- Heavy strands and light strands of a DNA duplex refer to the density differences that result when there is an asymmetry between base representation in the two strands such that one strand is rich in T and G bases and the other is rich in C and A bases. This occurs in some satellite and mitochondrial DNAs.
- The repeating units of arthropod satellite DNAs are only a few nucleotides long. Most of the copies of the sequence are identical.
In the arthropods, as typified by insects and crabs, each satellite DNA appears to be rather homogeneous. Usually, a single very short repeating unit accounts for >90% of the satellite. This makes it relatively straightforward to determine the sequence.
Drosophila virilis has three major satellites and also a cryptic satellite, together representing >40% of the genome. The sequences of the satellites are summarized in Figure 4.21. The three major satellites have closely related sequences. A single base substitution is sufficient to generate either satellite II or III from the sequence of satellite I.
The satellite I sequence is present in other species of Drosophila related to virilis, and so may have preceded speciation. The sequences of satellites II and III seem to be specific to D. virilis, and so may have evolved from satellite I after speciation.
The main feature of these satellites is their very short repeating unit: only 7 bp. Similar satellites are found in other species. D. melanogaster has a variety of satellites, several of which have very short repeating units (5, 7, 10, or 12 bp). Comparable satellites are found in the crabs.
The close sequence relationship found among the D. virilis satellites is not necessarily a feature of other genomes, where the satellites may have unrelated sequences. Each satellite has arisen by a lateral amplification of a very short sequence. This sequence may represent a variant of a previously existing satellite (as in D. virilis), or could have some other origin.
Satellites are continually generated and lost from genomes. This makes it difficult to ascertain evolutionary relationships, since a current satellite could have evolved from some previous satellite that has since been lost. The important feature of these satellites is that they represent very long stretches of DNA of very low sequence complexity, within which constancy of sequence can be maintained
One feature of many of these satellites is a pronounced asymmetry in the orientation of base pairs on the two strands. In the example of the D. virilis satellites shown in Figure 4.20, in each of the major satellites one of the strands is much richer in T and G bases. This increases its buoyant density, so that upon denaturation this heavy strand (H) can be separated from the complementary light strand (L). This can be useful in sequencing the satellite.