Cot Analysis: Single‐copy versus Repetitive DNA

Abstract

DNA reassociation, analysed by Cot methods, has provided insights into the organization, uneven replication, evolution and expression of genomes, and into disease processes such as viral infection and cancer.

Keywords: cot curves; DNA reassociation; genome organization; genome complexity; molecular phylogeny

Figure 1.

The time course of reassociation is shown for bacterial and for calf DNA. The amount of reassociation is plotted against the Cot. The time course for bacterial (Escherichia coli) DNA, almost all of which is single‐copy DNA, plots as an S‐shaped curve (red). If calf DNA were also single‐copy DNA, it would plot as a similar curve diplaced to the right (green). The actual curve for calf DNA (blue) has a different shape, however. The shape of the curve indicates that the reaction takes place in two different stages, one early and one late; the midpoints of the two stages (broken vertical lines) are separated by a factor of 100 000. The early stage represents the reassociation of repeated DNA and the later stage that of single‐copy DNA. (From Britten and Kohne, ).

Figure 2.

Dissociation profiles reveal sequence divergence within a species. For simplicity, the species is considered to be haploid and to have only single‐copy DNA sequences. In assay no. 1, DNA from several individuals is dissociated, reassociated separately to a specified Cot value, mixed and then subjected to a dissociation profile (red line). In assay no. 2, the DNA samples are first mixed, then dissociated, reassociated to the specified Cot value and subjected to a dissociation profile (blue line). In assay no. 1, all duplexes are composed of single strands from the same individual. In assay no. 2, most duplexes (the fraction depending on the number of individuals tested) are composed of single strands from different individuals. The duplexes derived from different individuals contain base mismatches absent from duplexes derived from a single individual. The decrease in thermal stability that occurs when the DNA is from different individuals gauges DNA sequence polymorphism within the species. This technique also has been used to gauge sequence divergence in diploid species containing repetitive DNA.

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References

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Further Reading

Britten RJ and Davidson EH (1976) Studies on nucleic acid reassociation kinetics: empirical equations describing DNA reassociation. Proceedings of the National Academy of Sciences of the USA 73(2): 415–419.

Britten RJ, Graham DE and Neufeld BR (1974) Analysis of repeating DNA sequences by reassociation. Methods in Enzymology 29: 363–418.

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How to Cite close
Graham, Geoffrey J(Apr 2001) Cot Analysis: Single‐copy versus Repetitive DNA. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0001161]