Friday, June 10, 2016

First Post of 2016! June 10th, 2016

Summer research kicked-off this week for both Savannah and I, as we began to work on new experiments. I focused on two projects this week: analyzing data that Abby took during the summer of 2014, and doing preliminary reading on nucleosome core particles (NCPs). I will be working on both projects throughout the summer.
                The data Abby took in 2014 is very similar to the data I analyzed last summer, except there was ion competition between a monovalent and a trivalent cation charge neutralizing a hexagonal array of DNA (as opposed to divalent and trivalent). Abby had already computed the average concentrations of each element in the samples, and I was just compiling the data into graphs (see below). Problems with this such “raw analysis” of the data is evident though: the total cation-to-anion charge ratio easily exceeds one. This problem arises because the trivalent ion dissociates into a divalent ion in high chloride concentrations, which is not taken into account in the graphs below. But evening knowing the dissociation constant, simple chemistry cannot be done to determine the respective concentrations of the divalent and trivalent cations because trivalent ions favorably bind to DNA. Therefore, more theoretical work must be done to understand the system.
                Primarily throughout the summer, I will be working on the nucleosome core particle experiment. Last summer, Abby set the foundation by writing a procedure to make the NCPs, and doing some preliminary experiments with them. I plan to build off Abby’s work by improving the NCP procedure and doing more experiments with them. This week, I read and tried to understand her procedure, and hopefully next week I will start making the NCPs!

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