Monday, March 1, 2010

Ideas dump

I'm looking over some old brainstorms, because of course I'm not busy at all, no sir, ahahaha... Anyway. I keep getting neat ideas, and I'm going to put some of them here so that (1) I don't forget them before I find time to investigate and (2) maybe someone will actually look at them and think about them. Also, I apologize for not explaining these ideas for the benefit of biology neophytes.

  • Enzymes that bind DNA and perform actions including cutting/pasting DNA or recruiting other enzymes. Can you inhibit their action by adding short pieces of RNA (or similar) with the same sequence as their binding site?

  • RNAi seems to exist in bacteria, kind of (not as much as in C.elegans). Is it useful for creating synthbiological devices? I don't recall seeing any; what's the roadblock?

  • In particular, RNAi could be a neat way of getting around the crosstalk/specificity problem, since it's very sequence-specific and designing RNA sequences is easier than designing proteins.

  • What would it take to drive localization to a synthetic organelle?

  • Need to learn more about riboswitches. All the riboswitches I've seen so far are the kind that respond to a small molecule. Hmm: can you make a riboswitch that responds to a short ssRNA??

  • What are the primitives of biological circuits? In a regime where it's easier to build monolithic black boxes than to reuse parts, how do things like two-component signaling evolve, that almost look intelligently designed with modularity etc?

  • I think I'm on an RNA kick. Is this justified?

  • Whoa, DNA scaffolds? Clever! read this at some point

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