Cutting a DNA fragment:
The frequency at which a R. E. will cut a DNA fragment is a
direct function of the length of the recognition sequence. As a
particular base position in a DNA strand can be occupied by any
of the four nitrogenous bases A, T, C or C, probability of repeating
a 6 bp segment of defined sequence is 4b or 4096. Therefore a
hexacutter will cut DNA once in every 4096 bp and a tetracutter
will cut DNA once in every 44 or 256 bp distance. This is true for a
DNA strand with random nucleotide distribution. If GC content
is higher, as observed in many repetitive DNA sequences,
probability will increase for those enzymes that have GC rich
recognition sequences and will decrease for others. Depending
on the distance between two cuts, the restriction endonucleases
are classified asfrc’quent cutters (Snu3A) or rare cutters (Not I).
The frequency at which a R. E. will cut a DNA fragment is a
direct function of the length of the recognition sequence. As a
particular base position in a DNA strand can be occupied by any
of the four nitrogenous bases A, T, C or C, probability of repeating
a 6 bp segment of defined sequence is 4b or 4096. Therefore a
will cut DNA once in every 44 or 256 bp distance. This is true for a
DNA strand with random nucleotide distribution. If GC content
is higher, as observed in many repetitive DNA sequences,
probability will increase for those enzymes that have GC rich
recognition sequences and will decrease for others. Depending
on the distance between two cuts, the restriction endonucleases
are classified asfrc’quent cutters (Snu3A) or rare cutters (Not I).
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