Scarlett S. Senior Project
Advisor: Mr. Anoop Patel
My research project involves manipulating samples that contain droplets made of a soap-like material suspended in a buffer solution, with DNA attached to the surface of the droplets that allows them to bind to each other at certain temperatures. By adding a magnetic fluid to the droplets, we can manipulate the droplets into aligning into long chains under a magnet, instead of clumping into aggregates. Furthermore, by varying properties of the droplet solution such as the concentration of droplets or the concentration of magnetic fluid, we are able to observe how different circumstances lead to differences in chain formation and average chain length, and eventually we will be able to better control the length and distribution of the chains we form. This will help aid an existing algorithm that allows for programmable chains that fold into specific geometries in a way that mimics the biological folding of proteins.
Project Blog
Week 1: Senior Project Week 1 (4/2-4/5)
This week was my first week working at the NYU Center for Soft Matter Research. On Tuesday, my first day, I was given a tour of the facilities and introduced to the work that each of the team members was doing. I also learned more about the specific project I would be working on, which involves creating droplets out of a soap-like substance and coating them with different types of DNA, then examining how the droplets interact with each other and what shapes they form. Specifically, we decided to try and create long chains of droplets that are a single droplet wide.
On Wednesday, I still didn’t have the lab training I needed to be able to perform experiments myself, so I observed as the team member I was working with showed me how to prepare the droplets that we would be examining. This process involves mixing two types of DNA with a buffer solution in 2 different tubes, and also incorporating two types of fluorescent dyes so that the droplets would be visible and distinguishable under a microscope. I was also taught how to use the microscope, which shows the droplets as a sea of blue and yellow bubbles that form chains and other shapes, and also takes time-lapse videos of the droplets forming the chains.
In order to manipulate the binding of the droplets, a couple of steps need to be taken. First, the temperature of the sample needs to be heated to around 50 degrees Celsius in order to break apart all of the bonds between the droplets, and then the droplets need to be forced into a linear alignment by a magnet, and then the sample can be cooled, allowing the droplets to rebind, but in a more linear structure, allowing long chains to be formed. Repeating this process over and over allows for different ways to create long chains to be explored.
On Thursday, we continued experimenting with the droplets, which is when we discovered a problem. In order to ensure that most of the droplet chains are only a single droplet long, the valence, or number of possible binding sites, of the droplets needs to be minimized. This is done by reducing the concentration of DNA mixed into the droplet sample. The problem with this is, in a sample of droplets, there is always a risk of two droplets merging together, or coalescing, and this risk becomes greater the less saturated the droplet surface is with DNA. Essentially, a sample full of droplets that has coalesced is unusable, so we decided that, in the future, we should add more types of DNA to the surface, but make it DNA that cannot bind to DNA on other droplets in the sample. I was also able to complete my lab training on Thursday.
On Friday, most of the morning was spent in a group meeting with the other members of the team. Although it was briefly interrupted by the earthquake, I got to hear even more about the work that other team members were doing, which was very interesting. I also received some valuable feedback on my project, which included a suggestion to instead of trying to maximize the length of the droplet chains, focus on creating chains of random sequences and examining the subsequent folding structure after removing the magnet. With this in mind, we did some more experimenting with droplet sequences under the microscope before heading home for the weekend.
Week 2: Senior Project Week 2 (4/8-4/12)
After receiving my lab training and observing the proper protocol for preparing the droplet solution and observing the droplets under the microscope, this week I was finally able to begin conducting experiments on my own. I started out this by week creating a test sample with the two-flavor droplets, diluting them each 10 times in the buffer, and running experiments under the microscope by heating the droplets to 50C, aligning them with a magnet into chains, and subsequently cooling the droplets to room temperature and removing the magnet to watch the droplets fold.
After I was sure I was familiar enough with this experiment design and protocol, we developed a game plan for what exactly our study would look like so I knew exactly how to design the experiments in the future. We decided we would be working with a single flavor of DNA, a palindrome sequence that binds with itself. We would keep the concentration of DNA on the droplets constant, and vary the volume fraction, or concentration of droplets in the buffer. Under the microscope, we would then repeat the same procedure of heating and aligning the droplets, and examine how the average chain length and time until steady state (a state where droplets are no longer actively forming chains) varied with volume fraction.
With this experiment design in mind, the team and I began examining the behavior of droplet samples with different volume fractions. By the end of the week, we had studied the behavior of droplets diluted 4x and 16x, and found that these seemed to be the approximate upper and lower bounds of concentrations that adequately made chains. 4x diluted droplets made very long chains, but were slightly too crowded in the sample and were beginning to form aggregates, and 16x diluted droplets were only able to make chains that were 3-5 droplets long. I am excited to see what more progress we make in the coming weeks with more samples of varying volume fractions.
Weeks 3-4: Senior Project Week 3 & 4 (4/16-4/26)
I have combined the blog post for this week and last week because I was only able to go into the lab for 2 days last week because of travel plans. I started the week of the 16th by preparing 4 batches of droplets with different volume fractions: One batch had droplets diluted twice in the buffer, one four times, one six times, and one eight times.
I kept the concentration of ferrofluid (the liquid that causes the droplets to align into chains under the magnet) constant, and over two days, cycled through heating the droplets, aligning them, cooling them, and removing the magnet to allow them to fold several times for each batch, while taking motion picture videos to allow me to gather data on the chains.
The next week, I maintained a similar experiment design, but this time varied the concentration of ferrofluid in the droplet solution, to observe how it affects chain formation and the average chain length of a sample. For this process, I made sure to keep the amount of time I kept the droplets at each step constant so that I would have accurate results.
I heated the droplets to 50C for 5 minutes, aligned them at 50C for 5 minutes, cooled the droplets to room temperature under the magnet for 10 minutes, kept them under the magnet at room temperature for 7 minutes, and removed the magnet, allowing them to fold for 5 minutes, and took separate videos of each step.
This phase of the experiment will continue on to next week, but so far, we have data on the average chain lengths at different ferrofluid concentrations that another member of the team was able to analyze, and I was able to present my findings at the weekly group meeting, so I am excited to see what other trends we begin to see as I repeat this process with varying concentrations.
Week 5: Senior Project Week 5 (4/29-5/3)
Last week's experiments found that changing the ferrofluid concentration had interesting effects on the rate at which the droplet chains began forming, so we decided to continue exploring that this week.
During the entire week, I tested samples with ferrofluid diluted 4 and 8 times. Instead of only aligning the droplets for 5 minutes and then cooling and folding them, I kept the sample at 50C for a full hour. This way, I could determine if/when the droplets reached a steady state where they no longer formed chains.
What we initially found by creating graphs with computer analysis of the images is that the samples with lower ferrofluid concentration formed chains at a slower rate than those with higher ferrofluid concentration.
Performing these experiments to gather enough data will be what I am focusing on for the next couple of weeks, so these blog posts may not have as much content as the previous weeks, where I was still being introduced to the lab and was designing the experiments.
Week 6: Senior Project Weeks 6, 7, 8 (5/6-5/23)
Apologies for the lack of blog posts! Throughout these past few weeks, I continuously performed experiments with the droplets where I varied either volume fraction or ferrofluid concentration and allowed the droplets to align at 50C for an hour, in order to determine the optimal conditions for creating chains of a certain length. Because of this, I haven't had many results to share as my time has mainly been focused on data collection.
With the help of a computer algorithm created by another member of the team, we began creating several graphs based on the videos of the chain alignment that showed values such as average chain length and average coordination number of droplets in a sample.
After identifying the optimal conditions for chain growth, I began exploring what could be done with these chains. An experiment I have begun performing involves aligning long chains in one direction, then cooling them and allowing them to fold, and then realigning them in the other direction in order to force the chains to begin turning and creating a spiderweb-like formation. This is something that I am still working on optimizing, but in the meantime, it creates some very interesting-looking videos!
Week 9: Senior Project Week 9 (5/26-5/31)
Unfortunately, my time at the lab will soon be coming to an end. This meant that I began to shift my focus from performing experiments and collecting data to analyzing the data and formulating my final presentation.
I only used the microscope once this week to redo the “spiderweb” chain alignment in order to get a clearer video to show during my final presentation. The rest of the week was spent sorting through all of the microscope videos and uploading ones that were of interest onto my computer so that I could include them in my presentation, and brainstorming with members of the team the narrative my presentation should follow.
Next week, I will spend all five days putting it all together into an amazing presentation that showcases all the work I have done these past two months!