[Hydrodynamics] Monday's hands-on lecture

[Borries Demeler]

Everyone,
On Monday, 2/12, we will meet first in SA7230 and go over the AUC project
we will set up in the lab, and then walk up to Quad 1 on Level 9.
Because we are a bit time limited, please make sure that everyone is on
time, and ready to do some lab work. If you have your own lab coat, please
bring it. If you don't have one, we can loan you one. The project we will
do on Monday is as follows:

1. using 2 spectrophotometers, we will first blank each spectrophotometer
with water and then measure the absorbance of our buffer
2. After blanking with our buffer, we will make a 0.8, 0.6, 0.4, and 0.2
dilution of a 1 OD260 nm DNA sample and a 1 OD280 nm protein sample. All
measurements will be recorded.
3. Next, we will show you how to assemble and disassemble an AUC cell. You
will get to do your own cell.
4. Once each of you has an assembled AUC cell, we will load both channels
with water (for practice).
5. One of the cells will be loaded with a 1:3 ratio of protein:DNA in one
channel, and a 3:1 ratio of protein:DNA in the other channel.
All lab work will be assisted by Sophia, Zach, Liam and Reece. You will
work in a group:

Sophia: Fatimah and Matt
Reece: Kate and Kenning
Liam: Anneke and Vinu
Zach: Uvi and Hanna

We will then set up the AUC run and run it overnight. On Wednesday we will
go over the data acquisition and analysis of the data, and you will use the
intrinsic extinction spectra to deconvolute the protein and DNA signals in
both samples. There will not be a homework on Monday, but there will be one
on Wednesday:

As homework, you will take both dilution sets and derive an
intrinsic extinction curve for both protein and DNA, and report the fitting
RMSD. Then you will analyze the two multi-wavelength datasets and report
DNA and protein ratios measured and determine if these molecules form a
complex.
I will upload all data to our download archive once they are available.

Please reply to this e-mail if you have any questions or comments.

-Borries
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