You wish to investigate proteins from human liver cells that bind to a specific short sequence of nucleotide bases you believe to be an enhancer element

Question

Design an experiment that would allow you to isolate and characterize human proteins that bind to the nucleotide sequence you are interested in. (Include at least two separate techniques in your answer.)
What will be an ideal response?

Answer 1

Answer: Students should recognize that they could start with cell lysate or the cytoplasmic portion of cell lysate from a human liver cell line. The lysate could be applied to an affinity chromatography column with the nucleotide sequence of interest bound to the column beads. Proteins that don't bind the sequence should wash off first; then the bound proteins will be washed off the column and be collected. The proteins in the second fraction (those that bound to the affinity column) could then be analyzed with SDS-PAGE, 2-D gel electrophoresis, tandem mass spectrometry, or other mass spectrometry techniques.