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Restriction Sites Plus 3

Restriction Calculations 3 — Advanced I

 
Calculate how frequently a given restriction site would be expected to occur in a stretch of DNA of a specific base composition (%GC).
Probabilities are not of the simple 1-in-integer type, so a slight variation from the previous mode of calculation is recommended. Round off answers to the nearest 10.

One site every base-pairs   
 
If the probability of finding a restrictions site at any position in DNA is ‘1 in x’, one can expect to find that site once every x base-pairs. This (overall) probability may be calculated by multiplying the probabilities of occurence of the base at each individual position in the site. In this case one is advised to express the probabilities as decimal fractions, e.g. in DNA of 50% GC, the probability of occurrence of each base is 0.25, and that of purines and pyrimidines 0.5. After multiplying these together one takes the reciprocal to get the frequency in base-pairs. The following is an example in DNA of a base composition that is not 50% GC:
  • Consider the site, AGCT, in DNA of base composition 60% GC.
  • The probability of occurrence of G and C is 0.3, and that of A and T is 0.2.
  • Hence the overall probability of occurrence is 0.2x0.3x0.3x0.2 = 0.0036.
  • AGCT therefore occurs 1 in every 1/0.0036 base-pairs = 1-in-278 or, rounded, 1-in-280 base-pairs. (cf. 1-in-256 in DNA of 50% GC.)
  • (NB. The probability of occurrence of Y or R in this example is 0.2 + 0.3 = 0.5. However it will have this value regardless of the base composition of the DNA.)