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“Men adjust their walking speed to match their romantic (female) partner’s pace — a phenomenon not seen when guys walk with female friends”1.

You may be thinking what on earth does it have to do with electrophoretic mobility??? Well, think about it. That same effect is pretty much what you can see in a classic EMSA (Electrophoretic Mobility Shift Assay), when a rather physical non-loving kind of interaction between nucleic acids and proteins is observed.

Well known is the relationship between electrophoretic mobility and size: bigger molecules have slower mobility than small ones. In the case of men, much of what determines walking speed is height: the longer your legs are, the faster you’re likely to walk — a fact that means men, on average, have a higher optimal speed than women do.

But the interesting thing is that researchers discovered that when a lovely-dovey couple walked together, the man slowed his pace to match his female’s optimal speed. In the same way, when nucleic acids interact with proteins, they slow down in an electrophoretic run compared to unbound nucleic acids. So you can say that we ladies are to proteins as men are to nucleic acids!

In 1981, while the world’s eyes where on Lady Di marrying prince Charles and Olivia Newton John’s hit ‘Physical’ was all over, a great technique to measure DNA-protein interactions, named EMSA, was published by two independent groups. And the story goes like this…

The research on protein-DNA interactions began in the early 1960s, when analyzing the binding of Lac and phage λ repressors to DNA. Back then, these complexes could be analyzed by a technique that arose from the discovery that certain membrane filters will retain DNA-protein complexes, but not free DNA2. So, by quantifying the retention of radiolabeled DNA fragments mixed with varying amounts of a protein of interest, it became possible to determine the stoichiometry and binding affinity of a protein for a given sequence. Anyway, filter binding remained impractical for the characterization of less stable complexes and non-DNA-protein complexes.

At the very beginning of the 1980s, Arnold Revzin and Mark Garner, at Michigan State University, knew of a study that showed that the ternary transcription elongation complex—DNA bound to RNA polymerase with a nascent RNA chain—was sufficiently stable for visualization by gel electrophoresis3. Combining purified protein with DNA restriction fragments containing appropriate binding sites and then running the mixture on a polyacrylamide gel, Revzin and Garner observed an amazing result: protein-DNA complexes forming distinctly ‘shifted’ higher molecular weight bands on the gels. Thus was born the electrophoretic mobility shift assay (EMSA)4. 

But they were not the only one working on it. Michael Fried and Donald Crothers at Yale also had developed their version of EMSA. Initially, Fried had speculated that only free DNA would be amenable to electrophoresis, and that DNA-protein binding could be quantified by determining how much DNA did not enter the gel, a very interesting thought by the way. But what they saw instead was a variety of shifted bands that appeared to correlate with the number of repressor molecules bound to each DNA fragment. (That’s when Crothers said to Michael “forget what you’re doing-follow this up!”). Their paper also offered some important extensions of Garner and Revzin’s assay, using radioactive labeling rather than ethidium bromide staining to detect shifted bands, and demonstrating he capabilities of EMSA as a means for measuring the relative binding constants and stoichiometry of protein-DNA interactions5.

Despite its popularity and application depth, EMSA is typically limited to semiquantitative interaction analysis. Nowadays, MicroScale Thermophoresis (MST) appears a solution-based method with high sensitivity that provides reliable quantitative information on molecular interactions such as protein-nucleic acids, based on a simple protocol, making measurements very fast and efficient with low sample consumption. This technique relies on binding-induced changes in thermophoretic mobility, which depends on several molecular properties, including not only size, but also charge and solvation entropy6.

Science and lab techniques evolve, it can go from electrophoresis to MicroScale thermophoresis, but I will continue to find parallels among life and and science.

 

  1. Wagnild J. and Wall-Scheffler CM (2013). PLoS One 8(10): e76576.
  2. Jones, G.W. and Berg, P. J. (1966). Mol. Biol. 22, 199–209.
  3. Chelm, B.K.and Geiduschek, E.P. (1979). Nucleic Acids Res. 7, 1851–1867.
  4. Garner, M.M. and Revzin, A. (1981). Nucleic Acids Res. 9, 3047–3060.
  5. Fried, M. and Crothers, D.M. (1981). Nucleic Acids Res. 9, 6505–6525.
  6. Seidel SAI, Dijkman PM, Lea WA, et al. (2013). Methods. 59(3): 301-315.