Lab techniques – The Bumbling Biochemist

note: if you’re looking for posts on recombinant protein expression & purification see the Protein expression and purification page

Agarose gel electrophoresis

with comparison to SDS-PAGE

Polyacrylamide gel polymerization

Coomassie Brilliant Blue – SDS-PAGE staining

Silver staining

Hot Start PCR, heated lids, polymerase options, etc. – basically some random PCR stuff to get the best chance at a successful PCR experiment!

Ways to measure “expression”

Ribosome footprinting/profiling

RNA extraction/purification

Desalting & buffer exchange gel filtration columns

Transfection methods

Antibiotic selection science

Minipreps (alkaline lysis)

interpreting clone sequencing

Measuring protein concentration – the many ways…

Approaches to studying protein-protein & protein-nucleic acid interactions: an overview/outline

Slot blot double filter-binding assay

Liquid Scintillation Counting – a scintillating look inside of a way to measure radioactive decay!

Experimental design: variables, controls, replicates, etc.

Equipped to experiment: lab equipment

Intro to protein crystallization (the actually getting crystals stuff and why it’s so hard)

Vapor diffusion crystallization – theory & practice

Native PAGE (PolyAcrylamide Gel Electrophoresis) & Blue Native PAGE

Fluorescent nucleic acid stains

spin-column PCR purification (clean-up)

Formaldehyde protein/nucleic acid & protein/protein crosslinking biochemistry

Radiolabeling nucleic acids

molecular cloning

Bacterial transformation – heat shock & chemically-competent cells

Blue-white screening

checking your cloning worked

Site-directed mutagenesis

Nucleic acid spectroscopy: Beer’s Law and Beyond!

EMSA (gel shift assay)

DNA fingerprinting, analytical restriction digest, Restriction Fragment Length Polymorphism (RFLP) analysis, etc.

Experiment-ing: organizedly planning out, preparing for, performing, & writing notes for experiments

Stock up on stock solutions

Serial dilutions of your solutions!

X-ray crystallography

Protein crystallization – Give your protein a nice cocktail!: precipitants, crystallization diagrams, screening and optimization