A calculation of fragment lengths obtainable from human DNA with 78 restriction enzymes: an aid for cloning and mapping.

The optimal choice of restriction enzymes to be used with mammalian DNA is critical for construction of subgenomic libraries pulse field gel electrophoresis, RFLP studies and other applications. For this purpose we have grouped 78 restriction enzymes representing the majority of known recognition sequences according to the expected average fragment length S (in bp) and provided estimates of the number of different fragments N and the maximal length of fragments Dmax obtainable with each. The frequencies of 16 possible dinucleotides in human DNA (Swartz, J., Trautner, M. and Kornberg, A. (1962).J.Biol. Chem., 237, 1961.) do not meet the expectation of randomness for a DNA having a GC content of 39,4%. We have defined S as the inverse of the product of the frequencies of dinucleotides forming the restriction site and the probabilities of their association. Thus S is highly sequence dependent. The results are applicable to all mammalian DNAs, since their dinucleotide frequences are similar. Due to the statistical nature of the calculation, the real values may differ if the sequences involved are not random for functional or structural reasons.