The Problem with Molecular Biology Techniques

I taught myself how to program a computer. It took a long time to become a fluent programmer, but there are a fair number of good books on most programming languages. Learning is a matter of patience, perserverance, and time spent in front of the computer.

When I began learning molecular biology techniques (e.g. cloning, sequencing, PCR, etc...), I disliked how much you have to rely on other people to show you things and explain things to figure out the different techniques - there isn't a molecular biology compiler that will print an error message saying, "warning your dNTPs have gone bad, please retry your PCR with freshly prepared dNTPs". It feels like you're constantly bothering other people. And if you ask two different people how to make a particular buffer or run a certain reaction, you'll get two slightly different methods - making it hard to know exactly what you should do.

There have been a few books more useful than others and a few mistakes that I now know how to avoid, so I put this kinda thing here when I think of it.

Common Mishaps

something won't go into solution
 Is the pH right? many things (e.g. EDTA!!!) won't go into solution until they are at a certain pH
 try heating it up a bit
 did you add too much? (you can check percent solubility on some MSDS sheets)
a protocol for TRIS says to add HCl until you reach a certain pH, but after adding TRIS you find the pH already too low.
 there are two kinds of TRIS 1=Tris Hydroxymethyl Aminomethane Hydrocloride and 2=Tris Hyroxymethyl Aminomethane. You used 1, but your protocol used 2.

Tricks to make life easier

Pipetting glycerol
  glycerol is commonly used in freezer stocks (300uL in 2mL total volume freezer stock), but its high viscosity makes it difficult to pipette. Typically glycerol is autoclaved to sterilize it. After the glycerol has cooled enough that you can touch the bottle without burning yourself, it is a good time to aliquot it to sterile freezer stock tubes, because hot glycerol pipettes like water.

Recommended reading

At the bench. A Laboratory Navigatora great book if you are just starting
Molecular Cloningthe standard molecular biology techiques, in 3 volumes. Hard to understand how to do many of the protocols when you're first starting, but a good source of detailed information later

Useful Links

Protocol Online Lot's of protocols and advice and the forums can sometimes be a useful place to debug problems, as someone may have had the same problem already. Kinda hard to locate stuff here though.
Oligonucleotide properties calculatorI use this when I design primers by hand for cloning genes
Primer3I use this to design any other type of primer. You give it a sequence and selection criterion (e.g. 59 < TM < 62) and it gives you good primers. There's a stand alone linux version for big jobs.
NEBcutterVery useful when doing anything with restriction enzymes