🧬 PCR Learning Laboratory

March 28, 2026 · View on GitHub

No installation needed — works directly in your browser

An interactive virtual lab to master Polymerase Chain Reaction (PCR) — entirely in your browser.

This educational platform simulates a complete PCR workflow with theory, calculations, realistic pipetting, thermal cycling design, gel interpretation, and a final assessment.

Perfect for biology, biotechnology, and medical laboratory science students.

🎯 What You'll Learn

By completing all modules, you will be able to:

Explain the molecular mechanism of each PCR step (Denaturation, Annealing, Extension)
Calculate exact reagent volumes using the C₁V₁ = C₂V₂ dilution formula
Set up a PCR reaction correctly (order and technique matter!)
Design a thermal cycling program and calculate primer Tm
Interpret agarose gel results and diagnose common failures
Understand real-world applications in diagnostics, forensics, and research

📚 Modules

Module	Focus	Key Skills
01 Theory & Concepts	What PCR is and how it works	Molecular mechanisms, exponential amplification, applications
02 Mix Calculations	Precision in reagent volumes	C₁V₁ = C₂V₂ formula, interactive calculator, practice
03 Virtual Lab Protocol	Hands-on pipetting simulation	Correct order, realistic pipetting, guided tutorial
04 PCR Programming	Thermal cycling design	Program builder, temperature profile, Tm calculator
05 Gel Electrophoresis	Result interpretation	Diagnose clean band, no band, multiple bands, smear
06 Assessment	Knowledge test	20-question quiz + Certificate (80%+ to pass)

🧪 Standard 50 µL PCR Reaction Mix

Component	Stock Concentration	Volume (µL)	Final Concentration	Role
Nuclease-Free Water	—	22	—	Solvent
2× Master Mix	2×	25	1×	Taq polymerase + dNTPs + buffer + Mg²⁺
Forward Primer	10 µM	1	0.2 µM	Binds to one strand
Reverse Primer	10 µM	1	0.2 µM	Binds to opposite strand
DNA Template	~50 ng/µL	1	~1 ng/µL	Target sequence
Total	—	50	—	—

Important: Always add Water first, then Master Mix → Primers → DNA Template last.

🔥 The Three Steps of PCR

Step	Temperature	Duration	What Happens
Denaturation	94–96°C	30 seconds	DNA double helix separates into single strands
Annealing	50–65°C	30 seconds	Primers bind to complementary target sequences
Extension	72°C	1 min/kb	Taq polymerase synthesizes new DNA strands

Amplification formula: Final copies ≈ Initial copies × 2ⁿ (n = number of cycles)

📊 Gel Electrophoresis Troubleshooting

Gel Observation	Likely Meaning	Common Causes	How to Fix
Single clean band at expected size	Successful PCR	Conditions optimized	—
No bands	No amplification	Bad primers, missing Taq, wrong Tm, no template	Check reagents, optimize annealing temperature
Multiple / extra bands	Non-specific amplification	Annealing temperature too low	Increase annealing temp by 2–5°C
Smear (no discrete bands)	Degraded DNA	Old or degraded template DNA	Use fresh high-quality DNA
Band in NTC	Contamination	Contaminated reagents or workspace	Use new reagents, clean area

🚀 How to Run the Lab

Quick Start: → Open PCR Learning Laboratory

Alternative (local):

Open index.html in any modern web browser (Chrome/Firefox/Edge recommended)
Start with Theory & Concepts, then follow the modules in order
Practice pipetting in the Virtual Lab (tutorial arrows will guide you)
Complete the quiz to earn your certificate

Fully client-side — works completely offline after the first load.

PCR powers COVID-19 testing, forensic DNA analysis, genetic research, and many other fields. This lab makes learning PCR visual, interactive, and practical so you truly understand the science instead of just memorizing steps.

Made with ❤️ for students who want to think and work like real molecular biologists.