User:Brigette D. Black/Notebook/Brigettes Notebook/2009/10/31/Further-ly Optimized Bulk Ideas

Try maybe two or three times as many MTs (4.213 uM) and the same concentration of kinesin (1: 12.6 ratio).


 * Gilbert:
 * 12uM tubulin
 * 0.2 uM Kinesin


 * Last Assay:
 * 1.51 uM tubulin
 * .33 uM kinesin

Last time, 3 uL produced (1.0666*10^-9) mols Pi which implies that the same number of moles of ATP were used per sample, or about (2.666 *10^-8) mols for the entire system. (2.666*10^-8 mols/ 75*10^-6 L = .356 mM used). To be on the safe side, let's use at least 2mM ATP.

Idea: Super PEM-T (2.37x as much taxol as regular PEM-T). Why? I have realized that diluting the reactions too much has lead to nothing but heartache and bad data. So if I am going to use more MTs, I don't want to end up over-diluting the reaction. Also, if I simply add 2.37 times as many MTs, I will have to add about 2.37x as much of everything else to accommodate for the volume change. So, less diluted, less kinesin, more rocking.

MT+ ATP concoction

 * (3uL each, make 25 uL extra total)
 * Total Volume needed: 100 uL


 * ATP :
 * 10uL (one aliquot) => 10 mM ATP (seems well over what is needed but still over what I think the malachite green + spectrophotometer can resolve well).


 * BME: 3 uL


 * MTs: 87 uL MTs (5 uL tubulin + 82 uL Super PEM)
 * 5.22 uM "Stock"
 * 4.514 uM in solution


 * Total volume: 100 uL

Save 25 uL to measure autohydrolysis. To this 25 uL, add 1.67 uL PEM (to keep concentrations the same as that in the reaction). 3 uL to 37 uL PEM in cuvette, develop and measure normally. (Makes 4 duplicated points)

Reaction

 * 70 uL MT+ATP (4.213 uM MTs + 9.333 mM ATP + 2.8 uL BME)
 * 5 uL kinesin (0.333 uM)


 * (ATP Background: 0.7 mM)

Add 3 uL reaction to 37 uL PEM. Develop and measure as usual. Makes 12 duplicated measurements.

Time Ideas

 * 0 min MTs+ATP
 * 30 min MTs+ATP
 * 60 min MTs+ATP
 * 90 min MTs+ATP


 * 0 min Reaction
 * 2 min Reaction
 * 4 min Reaction
 * 6 min Reaction
 * 10 min Reaction
 * 15 min Reaction
 * 20 min Reaction
 * 30 min Reaction
 * 45 min Reaction
 * 60 min Reaction
 * 75 min Reaction
 * 90 min Reaction

SUPER PEM-T

 * 2.37 uL 100 uM taxol per mL (make 1 mL to be safe). Add 997.6 uL PEM.