Trouble-shooting.

(also a science)

Things that didn’t go as expected • Gold color did not disappear

over 2 hour time rocking at room temperature

• After reduction and silver step, purple color did not develop

• Are there nanowires? What happened??

Dark orange – something’s not right

Gold – after two hours of rocking

Clear – what it is supposed to look like!

“Low hanging fruit”

• Phage titered correctly? Concentrations calculated correctly?– T/R lab, John and Bridget went through all of your

notebooks looking for these calculations – This is why you always right neatly and make sure

to read directions! Only one group remarked on the color change that took place.

– End result: even if there were slight calculation errors, all the phage added into the reaction mixture is in the correct order of magnitude

Too much gold for the ascorbic acid?

• Calculated the number of gold particles (based on molarity of gold solution)

• Calculated the number of nucleation sites (based on concentration of phage and number of p8 proteins)

• Phage reduces the gold that binds to the mutated p8 protein

• Calculated amount of ascorbic acid able to reduce the extra free gold in solution (if there weren’t enough phage)

• End result: reducing power is still in excess – this shouldn’t be a problem

Problem of “cutting corners * 1000”

• If we are an order of magnitude off in terms of phage and an order of magnitude off in terms of gold, does this make the experiment just fail?

• End result: Maybe, but nothing so drastic. This “cutting corners * 1000” is more likely to have an effect on the nanoscale and create nanoparticles instead of nanowires…it isn’t something that would change how we’d see the color change

Contamination?

• Belcher Lab has had issues with E4 contamination in the past– Remember E4?

• Normally perform a DNA sequencing analysis to check on this– How could this experiment be done?

• End result: phage contamination would not change the goldclear or the purple color change, so this isn’t contributing to our problem

pH?

• What if the pH of both the water and TBS is off? – Nanopure water vs. DI water

• End result: pH of both Belcher solutions and 20.109 solutions were similar (within 0.01)

What about the other solutions?

• Hmm, that gold looks sort of dark…• Absorbance on a spectrophotometer• Gold solution used T/R was significantly

darker (error in solution-making?)• Bridget re-made gold solution for W/F lab• Is this it??

Gold color didn’t disappear. Again. Now what?

• What about TBS? I mean, it’s a standard buffer, right?

• Apparently not. . .

Ionic Strength

General Equation: or

Biorad 1xTBS: pH = 7.5 0.020M TBS 0.5M NaCl

Rockland 1xTBS: pH = 7.5 0.1M TBS(HCl) 0.15M NaCl

Therefore,

IBiorad TBS = 0.518

IRockland TBS = 0.241

Qualitatively increased ionic strength results in:• Increased ionic charge shielding• Decreased ionic mobility (and diffusivity)

These factors should:•Decrease the ability of gold ions to penetrate CTAB bilayer• A high [NaCl] might lead to Na+ binding at p8