Fresh Wallaby Juice

Finished the first draft of the paper. At last. No idea how many changes my advisor’s going to want, but at least now I’m editing instead of writing from scratch – even when that turns into rewriting a paragraph, it’s amazing how much easier that *seems*.

Seminar today was Weihong Tan (of Florida), talking about DNA aptamers as molecular beacons. Mostly molecular beacons in general – that’s his thing and he’s sticking to it. Huge group, too, looked like the photo had 25+ people. He was one of the ones I would’ve considered as an advisor if I’d gone to UF for grad school, so it’s kind of interesting to ponder as a “what-if”. The work on developing massive libraries of aptamers for labeling cancer cells is interesting, although it’s pretty clearly in-progress.

However, seems like this would be mostly useful for searching the domain of all possible aptamers for key binding elements. Instead of assembling 25 bases at random, it’d seem rather better to identify a couple dozen sequences that are commonly found in “successful” aptamers, and then randomly(?) recombine two or three of those at a time to achieve really high binding affinity and specificity. Or just to start modeling what sort of cell-surface proteins these aptamers (or aptamer domains) might actually be binding to, since thse are presumably proteins expressed only in cancer cells. Someone asked that very question, but he kind of dodged it in his “answer”, so I’m not sure if they’re actually doing this or not. Then again, labeling is half the battle… the binding domain of a molecular beacon should also be the binding domain for targeted chemo agents or radioisotope treatment, for instance.

Tags: advisor, dna, search, writing