Interaction of endonuclease ecoRI with short specific and nonspecific oligonucleotides.
The interaction of EcoRI with different oligodeoxyribonucleotides (ODNs) was analyzed using the method of the slow step-by-step simplification in their complexity. Orthophosphate (KI = 31 mM), 2-deoxyribose 5-phosphate (KI = 4.6 mM) and different dNMPs (KI = 2.1-2.5 mM) were shown to be the minimal 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 approximately 2.0. Weak nonspecific electrostatic contacts of EcoRI with 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)n is no more than 2 orders of magnitude of a total ODN's affinity.
Kolocheva
T I
TI
Novosibirsk Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences.
Maksakova
G A
GA
Bugreev
D D
DD
Nevinsky
G A
GA
D001483:Base Sequence; D001665:Binding Sites; D015246:Deoxyribonuclease EcoRI / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D007700:Kinetics; D008024:Ligands; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D055672:Static Electricity; D013379:Substrate Specificity
D004791:Enzyme Inhibitors; D008024:Ligands; D009838:Oligodeoxyribonucleotides; D015246:Deoxyribonuclease EcoRI