Interaction of endonuclease EcoRI with short specific and nonspecific oligonucleotides

The interaction of EcoRI with different oligodeoxyribonucleotides (ODNs) wa s analyzed using the method of the slow step-by-step simplification in thei r complexity. Orthophosphate (K-I = 31 mM), 2-deoxyribose 5-phosphate (K-I = 4.6 mM) and different dN-MPs (K-I = 2.1-2.5 mM) were shown to be the mini mal ligands of the enzyme. The lengthening of a nonspecific d(pN)(n) (n = 1 -6) by one nucleotide unit resulted in the increase of their affinity by a factor of similar to2.0. Weak nonspecific electrostatic contacts of EcoRI w ith internucleotide phosphate groups of ODNs can account for about 5 orders of magnitude in the ligand affinity, whereas the contribution of specific interactions between EcoRI and d(pN), is no more than 2 orders of magnitude of a total ODN's affinity.