The Mechanism of the Supercoiled DNA Recognition by the Eukaryotic Type I Topoisomerases: I. The Enzyme Interaction with Nonspecific Oligonucleotides

Interaction of the DNA type I topoisomerases from the murine and human placenta cells with nonspecific oligonucleotides was analyzed. The contributions of strong and week nonspecific electrostatic, van der Waals's, and hydrophobic interactions, and hydrogen bonding of the enzymes to the complex formation with the single- and double-stranded DNAs were determined. The factors that determine the top-priority recognition of the topologically stressed DNA were revealed. The results were interpreted in comparison with the X-ray analysis data for human DNA topoisomerase I.     

Interaction of pro-and eukaryotic DNA repair enzymes with oligodeoxyribonucleotides containing clustered lesions

A study was made of the interaction of 8-oxoguanine-DNA glycosylases of Escherichia coli (Fpg) and human (OGG1), as well as apurinic/apyrimidinic endonucleases of yeast (Apn1) and E. coli (Nfo), with oligodeoxyribonucleotides containing 8-oxoguaine (oxoG) and tetrahydrofuran (F, a stable analog of an apurinic site) separated by various numbers of nucleotides. Inhibitor analysis showed that the affinity of Fgp for single-stranded DNA ligands is virtually independent of the relative positions of oxoG and F. K _M and k _cat were determined for all the four enzymes and all double-stranded substrates studied. The effect of the second lesion strongly depended both on the relative position of the lesion and the enzyme of interest. The highest drop in the affinity of Fpg and OGG1 for the substrate (1.6-to 148-fold) and in the reaction rate (4.8-to 58-fold) was recorded for the oligonucleotides in which F was immediately 3′ or 5′ of oxoG. Introduction of the second lesion barely affected K _M for nucleases Apn1 and Nfo. The reaction rate was five-to tenfold lower for the substrates containing two adjacent lesions. For all enzymes studied, an increase in the distance between two lesions in double-stranded DNA decreased their contribution to K _M and k _cat.     

Human milk lactoferrin binds two DNA molecules with different affinities.

Evidence is presented that lactoferrin (LF), an Fe3+-binding glycoprotein, possesses two DNA-binding sites with different affinities for specific oligonucleotides (ODNs) (Kdl = 8 nM; Kd2 approximately 0.1 mM). The high affinity site became labeled after incubation with affinity probes for DNA-binding sites; like the antibacterial and polyanion-binding sites, this site was shown to be located in the N-terminal domain of LF. Interaction of heparin with the polyanion-binding site inhibits the binding of ODNs to both sites. These data suggest that the DNA-binding sites of LF coincide or overlap with the known polyanion and antimicrobial domains of the protein.     

Correlated cleavage of single- and double-stranded substrates by uracil-DNA glycosylase

Uracil-DNA glycosylase (Ung) can quickly locate uracil bases in an excess of undamaged DNA. DNA glycosylases may use diffusion along DNA to facilitate lesion search, resulting in processivity, the ability of glycosylases to excise closely spaced lesions without dissociating from DNA. We propose a new assay for correlated cleavage and analyze the processivity of Ung. Ung conducted correlated cleavage on double- and single-stranded substrates; the correlation declined with increasing salt concentration. Proteins in cell extracts also decreased Ung processivity. The correlated cleavage was reduced by nicks in DNA, suggesting the intact phosphodiester backbone is important for Ung processivity.