IGEM:Harvard/2006/DNA nanostructures/Notebook/2006-7-21

Preliminary precipitation experiments

• Why precipitation? There are two problems with running a nanostructure and oligos together on a polyacrylamide gel with streptavidin. One is that it is unclear which band is which, although we believe that the slowest band (just below the well) is the nanostructure and the faster smear is the oligos. The other is that the presence of excess (unfolded) biotinylated oligos will compete with the nanostructure for oligo binding. Therefore, we should precipitate our nanostructures in order to a) determine which band are the nanostructures and b) prevent biotinylated oligo interference.
• Which precipitation protocol works best on our nanostructures? We should try all three of Shawn's protocols, and then run both the purified nanostructures, as well as the decanted supernatant, on an agarose gel to get a sense of purity/efficiency of each.