Archive for the ‘Failure’ Category

Update: Sterling silver as an electrode

January 14, 2012

Sterling silver wire does not work as a cathode or anode for gel electrophoresis.

Electrophoresis electrodes.

October 5, 2011

I have been trying to determine which materials work for electrophoresis electrodes.  My hope was that I could find something cheaper than platinum (I know it will work but it cost a lot).  Below are some things I have tried and the results.

  • Copper – Dissolves in solution and makes the solution blue-green (based on reports from various websites, only listed material I did not test).
  • Generic wire (22 gauge) – Mix of copper and iron.  Works as an anode but not a cathode.  As an anode copper leaked into solution and the wire became green and red striped, presumably because the braided strands were different materials.
  • Sterling silver (24 gauge) – Mix of silver (~90%), copper (~5%), and other elements.  Does not work for anode and I have not tested it as a cathode.  As an anode it leaked copper into solution, a black precipitate formed (steel was the cathode in this test) on top of both electrodes and the majority of the wire disintegrated.
  • Braided steel cable (around 1mm in diamter) – Intended as a “steel leader” for fishing.  Works as an anode but not as a cathode.  If it is used as a cathode it will disintegrate and break.
The failures I had have finally convinced me to purchased platinum wire.  The platinum will work for sure but I do not know if what I bought was thick enough so I will have to wait until it arrives in the mail.

LEGO electrophoresis box, as finished as it is going to get.

October 2, 2011

I kinda-sort finally finished the LEGO electrophoresis box.  Saying  ‘finished’ is a half-truth of sorts because I decided to abandon the nearly functional gel box.  Everything worked out but a few issues made the LEGO gel box more effort than it was worth. Keep reading for the details.

Final box

In the beginning….

When I originally set my mind to making the LEGO gel box I decided to test whether it was true that acetone would melt the ABS plastic (which the LEGO’s are made of) and thus fuse the bricks together and I wanted to test how nice of a gel could be cast.  The image below shows a still molten agarose gel being cast inside the rotatable gel mold.  To my delight, it was true that acetone would meld LEGO’s together and the LEGO’s worked great for casting a gel.

The prototype

I decided to class things up a bit and make the second version of the gel box all clean and spiffy looking (see image below).  The main impetus for using a single color LEGO brick was to avoid the color smearing that was inevitable.  The application of acetone melts and leads to smearing of the different colors.  In short, it looks dirty.

Black is the new black

Some assembly required….

The gel box can be assembled in an infinite number of ways and each person can go about things however they want.  The box I built was 12 LEGO pips by 28 pips and was 4 bricks tall.  Being the second attempt at a LEGO box I decided to step things up a noth and add 4 small protrusions on the inside of the box to hold the gel mold in place.  These protrusions stick out one LEGO pip and they do not obfuscate the electric field as the gel mold already blocks this area.

I entertained quite a few electrode placement variations before ultimately coming up with the design you see above.  I originality wanted the cables to plug into the side of the box, but the size of the banana plugs and the stubbornness of LEGO bricks to be drilled neatly prevented a side mount.  The LEGO plates I ended up using rest on top of the gel box and hang over it.  Take a look at the image below.

No electrodes

The image above is the gel box without electrode flaps and the image below is the box with electrode flapss.

With electrodes

Creating the electrode holders was easy.  Start with a LEGO plate that spans across the gel box and decide where to place the hole.  Once the spot has been chosen, drill a hole by starting with a small drill bit and moving up sizes until the hole is the needed size.  Starting out at the largest bore size will likely cause the plastic to crack or warp.

My reaction to drilling LEGO’s surprised me. -I was filled with a combination of childhood nostalgia and irrational love for LEGO which urged me to quit!   I nevertheless worked past my irrational love and generated the part you see below.

Drilled hole.

The next step is to attach the bannana jack.  The jack I bought attached to the LEGO plate by a screw on the underside (no gluing required).

Banana jack.

Electrodes attach to the jack similar to how the jack attached to the LEGO plate – via a screw pinching the material.  To make the electrode I stripped some wire and twisted it to form a cable.

Electrode

Once the electrodes are set-up its time to work on some finishing touches.  First, a gel tray or cast is needed.  The image below is the prototype tray I made, I chose this image over the new one I made because it is easier to see this one (on account of my camera being unable to image the black colors).  The mold is  a few LEGO plates, flanked on two sides by 1 pip wide bricks and covered with smooth plates.  The molds I built were 8 pips by 8 pips.

Mold

Building a lid for the gel box is critical, that is unless being electrocuted sounds appealing (note, the electricity could kill someone).  I lacked any single LEGO plate that could cover the entire span so I made my lid two LEGO plates thick and staggered multiply pieces so I could span the gap.  I lined the top of the gel box with smooth-topped plates and a couple normal plates so that the lid would attach but be easily removable.

Final box

After the box is assembled it is time to  weld all of the bricks.  When I chemically treated the gel box I used pure acetone and wiped all sides of the gel box.  I avoided welding the lid because there was no need to make it waterproof.

As an aside I recently read an article from MAKE magazine that gave a suggestion for making ABS glue.  They suggested adding ABS plastic flakes or pieces to a small bottle of acetone and letting the plastic dissolve over night.  The addition of plastics supposedly helps with the combining of the ABS plastic later on.  I have never tried this, but I will if I ever need to chemically weld plastics.

After acetone was dried up I performed a water test.  To my delight, the box held in water almost perfectly.  There were only three leaks present and all of them were at the junction between the walls of the box and the yellow base-plate.  I decided to be a cheapass and not purchase silicone to seal the bottom edge and I now regret this.  Instead of the silicone, I used a thick bead of PVC glue all around the bottom.  This was a bad idea.  The PVC blocked up two of the holes just fine, but the third was not stopped.  The problem was not the PVC glue sucked at sealing the bottom but that I could not cut out the PVC glue and re-seal the problematic spots (PVC glue melds with plastic).  When I tested the box after PVC glue treatment, the remaining leak was worse than the three original leaks, combined.  The problem was damage from transportation.  Going from my apartment to the lab led to the base-plate becoming even more loose and made the leaking worse.

The leak was the straw the broke the camels back and made me abandon the project. In my opinion,  if moving the gel box around could easily lead to leaks forming then the box was not worth the effort and I should probably just use a Rubber-Maid container or something.

The last problem I had was with chemistry.

The image below shows a electrochemical reaction that, while kind of interesting, was frustrating to encounter.  The twisted wire worked just fine for the anode, but the cathode  reacted to the current and chemicals.  I have no clue what exact reaction is occurring but the end result was the wire becoming a striped red and green color (which I think means the wire is made up of separate smaller wires wound together, probably copper and something else).

Frustrating reactions

(-)

All done.

The following two images are of the (mostly) finished gel box.  Despite the issues I had the box worked and so I am calling this a success even though I abandoned the project at the finish line.

In operation

 

Hooked up and with a lid

While I may have given up on using LEGO’s I have no given up on building a cheap box (<$10 a box).  Below is a preview of the new gel box I am working on and I will blog about it later.

Cheapo box

 

 

 

Yea…I am going to need a dremel.

September 20, 2011

Ugh, wow that is bad.

I tried to carve a gel comb out of a piece of LEGO.  Scissors, pliers, and a razor yielded a result that is less than satisfactory (see above).  I was really hoping to avoid buying a Dremel but the outcome of my first gel comb has convinced me to purchase one.