Spermidine increases the accuracy of type II restriction endonucleases. Suppression of cleavage at degenerate, non-symmetrical sites.

The non-specific cleavage of DNA by type II restriction endonucleases (BamHI, BsuRI, EcoRI, EcoRV, HindIII, PstI and SalI) can be effectively suppressed by spermidine in millimolar concentrations, regardless of whether the non-specific cleavage is induced by high concentrations of enzyme under optimal buffer conditions or by high pH, low ionic strength, organic solvents and Mn2+ ions. The increased specificity of restriction endonucleases in the presence of spermidine is due to an enhancement of the cleavage rate at the canonical site and a slowing down of the cleavage rate at related sites. It is argued that spermidine is essential for the high accuracy of restriction endonucleases in vivo.