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formaldehyde's function in Northern blot - (Nov/04/2006 )

why do we need to run a denaturing gel for northern blot? what is formaldehyde doing in this gel? does RNA need to be denatured and why?
Who can answer these questions?
thank you very much!


RNA is single stranded, and readily forms complex secondary structure, folding up into partial double helical domains. These structures migrate through the gel at unpredictable rates, so it is difficult to assign a length to RNA fragments by measuring gel migration distance. Further, the same fragment may fold up in multiple ways, leading to smeared bands. Formaldehyde denatures the RNA and forces it to adopt a linear arrangement, making it run more like a dsDNA fragment. Glyoxal can also be used, and is less of a pain to work with.