Browser-based design of loop-mediated isothermal amplification (LAMP) primer sets with template repeat masking and bisulphite support
- 1Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- 2National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
Abstract
Loop-mediated isothermal amplification (LAMP) requires four to six oligonucleotides to occupy six to eight defined regions of a target, with strict constraints on spacing and melting temperature. This makes manual design impractical; therefore, most users rely on a limited number of server-side design services. In this study, a browser-based LAMP primer set designer is presented that requires no installation or registration and does not transmit the target sequence. The tool generates six independent candidate lists per target and screens each candidate for melting temperature, linguistic complexity, simple sequence content, self-complementarity, and complementarity to existing user-owned oligonucleotides. The remaining candidates are then assembled into complete F3/F2/F1c-B1c/B2/B3 assays, optionally including loop primers. Any combination in which two members can form a stable duplex is first rejected by a fast combinatorial rule and then by the nearest-neighbor free energy of the most stable dimer that the assembled molecules can form at the reaction temperature. Regions of the template covered by dispersed repeats or low-complexity sequences are masked prior to design. The tool’s yield, parameter sensitivity, and masking behavior are reported, and its output is compared with an archived PrimerExplorer V5 design on an identical target. Four four-primer LAMP assays for transgene screening, which were designed using an earlier version of the same principles and validated experimentally, are also described. The tool is freely available at https://primerdigital.com/tools/lamp.html.
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BibTeX
@article{kalendar2026browserbased,
title = {{Browser-based design of loop-mediated isothermal amplification (LAMP) primer sets with template repeat masking and bisulphite support}},
author = {Ruslan Kalendar and Ruslan Kalendar},
journal = {Frontiers in Bioinformatics},
year = {2026},
month = oct,
doi = {10.3389/fbinf.2026.1992214},
url = {https://doi.org/10.3389/fbinf.2026.1992214},
note = {CC BY},
}
RIS
TY - JOUR
TI - Browser-based design of loop-mediated isothermal amplification (LAMP) primer sets with template repeat masking and bisulphite support
AU - Ruslan Kalendar
AU - Ruslan Kalendar
PY - 2026
DA - 2026/10/26
JO - Frontiers in Bioinformatics
DO - 10.3389/fbinf.2026.1992214
UR - https://doi.org/10.3389/fbinf.2026.1992214
AB - Loop-mediated isothermal amplification (LAMP) requires four to six oligonucleotides to occupy six to eight defined regions of a target, with strict constraints on spacing and melting temperature. This makes manual design impractical; therefore, most users rely on a limited number of server-side design services. In this study, a browser-based LAMP primer set designer is presented that requires no installation or registration and does not transmit the target sequence. The tool generates six independent candidate lists per target and screens each candidate for melting temperature, linguistic complexity, simple sequence content, self-complementarity, and complementarity to existing user-owned oligonucleotides. The remaining candidates are then assembled into complete F3/F2/F1c-B1c/B2/B3 assays, optionally including loop primers. Any combination in which two members can form a stable duplex is first rejected by a fast combinatorial rule and then by the nearest-neighbor free energy of the most stable dimer that the assembled molecules can form at the reaction temperature. Regions of the template covered by dispersed repeats or low-complexity sequences are masked prior to design. The tool’s yield, parameter sensitivity, and masking behavior are reported, and its output is compared with an archived PrimerExplorer V5 design on an identical target. Four four-primer LAMP assays for transgene screening, which were designed using an earlier version of the same principles and validated experimentally, are also described. The tool is freely available at https://primerdigital.com/tools/lamp.html.
SN - 2673-7647
ER -