The programs in this section can help you design primers for DNA sequencing, compatible primer pairs for PCR, and oligonucleotide probes for hybridization. They work by screening potential primers or probes for properties that are known to be important in priming or hybridization reactions and presenting you with a list of the candidates that pass the tests. Programs can examine a collection of candidates that you provide, or they can find candidates de novo if you provide a target nucleotide sequence.

Among the factors important in primer or hybridization reactions are the melting temperature of the oligonucleotide primer or probe (and that of the product in the case of PCR), and the G+C content of the oligos (and products). In the case of PCR, the difference in the melting temperatures of the primer pair members and between the primers and the product can also be important. The presence or absence of certain bases at the 3'-end of the oligo can be a factor in priming reactions. You can place constraints on all of these factors to fit the conditions of your reaction. Other constraints you can specify are a size range for the primers or probes, and for PCR reactions, a size range for the desired product, and a requirement that the primer pair brackets a certain region of the template sequence.

Complementarity is another factor to consider. These programs check potential primers for self-complementarity (and complementarity between PCR primer pairs) in order to eliminate primers that tend to form significant secondary structures or primer-dimer pairs. In the case of PCR primers, these programs can usually also eliminate primer pairs that have significant complementarity with the desired product. One thing that primer screening programs usually will not do is check to see if the candidate primers will bind to other locations in the template sequence; for this you will need to use a separate program (such as primersearch or stssearch or even BLAST) that looks for matches between oligos and a longer nucleotide sequence.

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