The coding sequence contained in the worm’s DNA is not final. During the creation of the messenger RNA that leaves the nucleus, segments of RNA marked by certain specific sequences are removed. The parts that get removed are called introns, and their surroundings, the parts of the coding sequence that stay, are called exons. Introns aren’t common in prokaryotes, but they do exist, particularly in the form of self-splicing introns, which are also found in eukaryotes, but aren’t very common in either case.

Eukaryotic genes with certain introns in them experience a significantly higher rate of expression than genes without introns; as a result, adding these introns to DNA can often improve the rate of production of imported proteins, and may prove useful to those looking to import BioBricks from the Registry of Standard Biological Parts. They may also be useful as a method for concealing ligation scars, promoters intended for other organisms, or other genetic elements that would benefit from being within the coding sequence, but would run the risk of causing a frameshift mutation or producing an undesirable amino acid sequence.

Self-splicing introns are possible because normal intron removal is accomplished by a set of RNA molecules that act catalytically (ribozymes). In normal splicing, these are found in the nucleus, in a complex called the spliceosome. This binds to the exposed pre-messenger RNA by complementary base-pairing and then twists it into the correct shape, snapping off the intron. In order for this to succeed, the middle of the intron must include at least one adenosine. One example of an intron sequence is:

caggtaagt … a … ttttgtttcagg

The parts in bold will be removed completely. The unbolded parts of this are not necessary, but appear in a substantial portion of C. elegans introns, especially the final G. Underlined text is absolutely or almost absolutely necessary; non-underlined text merely helps, although it is very common that the region just upstream from the end of the intron is pyrimidine-rich (lots of C and U/T). Again, this sequence does not require any specific reading frame to function, as intron removal occurs prior to translation. The rather short and simple content of the underlined text (which is the minimum required to define an intron) means that it is sometimes surprisingly easy for a point mutation to trigger a deletion by creating an intron, and this should be considered.