Single-copy sequences

In mammals, some 10% of the DNA is highly repetitive, a further 20% is moderately reiterated and the remainder represents non-repetitive or single copy sequences. The rate of renaturation of DNA has been used to estimate that 16% of the DNA in H. diminuta is repetitive (746). Furthermore, the rate of reassociation of the single copy component in this species has allowed calculation of its haploid genome size, which is approximately... 

In eukaryotic DNA, some DNA sequences are reiterated as many as 10 to 10 times in each cell. Whereas practically all of the DNA of E. coli is single-copy (sequences present only once in the genome), only about half of mammalian DNA and about a third of plant DNA fall into this category. 

Caccio S., Perani P., Saccone S., Kadi F., Bernardi G. (1994). Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates. J. Mol. Evol. 39 331-339. 

Those sequences that have the most copies in solution will reanneal fastest, as there is a greater chance of encountering their matching complementary pair, while the more complex single-copy sequences take the longest to reanneal. Hence a sample of DNA that contains both single-copy sequences and sequences with multiple copies will give a Cot plot that appears more like the one in Fig. 7-5. 

The Cot plot in Fig. 7-6 is from human DNA. What can be concluded from this analysis The human genome (and other mammalian DNA) has a population of sequences that appear in high copy number (30-40%) and a population that is composed of highly complex single-copy sequences. These have been divided somewhat arbitrarily into four groups (1) highly repetitive, (2) moderately repetitive, (3) small copy number, and... 

Fig. 7-6 The Cgt plot from a sample of human DNA that contained both single-copy sequences and sequences with multiple copies.

A crucial aspect of virtually all DNA-DNA hybridization studies is that they involve only so-called single-copy DNA (scDNA) or "unique DNA. Total genomic DNA is made single-stranded by heating and then allowed to reassociate into duplex DNA after cooling. Repeated copies of DNA sequences re-anneal faster than single-copy sequences due to their higher concentration in the solution. Thus, under controlled conditions and time, it is possible to remove excess copies of repeated sequences. 

Britten, R.J., A. Cetta, and E.H. Davidson. 1978. The single-copy sequence polymorphism of the sea urchin Strongylocentrotus purpuratus. Cell 15 1175-1186. 

The second class of rapidly reassociating DNA sequences make up between 20 and 25% of the mouse genome and reassociate at an average rate from a few to 100,000 times faster than would be expected for single copy sequences in a genome the size of a mouse. In RNA/DNA low Cot hybridization reactions, these repeated sequences are the major DNA component in the reaction. 

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