For real-time detection, LAMP fluorescent dye is read in the SYBR/FAM channel. Therefore, the ssDNA reporter should carry a fluorophore readable in a different channel, such as Texas Red, Cy5, or HEX. We recommend the following ssDNA reporter sequence, which will be read in the Texas Red channel: /5Alex594N/TTATTATT/3IAbRQSp/.
Reporters are typically 8–12 nucleotides long and may contain mixed T and A bases, poly-T, or poly-C. Longer reporters may improve kinetics but can increase background fluorescence. Avoid poly-G sequences and RNA-only or chimeric DNA–RNA reporters.
Compatible fluorophore/quencher pairs include:
- Alexa Fluor 594/Iowa Black RQ: Recommended when the FAM channel is used for an amplification readout, such as an intercalating dye
- 6-FAM/Iowa Black FQ: Compatible
- Cy5/Iowa Black RQ: Compatible
