Question

Write three characteristics that differentiate an agarose gel and a gel polyacrylamide
preparation

what it is used for

how analyze results

Answer 1

Electrophoresis with agarose and polyacrylamide gels is one of the most widely used tools in molecular biology. Since these gels are porous in nature, electrophoresis with agarose and polyacrylamide is standard method to seperate, identify and purify nucleic acids. There are many different characteristics of both these gels that differentiate them from each other.

• Agarose powder is dissolved in a buffer solution, microwaved, poured into the gel frame and allowed to set. Agarose gel runs horizontally i.e. the gel is flat on the table. On the other hand polyacrylamide gel sets by a chemical reaction after cross linking between acrylamide and bis-acrylamide. Polyacrylamide runs vertically i. e the gel is standing on the table.
• Agarose gels are used to resolve large fragments of DNA (50-20,000 base pairs). Proteins are also seperated by agarose gel electrophoresis based on charge and/ or size. Polyacrylamide gels are used for resolving shorter nucleic acids fragments (5-500 base pairs) and is generally used for analysing single stranded DNA. It is also used to seperate proteins based on their electrophoretic mobility.
• DNA and RNA in agarose gels are visualized by fluorescent dyes such as ethidium bromide, SYBR Green, GelRed etc and non-fluorescent dyes such as methylene blue, crystal blue etc. Fluorescent dyes are visualized in UV light while non-fluorescent dyes are viewed under natural light. For visualization polyacrylamide gels are stained with Coomassie brilliant blue R-250 (for proteins), ethidium bromide (for nucleic acid). After staining, destaining is also performed for proper visualization of bands.