Project Perseus

  Analyzing DNA-mercury Nanoparticles with Scanning electron Microscopy In the last post I discussed how I used fluorometry experiments to investigate the binding dynamics of DNA and mercury ions. In this post, I'm going to talk about how we visualized the DNA - mercury samples via Scanning Electron Microscopy (SEM) to get more information on the structure and morphology of the particles formed by these interactions. As they say, a picture is worth a thousand words! Remember how I said that the DNA forms some kind of hairpin or secondary structure around the mercury ions? Well using SEM we were able to visualize these structures more closely and see how they behave! How did I Prepare the Samples for Visualization? These samples, especially samples containing biological material like DNA, cannot just be thrown into the microscope and visualized. If that happened, the DNA would actually be invisible because of its inability to conduct electrons, since the conductivity of electrons is...

Investigating DNA - Mercury Binding Interactions using a Fluorescent Dye In my last post, I demonstrated that using a fluorescent dye that can insert between DNA bases can help me learn more about the intricacies of the DNA - mercury binding system including binding stoichiometry and affinity! Let's get right into this very colorful biochemistry! What Dye did I use? I mentioned it briefly in my last post, but for these experiments, I used an intercalating fluorescent dye called Thiazole Orange. Intercalating just means that the dye is able to insert itself in between the bases of a DNA molecule. The rationale behind using this method is that as our single-stranded DNA molecules in solution encounter mercury ions, they form a hairpin structure or some kind of secondary structure around the mercury ion per our hypothesis. Thus, the ssDNA's own bases then loop around and become in close contact with each other. Close enough for this dye to attach.  But how does the insertion of th...

   Starting Data Analysis and Obtaining Fluorometry Data This past week I decided to finally sift through the crazy DLS data and see if I could shed some light onto what in the world is happening. I've included links to the google CoLab sessions I used to code everything up and I highly recommend taking a look at those if you're interested. However, I've also included some of the primary charts/graphs right here on this post as well. Let's get started! Starting DLS Data Analysis My first step in data analysis was to assemble all of the raw excel sheets I exported from the DLS instrument into one coherent data-analysis-ready file. I deleted some redundant data and/or data that didn't really make sense or add any value to my current circumstances (like time data and viscosity for example). I mainly focused on intensity, amplitude, PDI (polydispersity index), and a whole host of other things that go into calculating the hydrodynamic radius. I stored the whole file as a...

  Continuing to Optimize Dynamic Light Scattering Signal In the last post I made detailing my time as an undergraduate researcher at the University of Mississippi, I described some of the difficulties I was facing in regards to the Dynamic Light Scattering (DLS) instrument.  Well, the drama and the trauma only increased this week, but needless to say, I've learned a lot more about DLS than I would have if everything had worked out perfectly the first time.  So what happened this week exactly? Reducing the Signal-to-Noise Ratio Pretty much the name of the game this week was to limit the noise that the DLS machine was picking up on. There were a lot of things that went into this and first and foremost I'll start with what I left off with last time: trying a new sample well plate with opaque walls instead of clear ones. My thought was that this would reduce the high intensities and the highly variable signals that I was getting from just de-ionized water and buffer alone. So...

  Learning and Experimenting with Dynamic Light Scattering This past week at my Ole Miss REU research program has been...interesting to say the least. Not in a bad way, just in a I'm-going-insane-because-all-my-data-is-wacky-no-matter-what-I-do kind of way. The purpose of these experiments that I've been trying to do involves gaining data about the size and distribution of DNA/mercury complexes in solution. I outlined in my first post of this series how Dr. Wadkins has demonstrated that mercury complexes with DNA and induces it to form secondary structures. It's also postulated that these structures can be thought of as fully-fledged nanoparticles.  Dynamic Light Scattering (DLS) is a common way to obtain data about nanoparticles. Therefore, getting usable data from the DLS instrument from my DNA/mercury samples was my first order of business in order to develop an idea of how increased mercury concentrations correlates with particle size in solution. I thought it would be ...

Working with Acutely Toxic Chemicals is Always a Fun Time... The first part of the drama that has been unfolding with my research with Dr. Wadkins has been due to a nasty little chemical called mercury(II) perchlorate trihydrate. This inorganic mercury salt is going to be our source of mercury ions in solution for when we titrate it with the DNA solution to observe the effects of heavy metal ion intercalation of DNA base pairs and subsequent secondary structure formation. Of course everything in life is hard, right? And nothing ever goes to plan. At least I think that's a safe motto to live by especially in scientific research. So what was going wrong? Mercury(II) Perchlorate is Hygroscopic What does it mean to be hygroscopic? It essentially means that it absorbs water like crazy! When we opened the bottle of the mercury salt, we discovered there was a thick aqueous layer of water on top of the actual salt and that the salt was nearly cemented to the bottom of the bottle. I tried m...

  Starting my Summer Research at Ole Miss At the time of this writing, it is May 2025 and I have just moved into my apartment at Ole Miss, the affectionate nickname of the University of Mississippi. I was selected to participate in a summer REU (Research Experience for Undergraduates) program working for Dr. Randy Wadkins. His bio and research summary can be found on the previous link.  Dr. Wadkins and I met a couple days ago over lunch and we talked about politics, science and other subjects. After researching the man for several months, it was quite an experience to finally meet him in person, as if the picture in his biography suddenly came to life and began talking about all the science I had merely read about from my computer screen. He was much more relaxed in person than I thought he would be, which I thought was a pleasant surprise. Too many times, accomplished scientists come across as pretentious or that they're condescending to lower planes of intellect when they b...

  Introduction to Biochemistry on Project Perseus Welcome to the Biochemistry category on Project Perseus! Here. I will attempt to write interesting posts about the subject, including other sub-categories such as molecular biology, cell biology, and the like. You can expect me to write about the future of cancer research, medicine, philosophies of disease treatment, and other big-picture topics. I will, of course, write posts on subjects of a more niche and particular nature, but since I am young in my biochemistry academic and research career, I will simply refrain about writing anything that I currently do not understand.  With that, I hope you enjoy reading my content. Cheers! Where thoughts orbit stars and dreams power suns...