INTERACTION OF HUMAN PLACENTAL URACIL DNA GLYCOSYLASE WITH SINGLE-STRANDED OLIGONUCLEOTIDES AND THEIR DUPLEXES

A study was made of the affinity of (pA)(n), (pU)(n), (pC)(n), d(pT)(n ), d(pC)(n), d(pA)(n), d(pU)(n), and their duplexes to uracil DNA glyc osylase [EC 3.2.2.3]. All oligonucleotides and duplexes were shown to inhibit the glycosylase-cataiyzed reaction competitively against DNA. The inhibition constants were determined for various oligonucleotides. It was shown that the enzyme has increased affinity to a single nucle otide unit in all substrates. The K-i ranged from 0.005 to 0.15 M, dep ending on the nature of the base. At n = 1-10, increasing the oligonuc leotide length by one unit raised the affinity to UDG by a factor of 1 .38-1.7 (f) owing to formation of weak contacts. Factor f practically did not depend on the nature and relative hydrophobicity of the base a nd sugar moiety, and corresponded to a free energy change of 0.27-0.43 kcal/mole. The data obtained indicate that UDG recognizes the substra te by forming a large number of weak contacts with ten of its nucleoti de units. Interaction of the enzyme with any nucleotide unit is a supe rposition of its weak ion-dipole and hydrophobic contacts with its str uctural elements.