Today's molecular bio lab is so loaded with cutting-edge hyper-tech, but in any lab big enough, you can locate a piece of equipment that seems out of date for a procedure that hasn't changed in fifty years. DNA is electrophoresed on agarose gels. Although part of the functionality of this old technology has been replaced by newer approaches over time, it has stubbornly persisted because of its affordability and adaptability. The balance of two opposing forces—the force of electric current versus the resistance of the agarose matrix—is essential to agarose gel electrophoresis. The sample is put into wells at the top of the cast gel, which is submerged in a tank of buffered electrolyte solution, and current is supplied. The agarose serves as a porous screen to prevent the current from dragging negatively charged oligonucleotides toward the positively charged side of the gel box. Although the resistance of the gel rises with oligo mass, oligo charge is precisely proportional to mass. Thus, as time passes, DNA gradually divides into discrete bands mostly based on its length. Smaller pieces of the same condition migrate more quickly and will thus appear closer to the oligo’s molecular weight. Migration speed does have some quirks, though. Uncoiling plasmid DNA (which has a single stranded cut or "nick") causes it to move more slowly than linear DNA of the same length. Plasmid DNA in the supercoiled state moves more quickly than linear DNA of the same length. Contrary to popular belief, under most circumstances, single stranded DNA will move more slowly than a double stranded segment of the same length. It is generally accepted that this is because ssDNA has less secondary structure and a more "open" conformation, which causes it to experience more resistance as it passes through the gel. Because the ladder is usually linear, supercoiled plasmid DNA will read shorter than it actually is, but nicked plasmid DNA will read longer. If you want to estimate plasmid length with precision, you can either linearize the plasmid using a supercoiled marker. A natural polymer called agarose, which was extracted from red seaweed, is utilized to create a gel. Gel is poured into a block or slab that is different heights, lengths, and thicknesses during gel electrophoresis. The gel serves as a support matrix when it is saturated with or immersed in an electrophoresis running buffer after setting. When an electric field is introduced to the apparatus, electrophoretic separation of the liquid samples takes place on a small portion of the gel. The components in the samples are propelled to migrate at various rates by the electric force that is generated.

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