Cot value and Cot Curve analysis is a technique for measuring DNA complexity based on renaturation kinetics. DNA is denatured and allowed to reanneal, with larger DNA taking longer. Cot value accounts for DNA concentration, time, and buffer effects, representing repetitive sequences - lower Cot means more repeats. Examples show bacteria have nearly all single-copy DNA, while mouse has varying proportions of single-copy, middle repetitive, and highly repetitive sequences. Cot curve analysis provides information on genome size, complexity, and proportions of sequence types.

1. Cot value and Cot Curve analysis
Unit-2|Core course-8
It is a technique for measuring the complexity (size) of DNA or genome. The technique was
developed by Roy Britten and Eric Davidson in 1960. The technique is based on the principle of
DNA renaturation kinetics.
Principle: The rate of renaturation is directly proportional to the number of times the
sequences are present in the genome.
Given enough time all DNA that is denatured will reassociate or reanneal in a given DNA sample.
The more the repetitive sequence the less will be the time taken for renaturation.
Procedure: The process involves denaturation of DNA by heating and allowed to reanneal by
cooling. The renaturation of DNA is assessed stereoscopically. Large DNA molecules take longer
time to reanneal.
What is cot value?
The renaturation depends on the following factors
DNA concentration, reassociation temperature,
cation concentration and viscosity.
Cot=DNA Concentration (moles/L) X renaturation
time in seconds X buffer factor (that accounts for
the effects of cations on the speed of renaturation).
Cot: Co=Concentration of DNA and t= time taken
for renaturation
Low cot value indicates a greater number of
repetitive sequences
High cot value indicates a greater number of unique sequences or less number of repetitive
sequences.

2. For example:
Bacteria- 99.7% Single Copy
Mouse - 60% Single Copy +25% Middle Repetitive+ 10% Highly Repetitive
How to calculate cot value?
Cot=DNA Concentration (moles/L) X renaturation time in seconds X buffer factor (that accounts
for the effects of cations on the speed of renaturation).
Nucleotide concentration = 0.050 M
Renaturation time = 344 sec
Buffer factor, 0.5 M SPB = 5.820
Cot value = 0.050X 344 X 5.820=100.000
Applications of Cot curve analysis:
Cot curve
Understanding genome size and complexity
Understanding complexity of sequences
Understanding relative proportion of single copy and repetitive sequences