The first good method of DNA sequencing was invented by Frederick Sanger (for which he eventually won the Nobel Prize in Chemistry). This method is still the most commonly used today, with a few changes. It is known as the dideoxy chain termination method. It utilizes ddNTPs (dideoxy nucleoside triphosphates) in some small percentage in a tube where DNA is undergoing replication using radiolabeled dNTPs (the normal constiutents of DNA, except with an isotope of phosphorus that is radioactive). Whenever the elongating DNA chain incorporates a ddNTP, chain elongation is stopped, because there is no 3' hydroxyl to attach the next nucleotide to. Originally this was done with 4 separate reaction tubes, one with ddATP, one with ddGTP, etc. After the reactions were complete, all the tubes would be run on a polyacrylamide gel, which is sensitive enough to tell a single nucleotide difference in sequence length, side by side. Based on the positions where chain termination occurred, you then know which base is at that position.

The modern method is to use ddNTPs with fluorescent molecules attached to them, a different color for each, and perform all the reactions at once in a single tube. This single tube can then be run on a gel, and a computer reads the fluorescence pattern to determine sequence. The new method has the benefits of being much faster and more sensitive than the original, as well as being able to read more bases than the 250-300 bases the original method was limited to.

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