|MadSci Network: Molecular Biology|
I think there are 2 questions here: why is methylene blue a good stain for DNA and why are you using it in your lab?
Let's look at methylene blue as a stain first. There are lots of different chemicals that will stain DNA. If you think about the structure of DNA, it's like a ladder, with the bases forming the "rungs". If you wanted to design something that binds specifically to DNA, you might design a molecule with a positive charge that can stick to the outside of the ladder (which is negative). You might also use a molecule that contained flat, ring-shaped structures which could bind to the bases in the DNA. This is how most DNA stains work-they bind across the "rungs", in a process called intercalation.
Have a look at this page, wich shows you the structure of methylene blue. Now go to this page or this page to read about the structure of DNA. Can you see how the rings of methylene blue might fit into the DNA structure?
The next question is why are you using it in your lab? One answer to this is that it is an easy stain to use. If you used a stain called ethidium bromide, you would have to look at your gel using ultraviolet light to see the staining. And ethidium bromide is also mutagenic and carcinogenic (meaning that it can cause mutations to your DNA and maybe cancer), so methylene blue is a lot safer for you to use.
I hope this answers your questions,
Try the links in the MadSci Library for more information on Molecular Biology.