The goal this week was to clean all of the unbound DNA out of a stable DNA-nanoparticle solution so that we can quantify the amount of DNA per nanoparticle. Due to the results we saw last week we used 10 ug/mL DNA in the same 0.3 nM CTAB gold nanoparticles. The protocol we came up with was to spin down the nanoparticles and then do 3 washes with TE+10mM NaCl followed by 2 washes with pure water. While doing this I encountered some aggregation and incomplete pelleting. The aggregation was reduced after each spin indicating that the spinning was clearing out any unstable particles from the solution. The incomplete pelleting was combated by spinning the collected supernatant 1-2 extra times and collecting the extra pellet and a hopefully clean supernatant. The result of this protocol modification was 3 times as many spins. Each spin took 40 minutes so the protocol took two very long days to complete. The result was two DNA-nanoparticle samples a sample washed by salt-TE buffer and water and a sample washed only with salt-TE. More aggregation was seen after adding cleaning with the water indicating that either the salt or the TE buffer is integral in maintaining the stability of the nanoparticle complexes.
I was going to start measuring the samples in the ICP but we were out of the argon and nitrogen gas. Instead I made 7 more sheared DNA samples, ran UV-vis on them and attempted to run them in an agarose gel. The UV-vis showed normal DNA spectra with DNA concentrations between 0.3-0.6 mg/mL. The agarose gel did not work and will need to be done again next week.