The primary factor dictating how far a protein will migrate during SDS-PAGE is the size of the protein. One of the key features of SDS-PAGE is that the protein sample is denatured and covered in a detergent prior to being run through the gel. This essentially eliminates any complications from the degree of folding or the number of subunits. In fact, subunits will migrate according to their own molecular weights.

SDS-PAGE requires a denaturing protein gel that separates proteins based on size. The primary ingredients are polyacrylamide and sodium dodecyl sulfate—SDS-PAGE refers to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In order to visualize the results, proteins separated via SDS-PAGE are transferred to a nitrocellulose membrane, where they are probed with antibodies for a specific protein of interest. 

Polyacrylamide gels allow for resolution of DNA strands down to single base pair differences. All these other options are applicable to any kind of gel electrophoresis. This property of polyacrylamide allowed for some of the earliest forms of Sanger sequencing, in which DNA sequences were read by their respective chain lengths across a 4 column gel (with one column each for adenine, cytosine, guanine, and thymine).

In order to study gene expression it would be useful to quantify the expression of a specific RNA transcript. All of the blotting techniques follow similar procedures, but differ in the macromolecule they separate or the information they obtain. Southern blotting is used for DNA fragments, western blotting is used for proteins, and eastern blotting is used to look at post-translational modifications. Northern blotting would be the most useful in this question, as it is used to look at RNA fragments.

Southern blotting is a technique used to detect a specific DNA sequence in a sample. The sample is run on an agarose gel and transferred to a membrane. A labeled nucleic acid probe is then incubated with the membrane. The probe carries a tag for identification and will only bind to the target region of DNA. If the tag is identified, then the researcher can conclude that the target gene is present in the sample.

Antibodies are most commonly used to detect specific proteins in western blotting. Biotin-binding proteins have wide uses in both detection and purification procedures. Phosphorous-32 is commonly used to label nucleotides (such as GTP) to perform enzymatic assays.

A Northern blot is very similar to a Southern blot, except it is used to identify RNA fragments rather than DNA fragments. A gel is used to separate the RNA fragments based on size. A radioactive probe can then be used to identify which known RNA sequences have been combined with an RNA fragment.

A Western blot is used to identify protein subunits and fragments. Eastern blots are used to identify protein modifications, such as glycosylation.

Northern blots are designed to detect the quantity and identity of mRNA transcripts in cells or tissue. Electrophoresis separates RNAs by size, and then hybridization is used to detect the mRNA sequence of interest. Southern blots detect DNA sequences, but give no information about whether they are transcribed or not. Western blots detect proteins, but we are not interested in translation. Neither thin-layer chromatography nor two-photon microscopy would tell us anything about the genetic processes occurring in the cell line. 

The only choice that would actually be useful in improving the purity of a protein sample would be column chromatography. It is possible to attach a specific ligand to your protein of interest to help separate it from a mixture via this method.

SDS-PAGE results in a separated, but denatured, protein sample. Detergents used in this process damage the protein structure, making it impossible to retain the native state. Southern blotting is a technique used to identify specific sequences of DNA in a sample and has nothing to do with increasing the purity of a protein sample. 

The fact that the two substances have the same R_f value is strong evidence that they are the same substance; however, it is not conclusive evidence. The researcher would have to verify these results with another test (such as NMR) to conclusively state that caffeine is present in his sample. R_f value is determined by polar and hydrophobic properties that may not be unique to a given compound. Many different compounds are capable of having the same or similar R_f values; therefore, his result does not conclusively show that caffeine is in his sample.

The Western blot test identifies antigens by separating them using electrophoresis on a gel, then transferring to a solid membrane by blotting. The process allows clinicians to establish is a specific protein or set of proteins is present in a sample.

Enzyme-linked immunosorbent assay (ELISA) methodology involves identifying the presence of antigens or antibodies in blood by binding them to enzymes that would result in a color change. In flow cytometry, cells are tagged with an antibody carrying a fluorescent label and passed through a detctor. In immuno-electron microscopy, antibodies are labelled with heavy metals and viewed with an electron microscope. Chemiluminescence is the emission of light as the result of a chemical reaction. Luminol is an example of chemiluminescence.