By week five enough of my materials had arrived to start experiments. I had obtained my gold nanoparticles and my PCR Primers, though not some specific thiol modified oligonucleotides. Just a recap, I’m working on a detection mechanism for Kaposi’s Sarcoma causing herpes virus based on changes in the optical properties of gold nano particles when they aggregate and are packed tightly together. By functionalizing the gold nanoparticles with two different oligonucleotides which are non complimentary and then introducing a third oligonucleotide which is complimentary to both the particles can be caused to aggregate. If this third oligonucleotide is from a virus such a scheme could be used to determine whether or not the virus is present.
Because the thiol modified oligonucleotides hadn’t arrived yet I started with regular oligonucleotides I had ordered with the same sequences which could be used for PCR. Using these PCR Primers I should be able to detect viral DNA using more conventional means and test whether or not my DNA sequences will actually detect KSHV and nothing else. DNA was extracted from two cell lines, one positive for KSHV and one not, and also from a mouse tail clipping. The DNA was prepared for PCR with my primers and the results were run through a gel.
The results came out positive; only the cell line positive for KSHV showed the PCR product while all other cell lines and a water control were negative. The product was the right size given the primers and was seen in both KSHV positive samples.
My clinical experiences continued on as normal this week and I observed more brain dissections and histology. Overall this was another successful week and I was happy to begin making real progress in my research.