Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Sterochemical Outcome and Kinetic Effects of Rp and Sp-Phosphorothioate Substitutions at the Cleavage site of Vaccinia Type I DNA Topoisomerase



J T. Stivers, B Nawrot, J. Jagadeesh, W J. Stec, S Shuman


To probe the mechanism of the reversible DNA phosphodiester bond cleavage and religation mechanism of the type I topoisomerase from vaccinia virus, we have synthesized DNA substrates carrying a single nonbridging Rp- or Sp-phosphorothioate (Ps) modification at the scissile phosphodiester (Pd) bond. Analysis of the stereochemical outcome of the net cleavage and rejoining reaction establishes that the reaction proceeds with retention of configuration, as expected for a double-displacement mechanism. Single-turnover kinetic studies on irreversible strand cleavage using 18/24 mer suicide substrates showed thio effects (KPd&/Ku)s^) of 340- and 30-fold for the Rp-Ps and Sp-Ps stereoisomers, respectively, but {nearly equal to} 10- fold smaller thio effects for the reverse single-turnover religation reaction (Rp-Ps = 30 and Sp-Ps = 3). As compared to the smaller suicide cleavage substrates, approach-to-equilibrium cleavage studies using 32/32 mer substrates showed 7-9-fold smaller thio effects on cleavage, similar effects on religation, and the same ratio of the Rp to Sp thio effect as the suicide cleavage reaction ({nearly equal to} 10). In general, thio effects of 2.4-6.2 fold on the cleavage equilibrium are observed for the wild-type and H265A enzymes, suggesting differences in the interactions of the enzyme with the nonbridging sulfur in the noncovalent and covalent complexes. Studies of the cleavage, religation, and approach-to-equilibrium reactions catalyzed by the H265A active site mutant revealed a stereoselective, 11-fold decrease in the Rp-thio effect on cleavage and religation as compared to the wild-type enzyme. This result suggests that His-265 interacts with the nonbridging pro-Rp oxygen in the transition state for cleavage and religation, consistent with the arrangement of this conserved residue in the crystal structure of the human topoisomerase-DNA complex. In general, the greatest effect of thio substitution and the H265A mutation is to destabilize the transition state, with smaller effects on substrate binding. The interaction of His-s65 with the pro-Tp nonbridging oxygen is inconsistent with the proposal that this conserved residue acts as a general acid in the strand cleavage reaction.
No. 18


site-directed mutagenesis, sterochemistry, thio effects, topoisomerase kinetics


Stivers, J. , Nawrot, B. , Jagadeesh, J. , Stec, W. and Shuman, S. (2000), Sterochemical Outcome and Kinetic Effects of Rp and Sp-Phosphorothioate Substitutions at the Cleavage site of Vaccinia Type I DNA Topoisomerase, Biochemistry (Accessed June 22, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created February 1, 2000, Updated February 17, 2017