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Full curriculum
  1. DNA damage and mutations as distinct genome changes
  2. DNA sequence substitutions, insertions and deletions
  3. The genetic code, codons and reading frames
  4. Coding-sequence consequences of base substitutions
  5. Coding-sequence consequences of insertions and deletions
  6. Homology, analogy and convergent evolution
  7. Sequence alignment as a hypothesis of positional homology
  8. Molecular sequence evidence for phylogenetic inference

Unit content

DNA sequence substitutions, insertions and deletions

Stable DNA sequence changes can be classified by what happens to the nucleotide sequence, independently of any later effect on a gene or phenotype.

A substitution replaces one nucleotide with another at a particular position. For example:

original:  A C G T A
changed:   A C A T A

The third nucleotide has been substituted.

An insertion adds one or more nucleotides:

original:  A C G T A
changed:   A C G G T A

A deletion removes one or more nucleotides:

original:  A C G T A
changed:   A C T A

Insertions and deletions are often grouped as indels.

These labels describe sequence structure only. The same class of change can have very different biological consequences depending on location. A substitution in one position may have little detectable effect, while another can alter a regulatory site or protein-coding sequence. Likewise, an indel can be harmless in one context and disruptive in another.

It is therefore useful to keep two questions separate:

  1. What changed in the DNA sequence? — substitution, insertion or deletion.
  2. What consequence does that change have? — a separate question determined by genomic context.

This distinction is important whenever DNA sequences are compared, including mutation analysis, genetics and evolutionary reconstruction.