A primer is a single-stranded DNA fragment that is complementary to a short sequence on the DNA strand to be copied. Primers are used to begin the process of copying a strand of DNA. Typically, primers are 15-30 bases long, and are designed to bind to unique DNA regions on the DNA strand (rather than to lots of sites).
Today, primers are designed using computer programs to optimize several features. Candidate sequences are identified from the ends of the DNA fragment you are trying to copy. These are put through a BLAST search to minimize binding to other parts of the DNA. The upstream primer and the downstream primer are designed to have similar "melting points" (the temperature at which the double-stranded DNA unravels) based on the number of A and T nucleotides versus G and C nucleotides. As and Ts have 2 hydrogen bonds while Gs and Cs have 3 hydrogen bonds, requiring more energy or heat to melt their bonds. Primers should not bind to themselves or to the other primer. |
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