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Research has been conducted on the reversible DNA phosphodiester bond cleavage. The synthesis of the DNA substrates that carry single nonbridging Rp- or Sp-phosphorothioate modification is analyzed.

Mg2+ stabilized, modification-dependent anticodon domain structures are the most efficient of anticodon conformations for ribosome binding. Base modification, which inhibits canonical hydrogen bonding, was observed with 95% of tRNA anticodon loop sequences that formed Watson-Crick base pairs across the loop.

The motional dynamics of 2-thiouridine and five 5-position derivatives and the six analogous uridines are investigated to elucidate the effect of thiolation on the conformation of transfer RNA. An examination of the dinucleosides s(super 2)UpU reveals that a neighboring nucleoside and its attached phosphodiester bond influence the conformations and dynamics of the ribose groups minimally. Moreover, it is the 2-position thiolation, instead on the 5-position alteration, that yields a more stable, motionally restricted, C(3') endo, gauche plus, anti conformer.

The reversible nucleophilic substitution reaction catalyzed by the vaccinia virus type IB topoisomerase is investigated. An energetic analysis of the combined effects of sulfur substitution and site-directed mutagenesis of active site residues of the enzyme has identified enzyme interactions with each oxygen in the ground state and transition state.

The substrate specificity of ChSI nuclease, obtained from wheat (Triticum vulgare) chloroplast, endonuclease toward various branched DNAs containing 5' flap, 5' pseudoflap, 3' pseudoflap, or single-stranded bulged structural motifs is investigated. The results show that ChSI is a 5' flap structure-specific endonuclease with nucleolytic activity toward single-stranded substrates.