My own personal brand of labelling obsessiveness:
- DNA shall have a light green dot on the top of it's tube if it is a maxiprep; bright orange if it is primer; dark green if it is a miniprep.
- Chemicals will be labelled on orange tape if sterile, and on green if they are not.
- E. coli stock will have a dark green dot on the top of its tube. M. smegmatis will have dark blue.
Neeraj's advice for revising my PCR:
- Titrating Mg, DNA, etc. is for when you don't get any bands; no good if you have too many bands.
- Use 30s instead of 1 minute for the three stages of PCR in general. Strongly binding primers will bind just fine in 30s, extension for 30s in 1 minute will reduce nonspecific large stuff, and 30s at denaturation will destroy less of the polymerase at each cycle.
- Can try adding 5M DMSO if there's still a lot of nonspecific junk.
- Can PCR straight out of E. coli and M. smegmatis: take a scoop of colonies from a plate, suspend in 100μL PBS+Tween, boil for 5-10 minutes, and use 1-2μL of that as the template in PCR reaction.