User:Nicole Bonan/Notebook/Chem 571 Lab Notebook/2015/10/13

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Objective

The purpose of today's lab was to measure the fluorescence of alpha-chymotrypsin blanks and AuNP fiber samples with 1µM alpha-chymotrypsin. Our goal was to determine the rate of AuNP fiber degradation by 1µM alpha-chymotrypsin.

Protocol

  1. We made a 1mL stock solution of our protease, alpha-chymotrypsin, by adding 1mL of 50mM phosphate buffer (pH=8) to one of the stock masses of alpha-chymotrypsin that we weighed out earlier in the semester. The final molarity of this sample was 47.656µM.
  2. We prepared AuNP fiber samples:
    1. We used the samples that Dr. Hartings synthesized on October 12. We had seven AuNP samples total, one for each incubation time that we were interested in:
      1. 10 min
      2. 15 min
      3. 30 min
      4. 45 min
      5. 1 hour
      6. 1.5 hours
      7. 2 hours
    2. We spun all the fiber samples down at 300 RPM for 10 minutes and pipetted off as much supernatant as we could.
  3. We calculated how much alpha-chymotrypsin stock and phosphate buffer we would need to add to each sample and blank. (Our goal was to make one AuNP fiber sample and one alpha-chymotrypsin blank for each of the incubation times listed in step 2. All of these solutions would have a concentration of alpha-chymotrypsin of 1µM. All solutions would be brought up to a total volume of 1mL using phosphate buffer).
    1. To determine how much of our stock of alpha-chymotrypsin we needed:
      Let
      M1=concentration of alpha-chymotrypsin stock=47.656µM
      V1=volume of alpha-chymotrypsin stock we need to add to the AuNP fiber sample
      M2=final concentration of alpha-chymotrypsin in the AuNP fiber sample=1µM
      V2=final volume of alpha-chymotrypsin sample=1mL
      M1V1=M2V2
      V1=(M2V2)/M1
      V1=[(1µM)(1mL)]/(47.656µM)
      V1=0.212mL=21.0µL
    2. We then subtracted the volume of alpha-chymotrypsin stock we needed to use (21.0µL) from the total volume of the solution (1mL, or 1000µL) in order to determine the volume of phosphate buffer to add:
      1000µL-21.2µL=979.0µL of phosphate buffer
  4. We added the calculated volumes to the samples and blanks. We put all of the samples and blanks into the 37 degree Celsius water bath, except for the 10 minute sample and blank, for their respective incubation times. We were careful not to disrupt the AuNP fiber pellet as we were adding each component, as we were trying to avoid breaking the fibers.
  5. As each sample and blank finished incubating, we:
    1. Spun down the AuNP fiber sample (but not the blank) at 12,000 RPM for 1 minute
    2. Combined, in a 600µL Eppindorf tube, the following:
      1. 20uL of the blank or sample
      2. 140uL of Assay Buffer
      3. 40uL of Assay Reagent
      4. Measured the fluorescence with an excitation wavelength of 390nm and an emission spectrum from 400 to 650nm
  6. We then repeated steps 4-5 for the 10 min sample and blank.

Data and Analysis

Figure 1: Raw Data: Fluorescence of alpha-Chymotrypsin Blanks as a Function of the Wavelength of Incident Light (nm)
20151101 1013 01 fluoresc blanks.png

The figure above shows the raw data for the fluorescence of the alpha-chymotrypsin blanks as a function of the wavelength of incident light. The different curves on the graph represent different incubation times, as indicated by the legend.


Figure 2: Raw Data: Fluorescence of AuNP Fiber Samples as a Function of the Wavelength of Incident Light (nm)
20151101 1013 02 fluoresc samples.png

The figure above shows the raw data for the fluorescence of the AuNP fiber samples, which incubated with alpha-chymotrypsin, as a function of the wavelength of incident light. The different curves on the graph represent different incubation times, as indicated by the legend.


Figure 3: Fluorescence Intensity of the alpha-Chymotrypsin Blanks and the AuNP Fiber Samples as a Function of the Incubation Time (min)
20151101 1013 03 fluoresc intensity both.png

The above figure shows the fluorescence intensity of both the alpha-chymotrypsin blanks (in blue) and the AuNP fiber samples (in red) as a function of the amount of time that the solutions were incubated. The fluorescence intensity was determined by doing the following:

  1. I corrected the alpha-chymotrypsin blanks for instrumental noise by subtracting the fluorescence for the last 0.5nm from all of the other fluorescence measurements for each blank
  2. I did the same correction for instrumental noise for the AuNP fiber samples
  3. I integrated the area under the fluorescence curve for each blank starting at 420nm. This gave the fluorescence intensity of each blank.
  4. I integrated the area under the fluorescence curve for each sample starting at 420nm. This gave the fluorescence intensity of each sample.
  5. I graphed both integrations

Interestingly, both the blanks and the samples seemed to reach a maximum fluorescence intensity at an incubation time between 30-45 minutes. The fluorescence intensity then decreased sharply for the blanks and then began to level off. The same pattern was observed in the AuNP fiber samples, though the drop in intensity was not as steep.


Figure 4: Fluorescence Intensity of the AuNP Fibers+Peptides as a Function of the Incubation Time (min)
20151101 1013 04 fluoresc intensity peptide.png


The above figure shows the fluorescence intensity of the AuNP fibers+peptides as a function of the amount of time that the solutions were incubated. The fluorescence intensity was determined by subtracting the fluorescence intensity of the alpha-chymotrypsin blanks from that of the AuNP fiber samples. This effectively subtracted out any fluorescence intensity in the fiber samples that would have been from the alpha-chymotrypsin, giving only the fluorescence intensity of the intact AuNP fibers and the chymotrypsin-digested AuNP fibers (peptides).


Figure 5: Concentration of AuNP Fibers+Peptide (mg/mL) as a Function of Incubation Time in alpha-Chymotrypsin (min)
20151101 1013 05 conc.png

The above figure shows the concentration of the AuNP fibers+peptides as a function of the amount of time that the solutions were incubated. The concentration of the AuNP fibers+peptides was determined from the data in Figure 4: these data points were divided by the slope of the calibration curve from September 30 (figure 4), which was 475965. This converted the fluorescence intensity to the concentration of AuNP fibers+peptides.