Skip to main content
SingaporeBiotechnologySyllabus dot point

How can we separate a mixture of DNA pieces by size and read the result as a pattern of bands?

Describe gel electrophoresis and explain how it separates DNA fragments by size

A focused answer to the O-Level outcome on gel electrophoresis. Loading DNA into a gel, applying an electric field, why smaller fragments travel further, and reading the bands.

Generated by Claude Opus 4.89 min answer

Reviewed by: AI editorial process; not yet individually human-reviewed

Have a quick question? Jump to the Q&A page

Jump to a section
  1. What this dot point is asking
  2. The answer
  3. Examples in context
  4. Try this

What this dot point is asking

This outcome asks you to describe gel electrophoresis and explain how it sorts DNA fragments by size. It is the standard way to look at DNA in a laboratory, turning an invisible mixture into a readable pattern of bands, and examiners reward a clear cause for why small fragments travel furthest.

The answer

What gel electrophoresis does

Gel electrophoresis separates a mixture of DNA fragments according to their size, producing a pattern of bands that can be read and compared.

The procedure

  1. Load the DNA. The fragments are pipetted into small wells at one end of a slab of gel.
  2. Apply an electric field. The gel sits in a tank with the negative electrode at the well end and the positive electrode at the far end.
  3. Let the DNA move. The field is left on for a set time, then switched off.
  4. Stain and view. The DNA is stained so the fragments appear as bands.

Why DNA moves toward the positive electrode

DNA carries a negative charge (from its phosphate groups), so it is attracted toward the positive electrode and moves through the gel in that direction.

Why fragments separate by size

The gel acts like a sieve full of tiny pores:

  • Smaller fragments slip through the pores easily and so travel further.
  • Larger fragments are held back and travel less far.

So after the run, fragments of the same size collect at the same place, forming a band. The band furthest from the wells contains the smallest fragments; the band nearest the wells contains the largest.

Reading the result

Each band is a group of fragments of one size. By comparing the positions of bands, or comparing them with a set of known-size markers run alongside, you can estimate fragment sizes and compare different DNA samples.

Examples in context

Example 1. Genetic profiling. In forensics, variable regions of DNA are amplified by PCR and then run on a gel. Because individuals differ in fragment sizes, each person gives a distinctive banding pattern, which is compared between a sample and a suspect.

Example 2. Checking a genetic engineering result. After cutting DNA with a restriction enzyme, scientists run the pieces on a gel to confirm the expected fragment sizes, checking that the cutting, or the insertion of a gene, worked as planned.

Try this

Q1. State why DNA fragments move toward the positive electrode during electrophoresis. [1 mark]

  • Cue. DNA is negatively charged, so it is attracted to the positive electrode.

Q2. Explain why smaller DNA fragments travel further through the gel. [2 marks]

  • Cue. The gel acts as a sieve; smaller fragments pass through its pores more easily, so they move faster and travel further than larger ones.

Q3. State what a single band on a finished gel represents. [1 mark]

  • Cue. A group of DNA fragments that are all the same size.

Exam-style practice questions

Practice questions written in the style of SEAB exam questions on this dot point, with worked answer explainers. The year tag is the paper they imitate, not the source.

Original6 marksDescribe how gel electrophoresis is used to separate a mixture of DNA fragments, and explain why the fragments separate by size.
Show worked answer →

Examiners want the procedure and the reason small fragments travel further.

The DNA fragments are loaded into small wells at one end of a gel. An electric field is then applied across the gel, with the negative electrode at the well end and the positive electrode at the far end.

Because DNA carries a negative charge, the fragments are attracted toward the positive electrode and move through the gel. The gel acts like a sieve: smaller fragments move through it more easily and so travel further, while larger fragments are held back and travel less far.

After a time the field is switched off. The DNA is stained so the fragments show up as a pattern of bands, with each band a group of fragments of the same size. The position of a band shows the size of its fragments.

What markers reward: loading DNA into wells, applying an electric field with DNA moving toward the positive electrode because it is negatively charged, the gel separating fragments by size with smaller ones travelling further, and staining to reveal bands whose position indicates fragment size.

Original3 marksA gel shows DNA bands at different distances from the wells. Explain how you can tell which band contains the smallest fragments.
Show worked answer →

The answer should link distance travelled to fragment size.

The band that has travelled the furthest from the wells contains the smallest fragments. This is because smaller fragments move through the gel more easily and quickly than larger ones, so they travel the greatest distance in the time the field is applied.

Conversely, the band closest to the wells contains the largest fragments, which are held back by the gel.

What markers reward: identifying the furthest-travelled band as the smallest fragments, with the explanation that smaller fragments move more easily through the gel and so travel further.

Related dot points