaporation dish and let sit for 10 min. You can measure the temperature of this mixture. It should measure ~ negative 40°C.
5. Next, calculate how much Ti(I-pro)4 you must add to your phage in order to achieve a 15:1 TiO2:phage ratio. The 15:1 gram ratio is based off of a calculation of the phage surface area to the surface area of the phage covered in TiO2, as the goal is to cover the phage completely with TiO2.
6. Quantities you need to know:
   • MW of phage = 1.8 x 10^7 g/mol
   • MW of Ti(I-pro)4 = 284.22 g/mol
   • MW of TiO2 = 80 g/mol
   • Concentration of Ti(I-pro)4 = 0.96 g/mL

 Think about the following progression:
 phage particle # --> moles phage --> weight phage --> weight TiO2 --> moles TiO2 = 
 moles Ti(I-pro)4 --> volume of Ti(I-pro)4 to add

1. Put on lab coat, gloves, and safety glasses for this next step. Add the calculated amount of Ti(I-pro)4 to the supercooled EtOH. Stir at least 5 minutes.
2. Add your complexed phage solution to the EtOH:titanium and stir vigorously for 20 minutes.
3. Remove the Erlenmeyer flask from the bath and place it back on the stir plate. Leave the mixture on the plate until it reaches room temperature. After a maximum of an hour your solution should turn grey (SWNT complexed phage) or white (gold complexed phage) indicating that the reaction has completed.

Part 2: Prepare a grid for TEM

Each group should prepare a TEM grid (so there might be 3 grids for each reaction of phage:SWNTs:TiO2). This will allow for some duplicates to be visualized in case the grid is damaged or different kinds of EM are being performed.

clever trick to keep the stirbar from falling out of your jar when you pour out the solution

1. Transfer the reaction to a 50 ml falcon tube. You can harvest the last few drops but not the stir bar using a larger magnet held to the bottom of the inverted jar (see image)
2. Vortex the nanowires for 1 minute and immediately remove 5 ul of the nanowire suspension to place on the TEM grid that you have balanced in the specialized tweezers. HINT 1: The grid is "sided" and you want the shiny edge side up. If you are uncertain as to which side has the shiny edge, try looking under the dissecting microscope (12X magnification) to find the numeral "1" on the correct side. HINT 2: Treat the grid with care and use the tweezers only on the edge to minimize damaging the delicate mesh.

   

   TEM grid balanced in tweezers

   
   
3. Allow the nanowires to settle onto the grid undisturbed for 5'. The EtOH will evaporate during this time. You can wick away any residual EtOH by touching the very edge of the grid with a Kimwipe.
4. Wash the grid by adding 5 uL of 100% EtOH onto the grid. After 30 seconds you can wick away the EtOH.
5. Wash the grid by adding 5 uL of sterile H₂O onto the grid. After 30 seconds you can wick away the water and transfer the grid to a holder to visualize next time.

Part 3: Wash your phage:SWNTs:TiO2 nanocomposites

1. Spin the remaining volume of nanocomposites in the clinical centrifuge at room temperature, 3000 rpm 10 minutes. At the end of this spin you should see dark material collected at the bottom of the tube. This is the material that will serve as the photoanode in our photovolatic device!
2. Decant the supernatant into a chemical waste bottle in the chemical hood. Resuspend the nanocomposite material in 20 ml dH₂O. Spin as before.
3. Decant the supernatant into the sink.
4. Hand the pellet of phage:SWNTs:TiO2 to the teaching faculty who will begin to prepare the paste needed to build them into the solar cell.

Part 4: Research pre-proposal

Pre-proposals will be due in lecture on M3D4 (11.29.12) at 11AM. That's coming up soon! Use your time today to look carefully at the requirements for this pre-proposal assignment. The requirements are posted here. Today you and your lab partner should work through the research topics you identified as interesting and decide on one (or at most two) that are worth researching more.
DONE!

ASSIGNMENT

Before M2D4 in lecture, every team must document a research pre-proposal by making and printing out a wiki page using the template found here.
Your pre-proposal will be evaluated based on its:

• • creativity and innovation with its context
  • clarity of goals and objectives
  • clarity of writing and figure
  • clarity of what results will achieve over current situation
  • format

The reader of your pre-proposal should leave with the feeling of "Great idea! I wish I'd thought of that..."

Reagents list

• 100% EtOH
• Ti(I-pro)4 msds

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