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Both have the same molecular weight, but because B has secondary (2') structure that makes it smaller than A, B will migrate faster than A in a gel. To prevent differences in shape (2' structure) from confusing measurements of molecular weight, the molecules to be separated must be in a long extend rod conformation - no 2' structure. In order to remove any such secondary or tertiary structure, different techniques are employed for preparing DNA, RNA and protein samples for electrophoresis.
Preparing DNA for Southern Blots
DNA is first cut with restriction enzymes and the resulting double-stranded DNA fragments have an extended rod conformation without pre-treatment...
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