DNA oligonucleotide mutations are caused spontaneously during the DNA replication process. Most DNA replicates precisely. Though rare, errors or mutations sometimes occur during this ongoing DNA replication process.

These are some of the more common causes of DNA oligonucleotide mutations:

1. Copying errors that produce mutations                      
2. Chemical volatility of purine and pyrimidine bases
3. Exposure of an organism to ultraviolet light, chemical carcinogens, or some other environment factor that triggers a reaction
4. Deamination of cytosine to uracil in the DNA double helix 

Most DNA oligonucleotide mutations get fixed immediately after they occur via an ongoing DNA repair process. During this DNA repair process, highly sensitive repair enzymes instantly repair and replace the replication errors, so they go largely unnoticed. However, some errors make it past these repair enzymes. These errors go on to become permanent mutations.