PCR and gel electrophoresis
About this app
An invented forensic case: choose primers, run the first three cycles by hand, start the programme, load the gel and read the bands against the marker under blue light. The strands count themselves: 2ⁿ − 2n target fragments, 2n long strands. Zooming into a band reveals billions of molecules of equal length.
With explain mode: an AI tutor walks you through the app, points out what matters in the scene and answers your questions.
From a stretch of DNA to a pattern
The polymerase chain reaction copies a chosen stretch of DNA. Each cycle consists of denaturation at 94–95 °C, annealing at 50–65 °C and elongation at 72 °C. Two primers delimit the target, their 3' ends pointing towards each other. Gel electrophoresis then separates the copies by length: DNA is negatively charged, migrates to the anode, and the agarose mesh slows long fragments more than short ones.
What the app shows
A thermocycler and a glowing gel are the main scene. Zooming into the tube leads to the molecular level, where template, long products and target fragments have separate colours. The counter works per starting duplex: 2n long strands, 2ⁿ − 2n target fragments, 2ⁿ as the approximation for large n. Zooming into a band shows that it consists of billions of molecules of equal length.
Try it yourself
Drag the temperature by hand through three cycles and see the first two target fragments after cycle 3. Choose a primer pair whose 3' ends point apart and the gel stays dark. Swap the poles, change voltage and run time, read the bands against the size marker and justify, in an invented case, whose DNA is on the cup. Seven exam questions give reasoned feedback.
Frequently asked questions
- How many DNA copies does PCR produce after n cycles?
- At full yield one duplex gives 2ⁿ duplexes. Of these, 2ⁿ − 2n are target fragments with exactly defined ends. The others contain one of the 2 template strands or one of the 2n long strands. After 30 cycles that means 1,073,741,764 target fragments, which is why 2ⁿ is used as an approximation.
- Why do short DNA fragments run further in a gel than long ones?
- Charge and mass both grow with length, so force per mass stays roughly equal. The agarose mesh acts as a sieve: long molecules get caught more often and move more slowly. Short fragments therefore end up closer to the anode.
- Is a band in a gel a single DNA molecule?
- No. A band holds very many fragments of equal length. The detection limit is about 1 ng, which at 232 base pairs means around 4 billion molecules. A single molecule would be invisible.
- What can I do in the app?
- You choose primers, drive the temperature by hand, start the programme, load the gel, set polarity, voltage and run time, read bands against the marker and justify the result of an invented case. An exam part with seven questions is included.
Subject: Biology (Gymnasium)
More from Biology (Gymnasium)
- Antigen & antibody
- Speciation through isolation
- Biological membranes
- Blood circulation and the cardiac cycle
- Genetic code wheel
- The inner clock: light, melatonin and the clock change
- The cell (3D)
- DNA double helix (3D)
A VisuApp by heyprof: interactive, free in your browser, no sign-up. What is a VisuApp? · All apps