Molecule of the Day

Ethidium is a dye that's used in molecular biology to allow DNA to be visualized. Regular DNA isn't colored; it absorbs ultraviolet but not visible light, so you need to use tricks like making the DNA radioactive (which makes it pretty easy to spot), or using dyes that selectively bind to DNA. Ethidium does this by slipping in between the base pairs of DNA, or "intercalating."

One ubiquitous method of visualizing DNA is called gel electrophoresis. You have no doubt seen this on some CSI-type show. The basic idea is this: you put DNA inside a water-based gel. DNA is negatively charged, so to get it to move, all you do is put it in a (DC) electrical field.

The gel is essentially Jell-O; a number of different things are used to make the water gel, but the idea is that you have a bunch of long, stringy molecules that will impede the DNA's progress through the gel. Smaller molecules are impeded less, so you end up having a method of separating DNA by size. How to visualize the DNA? Enter ethidium.

Soaking the gel in a dilute solution of ethidium (ethidium is a brilliant red color, the solution will just barely be reddish-orange) will allow the ethidium to bind to the DNA (concentrating the dye in the DNA). Additionally, ethidium can emit fluorescence. It doesn't do this very well when it's in water, but it does it very well when it's bound to DNA (about 15 times better). If you put your ethidium-stained gel in ultraviolet light, you will get pink-glowing DNA.

Public domain image from Wikipedia

A lot of people don't use ethidium to stain DNA these days because of a perceived safety hazard (the idea being that something that binds DNA is pretty likely to be mutagenic or carcinogenic). I tend to take this with a grain of salt (this may be wishful thinking, because I've probably handled more ethidium than a molecular biologist will in his lifetime!), but some of the "safer" alternatives are starting to become cheaper. Still something I always handle with a little extra care, but I think it got a bad name over the years.

There is another funny story behind ethidium. It has been used for years as a veterinary drug. I used to keep a bookmark for a webpage of someone making up a concentrated solution of ethidium and injecting it into a cow to freak out ethidium-phobes. Now, the best I can find is a manufacturer's site, lacking in pictures, an unfortunately named company, and (this one is new on me) references on thedental use of ethidium (one presumes the plaque staining described is done outside the mouth).