[Demelerlab] AUC Collaboration: Sizing Amyloid Beta derived Oligomers

Tue Jul 25 13:36:04 MDT 2023

I reran the UV-vis spectra of water + 0.1% TFA, 1 mM F19Cha, 3 mM F19Cha,
and 9 mM F19Cha all blanked against water and it worked much better this
time. The TFA absorbs negligibly above ~220 nm and absorbs weakly compared
to that of F19Cha. To get a 0.6 absorbance in a 3 mm centerpiece for the 1,
3, and 9 mM samples with less than 0.3 background absorbance, I would
recommend 268, 278, and 279 nm respectively. I'm open to adjusting the
wavelengths as you see fit. I've attached the Excel for the spectra below.
I think the reason why I got negative absorbance last time was because the
nanopure water that I was blanking with had some quality control issues.

Please feel free to reach out if there's anything you need from my end!

Best,
Jason
[image: image.png]

Best,
Jason

On Fri, Jul 21, 2023 at 10:47 AM James S. Nowick <jsnowick at uci.edu> wrote:

> Wonderful! Thanks, Bruce!
> James
>
> On Jul 21, 2023, at 10:21 AM, Bowler, Bruce <Bruce.Bowler at mso.umt.edu>
> wrote:
>
> Hi Borries,
>
> The samples arrived about an hour ago and are in my -20 freezer.
>
> I will mostly be around my lab until about 2:45 pm today.
>
> Cheers,
> Bruce
>
> *From:* Borries Demeler <demeler at gmail.com>
> *Sent:* Wednesday, July 19, 2023 9:26 PM
> *To:* Jason Zhu <jasonz13 at uci.edu>
> *Cc:* James S. Nowick <jsnowick at uci.edu>; Henrickson, Amy <
> amy.henrickson at uleth.ca>; demelerlab at biophysics.uleth.ca;
> maduni.ranasinghe at uleth.ca; Bowler, Bruce <Bruce.Bowler at mso.umt.edu>;
> Frederick, Ariel <ariel.frederick at umconnect.umt.edu>
> *Subject:* Re: AUC Collaboration: Sizing Amyloid Beta derived Oligomers
>
> Perfect! Thanks so much, and thanks to Bruce for handling our samples, I
> will check in with you during the morning session of our workshop. Amy,
> please remind me in case I forget.
> Thanks, -Borries
>
> On Wed, Jul 19, 2023 at 9:24 PM Jason Zhu <jasonz13 at uci.edu> wrote:
>
> Hi Bruce, Ariel, and Borries,
>
> The peptide (F19Cha) should ship tomorrow (Thursday) morning and arrive
> before 10:30 am on Friday. I've attached the shipping label and
> instructions for how much water to add to make 1, 3, and 9 mM samples.
>
> Best,
> Jason
>
> On Wed, Jul 19, 2023 at 11:59 AM James S. Nowick <jsnowick at uci.edu> wrote:
>
> Hi All,
>
> The bottom line is that the absorbance of trifluoroacetate should be
> negligible with respect to the peptide. The peptide absorbs so strongly at
> 214 nm that you will need to go to longer wavelengths. Alternatively, I
> think interference optics might be a good option.
>
> Best,
> James
>
>
>
> On Jul 18, 2023, at 7:57 PM, Jason Zhu <jasonz13 at uci.edu> wrote:
>
> Hi Borries and James,
>
> I tried running different TFA concentrations on the nanodrop and got very
> noisy UV-Vis spectra that I don't fully trust. I enabled the automatic
> baseline correction and automatic pathlength adjustment settings on the
> nanodrop which seems to have helped with the negative absorbance values
> that don't make physical sense. I will meet with James tomorrow morning and
> will work out the details of getting accurate absorbance values for both
> TFA and F19Cha then.
>
> <image.png>
>
> I plan on weighing out the peptides, labeling them, and shipping them by
> the end of the day Wednesday (tomorrow). I'll send an update once we figure
> out the ideal wavelength for the different concentrations we plan to run at
> each concentration and when the peptide is on its way.
>
> For lyophilized powder, 4C should be adequate. F19Cha isn't prone to
> oxidizing from my experience working with it.
>
> Best,
> Jason
>
> On Tue, Jul 18, 2023 at 2:38 PM Borries Demeler <demeler at gmail.com> wrote:
>
> Hi Bruce and Ariel:
> We would like to have some samples shipped to U of Montana, and I would
> like to pick them up on Friday, if this is possible? The samples are
> lyophilized peptide samples and can probably be stored at 4C. I will be in
> Missoula on Friday  and Saturday, all day, our entire lab will actually be
> in Missoula for a vaccine development workshop with the CTM group. Thanks
> for helping again with the samples!!
>
> James and Jason:
> Regarding the sample shipment, you can overnight them as a
> lyophilized powder to:
>
> University of Montana
> Dept. of Chemistry &Biochemistry
> c/o Bruce Bowler or Ariel Frederick
> 23 Campus Drive
> Missoula, Montana 59812
>
> Please weigh them out and indicate on your shipping list with what volume
> they need to be suspended to get the desired concentrations. Our loading
> volume will be 110 ul, and we would like to know the wavelength to use
> where we would get 0.6 OD in a 3 mm pathlength centerpiece, with no more
> than 0.3 OD of background absorbance from the buffer (when blanked against
> water). We can use different wavelengths for each sample to optimize the
> absorbance for each concentration.
>
> The speed will be 60 krpm, so they should be measured in the An60Ti rotor,
> at 20C.
>
> Please ship so they will be available for pickup by us on Friday this
> week. Please indicate the storage conditions - I assume for the lyophilized
> powder 4C is adequate?
>
> Thanks, -Borries
>
>
> James S. Nowick
> Distinguished Professor
> Department of Chemistry & Department of Pharmaceutical Sciences
>
> Department of Chemistry
> 4126 Natural Sciences 1
> University of California, Irvine
> Irvine, CA 92697-2025
>
> Phone:  (949)  824-6091
> e-mail: jsnowick at uci.edu
> Faculty Web Page: http://tinyurl.com/jsnowick/
> <https://urldefense.com/v3/__http://tinyurl.com/jsnowick/__;!!CzAuKJ42GuquVTTmVmPViYEvSg!N1pni7MvQC2b2B8UkuEuyJfTSy3SNOX8O3u82A0rJS42kQP5CMvnPCF331ntQaU-5VV5CG3ejXgg-gw0D2sQwB0-qA$>
> Research Group Web Page: http://tinyurl.com/nowickgroup/
> <https://urldefense.com/v3/__http://tinyurl.com/nowickgroup/__;!!CzAuKJ42GuquVTTmVmPViYEvSg!N1pni7MvQC2b2B8UkuEuyJfTSy3SNOX8O3u82A0rJS42kQP5CMvnPCF331ntQaU-5VV5CG3ejXgg-gw0D2ux34kS7g$>
> Pronouns: he/him/his
>
>
> James S. Nowick
> Distinguished Professor
> Department of Chemistry & Department of Pharmaceutical Sciences
>
> Department of Chemistry
> 4126 Natural Sciences 1
> University of California, Irvine
> Irvine, CA 92697-2025
>
> Phone:  (949)  824-6091
> e-mail: jsnowick at uci.edu
> Faculty Web Page: http://tinyurl.com/jsnowick/
> Research Group Web Page: http://tinyurl.com/nowickgroup/
> Pronouns: he/him/his
>
>
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