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DNA has a negatively charged phosphate backbone and moves toward the positive electrode in the appropriately assembled gel system. The agarose matrix impedes different-sized fragments differently, so shorter fragments generally travel farther under comparable conditions. Record gel and run conditions because migration is not determined by fragment length alone.
Video by Bio-Rad Explorer. Use the demonstration alongside this lesson’s specification reference and written explanations.
Viewing focus: Explain charge-driven DNA separation through a gel
After watching, attempt these questions before opening the answers. You can also use the written lesson below.
After watching 1: Which electrode does DNA normally move toward?
The positive electrode. The phosphate backbone contributes negative charge.
After watching 2: Why use a reference ladder on the same gel?
To compare unknown migration with known fragment sizes. A same-run reference controls relevant migration conditions.
What you'll be able to do
DNA has a negatively charged phosphate backbone and moves toward the positive electrode in the appropriately assembled gel system. The agarose matrix impedes different-sized fragments differently, so shorter fragments generally travel farther under comparable conditions. Record gel and run conditions because migration is not determined by fragment length alone.
Use the teacher-approved loading, electrical supply, staining and viewing arrangements. A tracking dye helps follow progress but is not necessarily a DNA fragment. Do not infer that every visible coloured mark represents DNA without the method’s detection evidence. Treat any image supplied for analysis as a provided result rather than claiming to have generated it.
A ladder contains fragments of known sizes and supports interpolation of an unknown’s migration. Over a justified range, log fragment size may relate approximately linearly to distance. This does not mean base-pair size is always linear with distance, so an arithmetic midpoint can give an incorrect estimate.
Compare samples under the same conditions and use suitable known/reference and contamination controls. Smearing can reflect several limitations, including sample quality or inappropriate loading. An absent band may indicate low amount, a detection problem or a true absence of that fragment; a functioning control is needed before choosing among these explanations.
A single matching band supports a shared fragment size within the resolution of the method, not a unique identity. A fuller DNA-profile comparison uses several informative loci and appropriate interpretation of the population and candidate evidence. Band intensity is not automatically a precise molecule count without calibration.
Retain the original image, lane labels and analysis decisions. Different exposure or contrast settings can affect apparent faint bands. A clear written conclusion states which lanes match by the chosen criteria, which differ and what further evidence is required; it does not silently remove uncertain bands to force a match.
Attempt these problems on paper before opening the worked reasoning. Explain your steps as well as giving a final answer.
Common mistakes to avoid
Key takeaways
Question 1: Two samples each have one band at the same position. Is a unique common origin established?
No. State the limited matching-size inference and seek independent evidence.
Check the assessed scope and practical or mathematical requirements.
An external explanation or interactive activity to use alongside the lesson. It may include extension material.
Close the notes and answer from memory. Revisit any explanation you cannot yet reconstruct.
Test yourself
Answer a few questions, then review anything you missed.
Start with the quiz above to check the key ideas. You can also choose another topic from the practice library.