Agarose vs Polyacrylamide Gels Agarose Horizontal or vertical? One molecule or lots of molecules? Why are they poured horizontal or vertical? Separates large molecules or small ones? Lets you tell small differences between sizes of bands? Can be reheated and poured? Powder is toxic? Solid is toxic Type of molecules run in this type of gel Big gaps or small gaps in gel? Special uses of this gel? Things to know when running the gel Things to know when handling the gel Advantages to using this gel Disadvantages of using this gel Expense? Polyacrylamide Horizontal Vertical Lots of molecules held together by One large molecule intermolecular forces Because you can. It’s easier to Need glass plates for pour a horizontal gel than it is to structure- very thin gels that pour a vertical gel. need support. Air speeds up polymerization. If the gel was poured open to air, it would not solidify evenly. Both, but better for large Both, but better for small molecules molecules No Yes Yes No No No Mostly DNA Yes No DNA or proteins Bigger gaps than with polyacrylamide Smaller gaps Make sure buffer covers wells when running. If the gel runs too hot, the agarose might melt. Sequencing gels, protein gels Make sure buffer covers wells when running. Check for leaks before running. Gel easily breaks where wells are. Gel easily rips. Can re-pour the gel if you goof. Can decide if you want lots of narrow lanes or a few wide lanes. Fewer ingredients to mix. Can’t tell small differences between band sizes. Bands are usually not as sharp as with polyacrylamide. Easy to stain. Can dry down the gel to save a copy. Agarose is about $1 a gramconsidered expensive. Need to know concentration needed before buying the gels. Need to know number of samples so that you can buy enough lanes for samples. If you are making them yourself, they take a long time to make and are challenging to pour. Gels usually bought prepoured. Cost $5-7 per gel.