Why does LAMP need six primers?

LAMP recognises six regions of the target with four core primers, which is what gives it its specificity, and the two optional loop primers add priming sites that make the reaction faster.

Can I design an RT-LAMP set against an RNA virus?

Yes. An RNA target is read as its cDNA, because RT-LAMP reverse-transcribes the target first and all six primers are DNA oligos annealing to that cDNA.

How long should the target be?

Gene-sized. LAMP amplifies 120 to 160 bases, so the region you select should be the window you actually want to amplify rather than a whole genome.

Amplify · experimental

LAMP primer set

Design a complete loop-mediated isothermal amplification set against a region of an open sequence: the four core primers that recognise six regions of the target, the two optional loop primers that accelerate the reaction, and every measurement that decided them. LAMP runs at one temperature, so the assay needs a heat block rather than a thermal cycler — which is why it is the method behind most field and point-of-care tests.

Open Primer Designer Open the Primer test sample

Real sequences (GenBank plasmid, FASTA, and a protein family) for the Primer Designer

What it does

01A complete six-primer LAMP set: F3, FIP, BIP, B3 and the two optional loop primers
02Criteria from the inventors own design guide, every window shown and adjustable
03The GC-content preset the target selects, stated before the run
04Secondary-structure screening of the inner primers
05RNA targets read as cDNA, so an RT-LAMP set can be designed directly on a viral genome
06All six binding regions drawn on the sequence map, each named and coloured

What it runs on

Design criteria come from the PrimerExplorer V5 guide published by the developers of the method, applied over the same golden-validated melting-temperature and secondary-structure engines the other primer tools use. The panel runs on @ports/enzymes, @ports/oligo-structure, @ports/primer.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Why does LAMP need six primers?: LAMP recognises six regions of the target with four core primers, which is what gives it its specificity, and the two optional loop primers add priming sites that make the reaction faster.
Can I design an RT-LAMP set against an RNA virus?: Yes. An RNA target is read as its cDNA, because RT-LAMP reverse-transcribes the target first and all six primers are DNA oligos annealing to that cDNA.
How long should the target be?: Gene-sized. LAMP amplifies 120 to 160 bases, so the region you select should be the window you actually want to amplify rather than a whole genome.

Also searched as

LAMP primer design · PrimerExplorer alternative · loop mediated isothermal amplification primer design · design FIP BIP primers · F3 B3 FIP BIP LF LB design · RT-LAMP primer design · isothermal amplification primer designer · LAMP assay design online