PCR, electrophoresis and DNA profiles

What you’ll learn

• Explain DNA amplification at the level of its main stages.
• Interpret separation of DNA fragments by size.
• Evaluate identification and relatedness evidence.

Understand the idea

PCR amplifies a selected DNA region in repeated cycles. Double-stranded DNA separates, primers bind to complementary flanking sequences, and a DNA polymerase extends from them using nucleotides. A heat-stable polymerase remains functional through repeated heating. Under an ideal model the target copy number doubles per cycle, but actual reactions eventually depart from ideal efficiency. PCR makes a small starting sample detectable; it does not guarantee that it came from the intended source.

DNA has a negatively charged phosphate backbone and migrates towards the positive electrode in gel electrophoresis. The gel impedes larger fragments more strongly, so shorter fragments usually travel farther in a fixed time under the same conditions. A reference ladder permits size estimates. Fluorescent or other detection methods reveal bands; a band position indicates fragment length, not the full DNA sequence.

Profiles compare variable DNA regions across samples. In a simple inheritance comparison, each child’s allele at a locus should be attributable to one biological parent or the other. Using multiple independent loci strengthens discrimination. A match supports common origin or relatedness but requires probability, contamination, mixture and chain-of-custody considerations; a profile alone does not establish how or when DNA reached a scene.

Key formulae

$$N_n=N_0\,2^n\quad\text{under ideal PCR doubling}$$

Worked example

At one DNA locus a child has alleles 12 and 15; the mother has 10 and 12. One possible father has 15 and 17, and another has 11 and 16. Interpret this locus.

1. The mother can supply the child’s allele 12.
2. The other inherited allele is 15, so the biological father must be capable of supplying 15 under the simple inheritance model.
3. The first candidate is compatible; the second is not compatible at this locus.

Answer: This locus supports the first candidate and excludes the second under the stated model; several loci and careful sample controls are needed for a reliable conclusion.