C0t filtration, or CF, is a technique that uses the principles of DNA renaturation kinetics (i.e. Cot analysis) to separate the repetitive DNA sequences that dominate many eukaryotic genomes from "gene-rich" single/low-copy sequences.
[1][2] This allows DNA sequencing to concentrate on the parts of the genome that are most informative and interesting.
Briefly, when sheared genomic DNA in solution is heated to near boiling temperature, the molecular forces holding complementary base pairs together are disrupted, and the two strands of each double-helix dissociate or ‘denature.’ If the denatured DNA is then slowly returned to a cooler temperature, sequences will begin to ‘reassociate’ (renature) with complementary strands.
In CF, genomic DNA is heat-denatured and allowed to renature to a Cot value (Cot = DNA concentration x time x a factor based on the cation concentration of the buffer) at which the majority of repetitive elements have reassociated but single and low-copy elements remain single stranded.
CF is most accurately performed if fractionation is based upon the results of a Cot analysis.