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PCR Amplification Step-Through Simulator

Run the PCR Amplification Step-Through Simulator Fullscreen

About This MicroSim

Forensic DNA analysis usually starts with a tiny amount of DNA — sometimes just a few cells from a touched surface. Before it can be profiled, that DNA has to be amplified into millions of copies. The tool that does this is the polymerase chain reaction (PCR), and it works by repeating the same three temperature steps over and over:

  • Denaturation (94 °C) — heat unzips the double helix into two single strands.
  • Annealing (60 °C) — short primers bind to where copying should start.
  • Extension (72 °C) — Taq polymerase builds a new strand from each primer.

Each complete cycle doubles the DNA. This MicroSim lets you step through the cycle one stage at a time and watch the molecule transform, with the temperature and copy count shown the whole way.

How to Use It

  1. Press Next Step to move through Denaturation → Annealing → Extension, one stage at a time. Try to predict what the DNA will do before each reveal.
  2. Watch the Molecular View:
  3. Denaturation: the gray base-pair bridges break and the red and blue strands drift apart.
  4. Annealing: yellow primers slide in and bind to each strand.
  5. Extension: a light-purple new strand grows from each primer while a gray polymerase rides the growing end.
  6. Read the side panel: the temperature gauge, the current step name and description, the cycle counter, and the copies counter.
  7. Press Run Cycle to auto-play all three steps, or Run 5 Cycles to watch the copy count grow exponentially (×2, ×4, ×8, ×16, ×32).
  8. Click any DNA part — template strand, primer, new strand, or polymerase — to read its definition.
  9. Press Reset to start over.

What You Can Learn

  • Explain what happens to the DNA at each PCR step and the temperature it needs.
  • Describe the jobs of the template strand, the primers, and Taq polymerase.
  • Explain why each cycle doubles the DNA, giving exponential amplification.

You can embed this MicroSim on your own web page with this iframe:

<iframe src="https://dmccreary.github.io/forensic-science/sims/pcr-amplification-simulator/main.html"
        width="100%" height="502" scrolling="no"></iframe>

Lesson Plan

Audience: High-school forensic science (grades 9–12) Time: 8–12 minutes Bloom level: Understand (L2) — explain.

Worked example. Press Next Step three times and narrate each stage: "Heat separates the strands… the primers bind… the polymerase copies." Note the cycle counter ticks to 1 and copies jumps to ×2. Then press Run 5 Cycles and watch the copy count race to ×32.

Guided questions:

  • Why must the temperature go up for denaturation but down for annealing?
  • What would happen to the reaction if you left the primers out?
  • After 10 cycles, how many copies would one starting molecule produce? (Hint: it's a power of two.)

Extension. Real PCR runs 28–35 cycles. Using the doubling rule, estimate how many copies 30 cycles makes from a single molecule, and discuss why that sensitivity is both PCR's greatest strength and a contamination risk in a forensic lab.

References

Specification

This MicroSim was generated from a specification in Chapter 8: Forensic DNA Profiling.

Design note: the strands, primers, and new DNA are schematic — straight colored lines rather than a true double-helix model — so the focus stays on what changes at each step. The temperatures (94/60/72 °C) and the doubling rule are accurate; the per-step animation timing is for clarity, not real reaction speed.