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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.

LAMP / Isothermal6-Primer SetsClient-Side

Try it out

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

  • 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

Don't 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

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

Frequently Asked Questions

Next Steps

LAMP Primer Tm & GC Checker

Validate existing LAMP primer sets for Tm, GC content, and length

Open app →

PCR Fidelity Estimator

Estimate mutation rates for PCR-based amplification comparison

Open app →

DNA / RNA Bio Converter

Convert between mass, moles, concentration, and copies for nucleic acids

Open app →

Isothermal Amplification Instruments

Heat blocks and water baths for LAMP reactions at 60–65 °C

Browse →

Gel Electrophoresis Systems

Verify LAMP products by ladder-pattern gel electrophoresis

Browse →

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