All subjects · Biology · WBI14 (Unit 4)

PCR, gel electrophoresis and DNA profiling

Forensic scientists can identify a person from a tiny sample of DNA. PCR makes many copies, gel electrophoresis separates fragments, and the pattern is a DNA profile.

The polymerase chain reaction (PCR)

PCR copies a section of DNA many times. The reaction mixture contains the DNA sample, primers (short single-stranded DNA complementary to each end of the target), free DNA nucleotides and Taq polymerase, a heat-stable DNA polymerase from a bacterium that lives in hot springs.

1. Denaturation at about 95 °C: hydrogen bonds break and the strands separate.

2. Annealing at about 55 °C: primers bind to complementary sequences at the ends of the target.

3. Extension at about 72 °C: Taq polymerase adds nucleotides from the primers, making new complementary strands.

Each cycle doubles the DNA, so after n cycles there are 2n copies of each starting molecule. 30 cycles take a few hours.

Gel electrophoresis

1. DNA is cut into fragments with restriction enzymes, or specific regions are copied by PCR.

2. Samples are loaded into wells in an agarose gel covered with buffer, beside a DNA ladder of known fragment sizes.

3. A current is passed. DNA is negatively charged (phosphate groups), so it moves towards the positive electrode (anode).

4. Smaller fragments move further through the gel's mesh.

5. The DNA is made visible with a stain or a fluorescent or radioactive probe.

DNA profiling

DNA profiling uses non-coding regions containing short tandem repeats (STRs): short sequences repeated many times. The number of repeats at each site varies between people, so fragment lengths differ. Looking at several sites gives a pattern of bands that is almost unique (identical twins share one).

Uses: matching DNA from a crime scene to a suspect; identifying bodies; and testing relationships, because each band in a child's profile must come from the mother or the father.

Worked example

A PCR starts with 5 molecules of target DNA. How many copies are there after 10 cycles?

  1. Each cycle doubles the number.
  2. 5 x 210 = 5 x 1024

Answer: 5120 copies.

Key idea: PCR: denature about 95 °C, anneal primers about 55 °C, extend with Taq polymerase at 72 °C; 2n copies after n cycles. Electrophoresis: negative DNA moves to the anode, smaller fragments further. STR profiles identify people and relationships.

Check yourself

  1. Starting from one DNA molecule, how many copies are there after 20 PCR cycles?
    Show answer

    1048576. 220 = 1 048 576.

  2. A sample has 50 target molecules. How many copies are there after 8 cycles?
    Show answer

    12800. 50 x 256 = 12 800.

  3. Why is Taq polymerase used in PCR?
    • It works best at 4 °C
    • It is not denatured at the high temperatures used
    • It cuts DNA at specific sequences
    • It joins Okazaki fragments only
    Show answer

    It is not denatured at the high temperatures used. It comes from a heat-loving bacterium, so it survives 95 °C.

  4. What happens during the 95 °C step of PCR?
    • Primers bind to the DNA
    • New nucleotides are added
    • Hydrogen bonds break and the DNA strands separate
    • Phosphodiester bonds form between fragments
    Show answer

    Hydrogen bonds break and the DNA strands separate. Heat separates the strands.

  5. What is the role of primers in PCR?
    • They bind to the ends of the target sequence so polymerase can start copying
    • They break the DNA strands apart
    • They stain the DNA
    • They cut DNA into fragments
    Show answer

    They bind to the ends of the target sequence so polymerase can start copying. Polymerase needs a short double-stranded start point.

  6. Why does DNA move towards the positive electrode in gel electrophoresis?
    • It is positively charged
    • It is pushed by the buffer flow only
    • Its phosphate groups make it negatively charged
    • It is attracted to the agarose
    Show answer

    Its phosphate groups make it negatively charged. Opposite charges attract.

  7. Which DNA fragments travel furthest through the gel?
    • The smallest fragments
    • The largest fragments
    • The most positively charged fragments
    • Fragments with the most guanine
    Show answer

    The smallest fragments. Small fragments pass through the mesh more easily.

  8. In a paternity test, how is a man shown to be the likely father?
    • His profile is identical to the child's
    • Every band in the child's profile not from the mother matches a band in his
    • He has more bands than the child
    • His profile matches the mother's
    Show answer

    Every band in the child's profile not from the mother matches a band in his. Each band comes from one parent.

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Last updated 7 November 2026. Spotted a mistake? Tell us.