Cot-curve

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Organization of DNA •

DNA reassociation kinetics –

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Allow DNA for a given species to denature (usually by heat) Time how long it takes for the DNA to renature Repetitive sequences renature faster than nonrepetitive(unique) sequences







Cot Curve







Types of DNA in genomes •

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Classification based on reassociation kinetics Three classes Highly repetitive: repetitive: About 10-15% of mammalian DNA Moderately repetitive: Roughly 25-40% of mammalian DNA. Single copy (or very low copy number): This class –

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Highly Repetitive DNA •

Often found as tandem repeats: Three types Satellite DNA: ranges from 100 kb to 1Mb in size; type of repeat found at centromere sequences Minisatellite DNA: ranges from 1 kb to 20 kb; type of repeat used for DNA fingerprinting and is the type of repeat found in telomere sequences Microsatellite DNA: 1 bp to 150 bp; the smallest –

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Other kinds of repetitive DNA •

Interspersed, Interspersed, genome wide: –

Retrotransposon (with (wi th LTR) LTR)

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Retroposon (no LTR) •

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LINES-long interspersed nuclear elements SINES-short interspersed nuclear elements (eg. Alu repeats)









Variation in genome size •

Due to differences differences in amount and kind kin d of repetitive sequences







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The human genome consists of all the DNA present in the cell. It can be divided into the nuclear genome genome







Cot Curves •

Cot curves are generated by shearing DNA to about 1000 bp length, then melting it, lowering the temp and allowing it to re-anneal, measuring the % still single stranded at various time points.







Cot Curves and Copy Number •

Number of copies of each sequence determines the rate: how many collisions does a given strand have to make before it







Complex Cot Curves •

For eukaryotic DNA, Cot curves are not simple sigmoid curves. cur ves. Computer analysis generally resolves them into 3 sections:















Highly Repeated Sequences







Satellite DNA







Mini- and Microsatellite







Moderately Repeated DNA

Cot-curve

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