Week 2: Data Time!

Learning to use the ITC over the past week and a half has been a long process. At the beginning of the week, I got some pretty terrible results. Here’s a small selection from the many failures I encountered.

Over time though, the results slowly got better. The goal is to have a smooth “hill” formed by the injection peaks which returns to a flat baseline about halfway to two-thirds of the way through the experiment. Here’s a few my good data sets, which I was able to collect some good numbers from.

I was able to gather four pieces of data from this. The first is the binding energy, Kd. This is a measure of how strong the bond between two chemicals is. The next important number is the stoichiometry of the reaction, n. This represents the ratio of chemicals needed for the reaction to take place. Third, we have the change in enthalpy, delta H. This value is related to both the change in temperature and pressure/volume during the reaction. The last constant is the change in entropy, delta S. This is more or less a measure of the increase in disorder caused by the reaction.

The following graphs were obtained by plotting the area under each injection peak versus its peak number, and then fitting a curve to the data points. This gave us some very consistent results which were also pretty accurate. This is a good sign for future tests!

First week into the process of preparing nucleosomes

On Monday, Dr. Andresen and I began the process of preparing nucleosomes. We began with 50mL of chicken blood which if you’re wondering the reason behind why we use chicken blood, it’s because unlike our red blood cells, chicken red blood cells have nuclei that contain nucleosomes.

First off, Dr. Andresen and I began the process of preparing nuclei. We made 500mL of KTM buffer, which contains Tris HCL, KCl, MgCl2 and PMSF, and combined 50mL of it with the 50mL of chicken blood. Then we spinned that using a Centrifuge machine. The Centrifuge machine separates the heavier stuff (the pellet) from the lighter stuff (the supernatant) by increasing the gravitational force.Therefore, for the first couple of spins it helped us separate the red blood cells (the pellet) from the extra stuff that the blood contains such as plasma (the supernatant). Then, we resuspended the cells in KTM buffer and Triton X. The Triton X is like a “soap” which helps “break” the cells in order to release the nuclei inside of them. We had to do this because we want what’s inside of nuclei, the nucleosomes.

Tuesday, we had a discussion about unproductive and productive stupidity in STEM. Right after the discussion, I actually made a mistake and added too much of one solution to a batch of KTM buffer that I needed to use in order to finalize the preparation of the nuclei. Dr. Andresen realized that I did this once he noticed how hard the pellet (which contained the nuclei) was since it wouldn’t dissolve in the KTM buffer. Therefore, I had to start all over. I was frustrated at the fact that I had ruined a day of work but it actually helped me get over the fear that I had of messing up. It began my journey of understanding that research is a process of trial and error and that my mistakes will only help me learn and grow.

For the remainder of the week, Dr. Andresen and I went from having nuclei to having chromatin. When we had the nuclei, we measured how much DNA we had using the UV/VIS machine, which told us the concentration of DNA we had. We had about 125mg of DNA. Then, we resuspended the nuclei with CaCl2 + ML buffer, which contains Tris HCl, NaCl, MgCl2 and PMSF, and heated it at 37 degrees Celsius for 35 minutes. We heated this because throughout the process, the solution actually eats at the membrane of the nuclei which then breaks the nuclei and releases the DNA and everything else in the nuclei. Then, we continued by doing different steps in order to get the chromatin which consisted of making other solutions, spinning it, and letting it sit overnight with different solutions in order to get rid of the extra stuff such as ions and molecules surrounding the DNA.

As of today, Friday, we have chromatin, which consists of DNA linking nucleosomes together. Ultimately, what we’re trying to do is get the nucleosomes, which is an octamer wrapped around twice by DNA, so we’ll have to cut the DNA linking the nucleosomes in order to get the nucleosomes alone. Also, today we measured how much DNA we have, which is approximately how much chromatin we have. We have 37mg of DNA which is about 30% of how much we had last time we had checked. We are hoping to at least have half of this amount by the end. However, during our group meeting today I found out that the next step is where things have gone wrong in previous years. Even so, I am hoping to have some nucleosomes next week.

Week #1: The Nano ITC

This week I’ve been spending a lot of time working with the Nano ITC, so I thought I’d take some time to explain a bit about how it works. After all, this is what I’ll be using all summer!

Thar she blows! The Nano ITC in all its glory!

The Nano ITC, which stands for Nano Isothermal Titration Calorimeter, is a fun little box that can tell us all sorts of things about chemical reactions. In understanding what this instrument does, I find it useful to break things down word by word. First up is “Nano,” which means it’s pretty small. In fact, the ITC only uses about 350 microliters of sample per trial. That’s about .0006 times the size of a Venti cappuccino at Starbucks! This lets us use a lot less sample to get the same information.

A view down the barrel of the ITC. At the bottom you can see the openings of the two chambers. The one in the center holds our sample and the one on the right holds our reference.

The second word in the name is “Isothermal,” literally meaning “same temperature,” which is exactly how the ITC works. Inside this box of wonder are two chambers, which are held at the same temperature throughout the experiment. As the temperature of our sample changes, it is checked against a reference solution placed in the other chamber, and the machine adjusts its temperature so the two match. The ITC measures the amount of power it takes to keep these two chambers at the same temperature, which gives us our results.

This is the syringe that the ITC uses to inject one of our solutions into the other.

The third word in the name is “Titration.” This is a fancy chemistry word that basically means we’re adding one chemical to another. The ITC uses a syringe to slowly inject small amounts of a solution into our sample. This causes a chemical reaction which we can collect data about. Also, we don’t actually have to do anything after we start the machine, since the ITC does it for us! Finally, we have “Calorimeter.” This just means that the ITC measures information about the thermodynamics of whatever chemical reaction is happening in the machine.
Putting all this information together, we see that the Nano ITC is a device that lets us measure thermodynamic data about a chemical reaction between two solutions. It does this by measuring the power it takes to keep our sample and a reference at the same temperature, and it doesn’t even need that much solution to do it! And there you have it! That’s a basic run-down of the Nano ITC. It’s a really powerful tool that can give us a ton of useful information. Hope you liked the explanation, and I’ll be back next week with some results from this week’s testing!

First Week – Creating Nanoparticles

This week I started making gold nanoparticles (NPs) using two different methods, using citrate and CTAB surface coatings. The first is very easy to make, simply by heating up a gold solution until it boils and injecting trisodium citrate into it. This makes a red colored solution which contains the nanoparticles. The second method is much harder. The first step is preparing a “seed” solution that contains very small nanoparticles and then scaling these up in order to become bigger and easier to work with. Once the seeds have been made, they must sit for a few hours to grow and then the particles can be made by adding the seeds to a mixture of a gold solution, silver nitrate, and ascorbic acid. This is a very sensitive process, especially when adding the silver nitrate and ascorbic acid and can be messed up easily, which is what makes it difficult. However, if made correctly, the particles will be coated in CTAB and should be a red/pink color. The ones I made this week (two batches of 8 samples each) were relatively red/pink, but a few samples were purple/blue, which indicates aggregation (some of the particles have clumped together). This isn’t what I want, as I want the particles to be as separate as possible in order to continue with my work wrapping DNA around each particle. If the particles are clumped, the DNA won’t be long enough to wrap around and will cause problems with my experiments. I also made two batches of citrate-coated particles, which look a little redder than the CTAB ones.

Citrate-coated NPs. The middle is a nice red color, but the others are an ugly dark purple which indicates aggregation of particles.

When I ran my samples through the UV-Vis machine, which measures the absorption spectrum of the particles (how much of each color in the visible light spectrum is absorbed by the solution), most seemed decent, with a good solid peak of about 530 nanometers. This means that the particles are mostly absorbing green light / reflecting red light, which explains why the solution looks red. I had a few that absorbed way too much of other colors, so I’m not going to be using them to continue my research.

Absorption Spectrum from the first batch of CTAB-coated NPs.

I also ran my samples through a DLS machine which measures the size of the particles. Most of them were around 40 nanometers in diameter, which is a little on the large side, but it’ll still work – I’ll just have to correct for this when measuring how long the DNA should be. I had a few that were way too large, so I won’t use these either.

The last analysis that I did is called zeta potential, and this basically measures the charge on the surface on the particles. Almost all of my particles performed well in this test and had the correct charge on their surface (about 30 millivolts). This is all well, however, the most important test is the absorption spectrum measurement, so all of the ones that did not do well in that test I will most likely be trashing. Next week, I’ll start wrapping DNA around my particles and hope that all goes well – if not, I may need to create new particles.

Last Week

So last week Monday morning came around and Professor Thompson had been too busy to prepare gold nano-particles for me. This was fine, I was ready to tackle the task on my own. The procedure involves bringing 100mL of a solution up to a boil and then pouring 3mL of another solution into it. The solution then proceeds to change colors several times, its actually pretty neat to watch. I ended up making a pretty concentrated batch of nano-particles. It even ended looking pretty good under the UV-Vis, so I decided to continue on with my project using them. I needed to find a good ratio of NPs and PAH because the two are pretty fragile. If not mixed together properly they can immediately aggregate and make the solution unusable. Also, if they are not in the proper ratio this can also cause it to become aggregated and then unusable. So I tried to make a 3x and a 5x diluted NPs solution with normal concentrations of PAH. Both seemed usable after mixing. I then tried out the new cleaning procedure that Professor Thompson had suggested. I would spin the solutions at very high speeds, 9000 rxg and 7000 rxg in order to get all of the excess PAH out of the solution. This maximized our risk of contamination by stray PAH particles. My problem with this procedure arose when I had to wash the pellets with DNA in them. After I started this centrifugal process, I found that the solutions were creating pellets that were virtually non-existent. This is not good, as it is one of our main goals to get good pellets here. I was thinking that these pellets could not form because I had diluted the initial amount of NPs in the beginning. Professor Thompson suggested it had something to do with my spinning procedure for the DNA washes. I’m now currently trying this new procedure, which includes longer times and a larger rxg, to get better pellets in my solutions.

Continuation of Week 6

Is finally Friday! Well that doesn’t matter, what matter is what I have accomplish this week. In terms of work, I have accomplish  a great deal but in terms of progress I could had accomplish more. I say this because we got our results from Monday and we didn’t get the results we wanted… again. This is really frustrating but like I said last time, researching is about learning from our mistakes and improving upon them even if it takes multiple failures. Once we saw our results, professor Andresen and I came out with a new method to try out it order to see if we were doing our trial digestion correctly. Instead of using our chromatin, we instead used sonicated DNA with our trial digestion to see if we get different results in our gel. In order to do this we must first shred DNA and we would be left with a solution of liquid DNA.Then I added 50 micro-liters of sonicated DNA into two micro-centrifuge test tubes. Once this was done, I diluted the micrococcal nuclease to 100x dilution and also diluted CaC12 in order to add to our two samples. I added 0.5 micro-liters of micrococcal nuclease to one sample and to the other sample I added 2.5 in order to have two different lengths of DNA. Once this was done, I put both solutions in the heater for 15 minutes at 37 degrees Celsius and when this was done I did the same procedure as the previous trial digestions. In the end had two different samples to test in our gel, but I also made some extra samples such as DNA ladder and just the shredded DNA and the same samples with just added DI water. I added this solutions into our gel,  and when the results were ready, we again got the results which was more frustrated because it still didn’t work. The results can be seen in the next picture. Figure #1

Figure #1: Results from Gel

From this picture, we can clearly see that we can’t  see any base pairs from our samples, only from our DNA ladder which is located to the left. This is the problem that we have been getting on our past trials and from this picture, we think that all of our samples are staying in the beginning of gel. In other words our micrococcal nuclease is not separating our chromosomes.
After this process was done, professor andresen and I decided to do one more trial with the past solutions but this time, instead of making 3% agarose gel, we will be making 1% gel. What this would do, it would make us see the base pairs stuck at the top of gel from the previous samples. For this new trial, I will use two samples with out the proteinase K trial digestion and two other samples with the full trial digestion. Unfortunately when I was moving the agarose gel to the special the machine that was gonna give me my results, the gel felt apart and what this meant was that I needed to redo my work all over again. which I eventually did.
The next day I ran the gel and while I was waiting for the gel to be done I prepared another trial digestion that I will do next week. This new trial digestion consisted of time intervals of 5, 10, 20, 40, and 60 minutes and 1.6 micro-liters of 100x diluted micrococcal nuclease.
Once the gel was done, I look at the results and they were a little better than previous results but it still didn’t show the base pairs that we want it to see. We are hoping that next week with this new trial digestion, we will be able to see the results we want to see. Its a struggle keep seeing how our trials always fail but even though its slowly, we are making progress and we will be able to find what is causing our results.

End week six

The last run of samples was supposed to be our most promising samples yet. It had looked like we were going to get not only quality data but in a large quantity as well. Unfortunately, something had gone awry. When we start with out citrate nano-particles they should be negative in charge, then we wrap them in PAH and they switch to positive charge, and then finally we wrap them in DNA and they switch charges a final time, back to negative. My first two Zeta tests were conclusive and yielded the expected results, however the final one simply doubled the number and did not switch the charge at all. Professor Andresen phoned a friend and we then scheduled a conference with Professor Thompson. Before we could have this conference however, I first had to prepare a power point presentation on my most recent bit of research. Dr. Thompson broke down several of the data pieces I am so accustomed to collecting and helped me better understand them. The UV-Vis is a lot more helpful then I know it to be, but I really need to learn how to overlay graphs on it, I am determined to learn this early next week when I have to use the machine again. The conference left me feeling very hopeful about the project. On Monday Professor Thompson is going to prepare more nanoparticles for me to use in my next batch of samples. He also suggested a much more appropriate way of preparing the PAH wrap and how to more properly purify them. I am hopeful that this will greatly improve the project. At the end of this week, I am wrapping it up by shearing DNA and looking forward to finally getting proper data next week.

Week six

So at my last post I had just found an appropriate mix of salts and nano-particles. This allowed me to then mix in my DNA and start performing equilibrium dialysis. However, I immediately ran into another big problem. What was I to re hydrate my solutions with? In the past, at this step I was not using citrate nanoparticles, but I was re hydrating with TEM buffer. I was uncertain if this would be efficient with these new particles. I decided to head to the science center and discus this problem with Rich, a fellow user of similar nano-particles. We threw a few ideas back in forth, but nothing seemed like an exceptionally good idea to re hydrate with. So I had to make a sacrifice, I gave up any hope of getting to use the ICP-OES this run in order to figure out what to re hydrate my samples with. I split my total solution of nano particles into three parts, one would be re hydrated  with mili-Q, another with TEM buffer, and a third with a solution that was 10^-2 M NaCl. Unfortunately I was only re hydrating with 4mL each when I typically do double that. Regardless, the results appeared to be conclusive, showing that the salt buffer worked the best.

So then I had to restart once again. This time, I took all of my gold nano particles and coated them with PAH. I then spun them in the centrifuge for an increasingly long period of time to siphon out the supernatant and continue spinning that. Finally, I recombined the pellets and diluted it back to 7mL with more nano particles. So I’m left with 1 super concentrated gold nano particle sample and 7 other slightly less concentrated samples. They were then all mixed with DNA and left to sit over night. Now I am currently trying to perform equilibrium dialysis, and hopefully after doing this I’ll finally be able to use the ICP-OES.

End of fifth week already?

Time surely flies by when you’re working full on. This week, I started working on another batch of ITC experiments after we figured out a number of flaws in our experimental protocols. Therefore, we decided to redo some of our previous experiments using different experimental parameters and protocols.
We decided that we would keep the relative concentrations of DNA and Cobalt Hexammine unaltered in the different ITC runs. The concentrations of DNA and Cobalt Hexammine used in the experiments were 2.5mM DNA+3mM Cobalt Hexammine, 5mM DNA+6mM Cobalt Hexammine, 10mM DNA+12mM Cobalt Hexammine. In addition, we decided to alter the experimental procedure a tad bit. We decided to form isotonic DNA+NaCl solutions using the dialysis method so that the concentrations of NaCl in all the samples are equal. The dialysis buffer was used for the serial dilution of the 120mM stock Cobalt Hexammine (instead of water as in the previous experiments).

After I prepared the batch of DNA samples (of different concentrations) using the regular method, I filled up dialysis tubes with 10ml of each sample. I left the tubes in a dialysis buffer of 10mM NaCl solution overnight. I used the same dialysis buffer for the serial dilution of the 120mM stock of Cobalt Hexammine in order to synthesize 10ml of 12mM,6mM and 3mM solutions respectively.

After the synthesis of the DNA samples and the Cobalt Hexammine solutions, I ran heat of dilution tests on the Cobalt Hexammine samples. Here are the results:

After running the heat of dilution experiments, I proceeded to start ITC runs with my DNA samples. I started off by using my 10mM DNA sample. Here’s the overlay for the raw heat data and the integrated heat data:
That’s all the highlights from week 5 folks. Stay tuned for more ITC results next week!