User:Anthony Salvagno/Notebook/Research/2009/01/29/Koch's Email

Email 1

Hey Ant, great email. I was just reminded that I think the "molecular cloning" books are in the lab. Those are fantastic resources for the kind of work you're going to be doing, including appendices about how to make buffers. Here're some things that came to mind that maybe you could look up:

• Multiple cloning site
• restriction endonuclease (e.g. XhoI)
• T4 DNA ligase and ligation reactions
• Agarose gel electrophoresis
• miniprep (plasmid DNA isolation from E. coli)

Another thing about a general strategy. Since you're like me, you're probably going to be made nervous by a bunch of steps in a row without any visible feedback (it all looks like water). A good way to keep track of things is to print out protocols and use a sharpie to check off steps. You could also do this electronically with, say, a PDF file. Just something so you can make a mark when you've done the step. Also, printing out the protocol, means planning it out ahead of time -- Kelly and Osley will love this if you can show them on paper what you're planning on doing. It's going to be annoying because Osley wants paper notebooks and obviously electronic is better for a variety of reasons. I don't know if you'll be able to convince her otherwise, unless your electronic notebook was just ridiculously good.

Also, I don't see any reason why you can't go public notebook if you feel like it. The only thing would be Adelman stuff which we'd need to talk with her about when the time comes.

--S

Email 2 (in conjunction to Kelly's email)

Sweet. Steps 1-6 are of equal difficulty (or easier than) to step 7, by the way. The ligation is not going to be easy. Some good steps to prepare for ligation:

1. Read Brandon's latest notebook entries (and Diego's)...this is where he has a gel indicating successful ligation
2. Read up on my old protocol: http://openwetware.org/wiki/Koch_Lab:Protocols#Labeling_DNA_for_unzipping
   

-> By the way, I have ALL KINDS of (stuff) in my notebook from grad school. I don't know how to transfer this kind of information, but let me know when you have the inkling that something I've done before would help.

Also, BTW: I'm not sure I agree that Kelly's ligation method is the best. It might be. So, it's going to help a lot if you take the time to understand both what he's saying with his ligation-on-beads method, and what sort-of worked for me in the past. We're coming from separate worlds, and you can maybe bridge our communication and recognize something very efficient between the two methods. This isn't supposed to mean anything besides just alerting you.

--S

My thoughts

More things to learn:

• I already read about restriction enzymes.
• Need to brush up on everything else.