Loop primers are used for the acceleration of LAMP reaction in addition to the regular LAMP primer (FIP, BIP, F3 and B3). For Loop primer designing, the information of not only the target sequence but the position of the FIP, BIP, F3 and B3 are required. This information is included in the Primer Information file, and is inputted into PrimerExplorer V3.
Download the Primer information file from the Selected Primer Sets page.
As double stranded DNA is in the condition of dynamic equilibrium at the temperature around 65°C, one of the LAMP primers can anneal to the complimentary sequence of double stranded target DNA, then initiates DNA synthesis using the DNA polymerase with strand displacement activity, displacing and releasing a single stranded DNA. With the LAMP method, unlike with PCR, there is no need for heat denaturation of the double stranded DNA into a single strand. The following amplification mechanism explains from when the FIP anneals to such released single stranded template DNA.
2. Because LAMP primers recognize 6 distinct regions, the specificity of LAMP is much higher than that of the other commonly used amplification techniques.
LAVA is designed to be a flexible tool for custom signature design, so it can fulfill varying signature design needs in a high-throughput informatics environment. LAVA was implemented in Perl because Perl interpreters are available for every major operating system, the wide use of BioPerl  in bioinformatics, and BioPerl's support for several different sequence alignment formats. To simplify discussion of signature design, we refer to LAMP primers as pairs of nested primers: inner, loop, middle, and outer, as shown in Figure . All signature results from LAVA are read in the 5' to 3' direction, even if the opposite strand is used to design a portion of the sequence, and are consistent with the traditional nomenclature in Notomi et al. .