March 15, 2014 (Vol. 34, No. 6)
Strong Points: Many customizable options
Weak Points: No in-page help of descriptions (separate help page)
Polymerase Chain Reaction (PCR): the technique we all love to hate. PCR is immensely useful, but notoriously finicky. One of the biggest (and most important) variables that determines the success or failure of the DNA amplification is the design of the oligonucleotide primers. Primer3web is an online primer design tool that allows users to find either an appropriate matching primer (if one primer sequence is already known), or a complete set of primers for a given user-inputted source sequence. The power of the Primer3web tool is the large number of customizable options for the primer design. These options include the usual suspects such as primer length, melting temperature, and product length, but they also include options relating to thermodynamic secondary structure properties (such as template mispriming and self-complementarity), reaction conditions, and customizable penalty weights for the primers.