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.