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LAMP / IsothermalFree in-browser calculator

LAMP Primer Set Designer.

Design complete LAMP primer sets (F3, B3, FIP, BIP, LF, LB) from a target DNA sequence. Sliding-window algorithm with Tm/GC optimization, Notomi distance constraints, top-N ranked alternatives, CSV export. All computation runs client-side.

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Validated2026-04-07
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Load example LAMP Primer Designer data to see the full workflow

Target Sequence

Paste your target DNA region (100–2000 nt, ACGT only). Whitespace and digits are stripped automatically.

Design Settings

Loop primers accelerate LAMP 2–3x

When to use

  • Design a complete LAMP primer set (F3, B3, FIP, BIP, LF, LB) from a target sequence
  • Point-of-care diagnostics requiring isothermal amplification
  • Field-deployable pathogen detection (no thermal cycler needed)
  • Rapid genotyping and mutation screening
  • Compare multiple primer set candidates ranked by quality score

Do not use for

  • PCR primer design — use a standard primer3-based tool or our PCR Fidelity Estimator
  • Targets shorter than 100 nt — LAMP needs 150–300 nt minimum
  • RPA (Recombinase Polymerase Amplification) — different primer requirements
  • Multiplexed detection of many targets — LAMP is best for 1–2 targets per reaction

Use all six primers for fastest results

A complete 6-primer set (F3, B3, FIP, BIP, LF, LB) amplifies 2–3x faster than the minimal 4-primer set. Loop primers are worth the extra cost.

LAMP is exquisitely sensitive to contamination

LAMP produces microgram quantities of DNA from femtograms of template. Always use dedicated pipettes, filtered tips, and physical separation of pre- and post-amplification areas.

Validate with known positive and negative controls

Non-specific amplification can occur with LAMP. Always run no-template controls (NTC) and confirm specificity by restriction digest or sequencing of the product.

Betaine improves GC-rich target amplification

If your target has high GC content (>60%), adding 0.8–1.0 M betaine to the reaction can improve strand displacement and reduce secondary structure interference.

Primer Tm should match reaction temperature

LAMP runs at 60–65 °C. Primer Tms outside this range reduce efficiency. If no sets score well at 60–65 °C, consider redesigning with a slightly wider range (58–68 °C).

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Method

Primer design follows Notomi et al. (2000) distance constraints and NEB LAMP guidelines. The algorithm scans F2 anchor positions across the target at 5 nt intervals, then picks optimal F1c, F3, B1c, B2, and B3 primers at each anchor by nearest-neighbour Tm (SantaLucia 1998). Loop primers (LF, LB) are designed in the gap regions between inner primer components. Sets are scored on Tm balance, GC content, inter-primer distances, and loop primer availability, then deduplicated and ranked.

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Validated

Last validated 2026-04-07. Calculations are designed for planning and documentation support; verify procurement decisions against manufacturer specifications or institutional SOPs.

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How to cite

How to Cite

ConductScience LAMP Primer Designer (v1.21.0). ConductScience, Inc. 2026. Available at: https://conductscience.com/tools/lamp-primer-designer

Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28:e63. doi:10.1093/nar/28.12.e63

Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes. 2002;16:223–229. doi:10.1006/mcpr.2002.0415

SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS. 1998;95:1460–1465. doi:10.1073/pnas.95.4.1460

How LAMP amplification works

LAMP uses a strand-displacing DNA polymerase (typically Bst) at a constant 60–65 °C. The reaction proceeds in two phases:

Starting phase: 1. F3 displaces the F2-primed strand, creating a single-stranded intermediate 2. FIP (F1c+F2) hybridizes: F2 binds sense strand, extends, then F1c folds back to form a loop 3. The B side mirrors this process, generating a dumbbell structure
Cycling phase: 1. The dumbbell self-primes from the 3′ stem-loop 2. Internal primers (FIP/BIP) bind loop regions and extend 3. Each cycle doubles the product and creates increasingly long concatemers 4. Loop primers (LF/LB) accelerate by providing additional priming sites

LAMP primer design guidelines

Good LAMP primers follow these rules (Notomi et al., 2000; NEB guidelines):

  • Tm range: 60–65 °C for all individual primers (using nearest-neighbour calculation)
  • GC content: 40–65% for each primer
  • F3/B3 length: 18–25 nt (outer primers, displacement function)
  • F2/B2/F1c/B1c length: 18–25 nt (inner primer components)
  • FIP/BIP length: 36–50 nt (composite F1c+F2 or B1c+B2)
  • LF/LB length: 15–25 nt (loop accelerators)
  • F2-to-F1c distance: 40–60 nt (governs initial stem-loop size)
  • F3-to-F2 gap: 0–20 nt (F3 must displace the F2-primed strand)

Troubleshooting LAMP reactions

Common issues and solutions:

  • No amplification: Check primer Tms, try 60–67 °C temperature range, increase polymerase/primer concentration, extend incubation to 60 min
  • False positives / contamination: LAMP produces large amounts of DNA — use separate areas for setup and detection, include no-template controls
  • Slow reaction: Add loop primers (LF/LB) for 2–3x speedup, optimize MgSO4 concentration (6–8 mM)
  • Non-specific amplification: Redesign primers (try alternative sets from this tool), reduce primer concentration, add betaine (0.8–1.0 M)
  • Target too short: LAMP needs 150–300 nt of target region; if your gene region is shorter, extend upstream/downstream

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